Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Targeting microbiota in dietary obesity management: a systematic review on randomized control trials in adults

Obesity is an alarming public health problem. Tailored nutritional therapy is advisable since emerging evidence on complex cross-talks among multifactorial agents. In this picture, the gut microbiota is highly individualized and intricately dependent on dietary patterns, with implications for obesity management. Most of the papers on the topic are observational and often conflicting. This review aimed to systematically organize the body of evidence on microbiota deriving from dietary trials in adult obesity giving the most certain phylogenetic, and metabolomic signatures in relation to both the host metabolism and phenotype changes published until now. We retrieved 18 randomized control trials on 1385 subjects with obesity who underwent several dietary interventions, including standard diet and healthy dietary regimens. Some phyla and species were more related to diets rich in fibers and others to healthy diets. Weight loss, metabolism improvements, inflammatory markers decrease were specifically related to different microorganisms or functions. The Prevotella/Bacteroides ratio was one of the most reported predictors. People with the burden of obesity comorbidities had the most significant taxonomic changes in parallel with a general improvement. These data emphasize the possibility of using symbiotic approaches involving tailored diets, microbiota characteristics, and maybe drugs to treat obesity and metabolic disorders. We encourage Authors to search for specific phylogenetic associations beyond a too generally reported Firmicutes/Bacteroides ratio.

Research progress on the correlation between gut microbiota and preeclampsia: microbiome changes, mechanisms and treatments

Preeclampsia is a specific disease during pregnancy and is a significant factor in the increased mortality in perinatal women. Gut microbiota, an intricate and abundant microbial community in the digestive tract, is crucial for host metabolism, immunity, and nutrient absorption. The onset and progression of preeclampsia are closely correlated with the changes in maternal gut microbiota. Research purpose was to compile the existing bits of present scientific data and to close the gap in the knowledge of changes in gut microbiota in preeclampsia and their association with preeclampsia. We searched studies from two electronic databases (PubMed and Web of Science) included from 2014 to 2023. This review is divided into three parts. In the first part, the author elaborates longitudinal differences of maternal gut microbiota during different gestation periods. In the second part, we discuss that gut microbiota can lead to the occurrence of preeclampsia by systemic immune response, influencing the release of active peptides, short-chain fatty acids, trimethylamine-N-oxide (TMAO) and other metabolites, vascular factors and Microorganism-immune axis. In the third part, we proposed that a high-fiber diet combined with drugs and microecological regulators may be therapeutic in enhancing or preventing the emergence and evolution of preeclampsia, which needs further exploration. Although the pathogenesis of preeclampsia is still nebulous and there is no clear and valid clinical treatment, our study provides new ideas for the pathogenesis, prevention and treatment of preeclampsia.

Lonicera caerulea L. polyphenols improve short-chain fatty acid levels by reshaping the microbial structure of fermented feces in vitro

Increasing evidence suggests that the pathogenesis of type 2 diabetes mellitus (T2DM) is closely related to the gut microbiota. Polyphenols have been shown to alleviate T2DM, but the effects of L. caerulea L. polyphenols (LPs) on the gut microbiota and metabolites remain elusive. In this study, the inhibitory effects of fermented L. caerulea L. polyphenols (FLPs) and unfermented L. caerulea L. polyphenols (ULPs) on α-amylase and α-glucosidase and the impact of LP on the gut microbiota and metabolites were investigated. Furthermore, the relationship between the two was revealed through correlation analysis. The results showed that ULP and FLP had the highest inhibitory rates against α-amylase and α-glucosidase at 4 mg ml-1, indicating a strong inhibitory ability. In addition, LP plays a regulatory role in the concentration of short-chain fatty acids (SCFAs) and tends to restore them to their normal levels. LP reversed the dysbiosis of the gut microbiota caused by T2DM, as evidenced by an increase in the abundance of bacterial genera such as Lactobacillus, Blautia, and Bacteroides and a decrease in the abundance of bacterial genera such as Escherichia-Shigella and Streptococcus. Similarly, after LP intervention, the relationships among microbial species became more complex and interconnected. In addition, the correlation between the gut microbiota and metabolites was established through correlation analysis. These further findings clarify the mechanism of action of LP against T2DM and provide a new target for T2DM interventions.

Gut microbiota-derived short chain fatty acids act as mediators of the gut-brain axis targeting age-related neurodegenerative disorders: a narrative review

Neurodegenerative diseases associated with aging are often accompanied by cognitive decline and gut microbiota disorder. But the impact of gut microbiota on these cognitive disturbances remains incompletely understood. Short chain fatty acids (SCFAs) are major metabolites produced by gut microbiota during the digestion of dietary fiber, serving as an energy source for gut epithelial cells and/or circulating to other organs, such as the liver and brain, through the bloodstream. SCFAs have been shown to cross the blood-brain barrier and played crucial roles in brain metabolism, with potential implications in mediating Alzheimer's disease (AD) and Parkinson's disease (PD). However, the underlying mechanisms that SCFAs might influence psychological functioning, including affective and cognitive processes and their neural basis, have not been fully elucidated. Furthermore, the dietary sources which determine these SCFAs production was not thoroughly evaluated yet. This comprehensive review explores the production of SCFAs by gut microbiota, their transportation through the gut-brain axis, and the potential mechanisms by which they influence age-related neurodegenerative disorders. Also, the review discusses the importance of dietary fiber sources and the challenges associated with harnessing dietary-derived SCFAs as promoters of neurological health in elderly individuals. Overall, this study suggests that gut microbiota-derived SCFAs and/or dietary fibers hold promise as potential targets and strategies for addressing age-related neurodegenerative disorders.

Gut microbiota diversity before allogeneic hematopoietic stem cell transplantation as a predictor of mortality in children

The correlation existing between gut microbiota diversity and survival after allogeneic hematopoietic stem cell transplantation (allo-HSCT) has so far been studied in adults. Pediatric studies question whether this association applies to children as well. Stool samples from a multicenter cohort of 90 pediatric allo-HSCT recipients were analyzed using 16S ribosomal RNA amplicon sequencing to profile the gut microbiota and estimate diversity with the Shannon index. A global-to-local networking approach was used to characterize the ecological structure of the gut microbiota. Patients were stratified into higher- and lower-diversity groups at 2 time points: before transplantation and at neutrophil engraftment. The higher-diversity group before transplantation exhibited a higher probability of overall survival (88.9% ± 5.7% standard error [SE] vs 62.7% ± 8.2% SE; P = .011) and lower incidence of grade 2 to 4 and grade 3 to 4 acute graft-versus-host disease (aGVHD). No significant difference in relapse-free survival was observed between the 2 groups (80.0% ± 6.0% SE vs 55.4% ± 10.8% SE; P = .091). The higher-diversity group was characterized by higher relative abundances of potentially health-related microbial families, such as Ruminococcaceae and Oscillospiraceae. In contrast, the lower-diversity group showed an overabundance of Enterococcaceae and Enterobacteriaceae. Network analysis detected short-chain fatty acid producers, such as Blautia, Faecalibacterium, Roseburia, and Bacteroides, as keystones in the higher-diversity group. Enterococcus, Escherichia-Shigella, and Enterobacter were instead the keystones detected in the lower-diversity group. These results indicate that gut microbiota diversity and composition before transplantation correlate with survival and with the likelihood of developing aGVHD.

Gut-Brain Axis a Key Player to Control Gut Dysbiosis in Neurological Diseases

Parkinson's disease is a chronic neuropathy characterised by the formation of Lewy bodies (misfolded alpha-synuclein) in dopaminergic neurons of the substantia nigra and other parts of the brain. Dopaminergic neurons play a vital role in generating both motor and non-motor symptoms. Finding therapeutic targets for Parkinson's disease (PD) is hindered due to an incomplete understanding of the disease's pathophysiology. Existing evidence suggests that the gut microbiota participates in the pathogenesis of PD via immunological, neuroendocrine, and direct neural mechanisms. Gut microbial dysbiosis triggers the loss of dopaminergic neurons via mitochondrial dysfunction. Gut dysbiosis triggers bacterial overgrowth in the small intestine, which increases the permeability barrier and induces systemic inflammation. It results in excessive stimulation of the innate immune system. In addition to that, activation of enteric neurons and enteric glial cells initiates the aggregation of alpha-synuclein. This alpha-synucleinopathy thus affects all levels of the brain-gut axis, including the central, autonomic, and enteric nervous systems. Though the neurobiological signaling cascade between the gut microbiome and the central nervous system is poorly understood, gut microbial metabolites may serve as a promising therapeutic strategy for PD. This article summarises all the known possible ways of bidirectional signal communication, i.e., the "gut-brain axis," where microbes from the middle gut interact with the brain and vice versa, and highlights a unique way to treat neurodegenerative diseases by maintaining homeostasis. The tenth cranial nerve (vagus nerve) plays a significant part in this signal communication. However, the leading regulatory factor for this axis is a diet that helps with microbial colonisation and brain function. Short-chain fatty acids (SCFAs), derived from microbially fermented dietary fibres, link host nutrition to maintain intestinal homeostasis. In addition to that, probiotics modulate cognitive function and the metabolic and behavioural conditions of the body. As technology advances, new techniques will emerge to study the tie-up between gut microbes and neuronal diseases.

Revealing the beneficial effects of a dairy infant formula on the gut microbiota of early childhood children with autistic spectrum disorder using static and SHIME® fermentation models

This study evaluated the impact of the Milnutri Profutura® (MNP) dairy infant formula on the gut microbiota of early childhood children (three to five years) with Autistic Spectrum Disorder (ASD) using static fermentation (time zero, 24, and 48 h) and the Simulator of the Human Intestinal Microbiol Ecosystem (SHIME®) (time zero, 72 h, and 7 days). The relative abundance of selected intestinal bacterial groups, pH values, organic acids, and sugars were verified at time zero, 24, and 48 h using flow cytometry and measurements. In addition, the diversity and changes in the gut microbiota, and the amounts of acetic, butyric, and propionic acids and ammonium ions (NH4+) in fermentation using the SHIME® were measured at time zero, 72 h, and 7 days. MNP increased Lactobacillus/Enterococcus and Bifidobacterium populations and decreased Bacteroides/Prevotella, Clostridium histolyticum and Eubacterium rectale/Clostridium coccoides populations (p < 0.05) at 24 and 48 h of static fermentation, showing a positive prebiotic activity score (65.18 ± 0.07). The pH, fructose and glucose decreased, while lactic, butyric, and propionic acids increased (p < 0.05) at 48 h of static fermentation. MNP increased (p < 0.05) the Firmicutes phylum during the fermentation in SHIME®. MNP decreased the diversity at 72 h of fermentation, mostly by the increase (p < 0.05) in the Lactobacillus genus. Microbial groups considered harmful such as Lachnospiraceae, Negativicoccus, and Lachnoclostridium were inhibited after administration with MNP. Propionic and butyric acids increased at 72 h and NH4+ decreased (p < 0.05) at the end of fermentation with MNP. The results indicate MNP as an infant formula which may benefit the gut microbiota of children with ASD.

Gut microbiota controls the development of chronic pancreatitis: A critical role of short-chain fatty acids-producing Gram-positive bacteria

Chronic pancreatitis (CP) is a progressive and irreversible fibroinflammatory disorder, accompanied by pancreatic exocrine insufficiency and dysregulated gut microbiota. Recently, accumulating evidence has supported a correlation between gut dysbiosis and CP development. However, whether gut microbiota dysbiosis contributes to CP pathogenesis remains unclear. Herein, an experimental CP was induced by repeated high-dose caerulein injections. The broad-spectrum antibiotics (ABX) and ABX targeting Gram-positive (G+) or Gram-negative bacteria (G-) were applied to explore the specific roles of these bacteria. Gut dysbiosis was observed in both mice and in CP patients, which was accompanied by a sharply reduced abundance for short-chain fatty acids (SCFAs)-producers, especially G+ bacteria. Broad-spectrum ABX exacerbated the severity of CP, as evidenced by aggravated pancreatic fibrosis and gut dysbiosis, especially the depletion of SCFAs-producing G+ bacteria. Additionally, depletion of SCFAs-producing G+ bacteria rather than G- bacteria intensified CP progression independent of TLR4, which was attenuated by supplementation with exogenous SCFAs. Finally, SCFAs modulated pancreatic fibrosis through inhibition of macrophage infiltration and M2 phenotype switching. The study supports a critical role for SCFAs-producing G+ bacteria in CP. Therefore, modulation of dietary-derived SCFAs or G+ SCFAs-producing bacteria may be considered a novel interventive approach for the management of CP.

Gut-derived short-chain fatty acids bridge cardiac and systemic metabolism and immunity in heart failure

Heart failure (HF) represents a group of complex clinical syndromes with high morbidity and mortality and has a significant global health burden. Inflammation and metabolic disorders are closely related to the development of HF, which are complex and depend on the severity and type of HF and common metabolic comorbidities such as obesity and diabetes. An increasing body of evidence indicates the importance of short-chain fatty acids (SCFAs) in regulating cardiac function. In addition, SCFAs represent a unique class of metabolites and play a distinct role in shaping systemic immunity and metabolism. In this review, we reveal the role of SCFAs as a link between metabolism and immunity, which regulate cardiac and systemic immune and metabolic systems by acting as energy substrates, inhibiting the expression of histone deacetylase (HDAC) regulated genes and activating G protein-coupled receptors (GPCRs) signaling. Ultimately cardiac efficiency is improved, cardiac inflammation alleviated and cardiac function in failing hearts enhanced. In conclusion, SCFAs represent a new therapeutic approach for HF.

The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella

Propionate is a microbial metabolite formed in the gastrointestinal tract, and it affects host physiology as a source of energy and signaling molecule. Despite the importance of propionate, the biochemical pathways responsible for its formation are not clear in all microbes. For the succinate pathway used during fermentation, a key enzyme appears to be missing-one that oxidizes ferredoxin and reduces NAD. Here we show that Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)] is this key enzyme in two abundant bacteria of the rumen (Prevotella brevis and Prevotella ruminicola). We found these bacteria form propionate, succinate, and acetate with the classic succinate pathway. Without ferredoxin:NAD+ oxidoreductase, redox cofactors would be unbalanced; it would produce almost equal excess amounts of reduced ferredoxin and oxidized NAD. By combining growth experiments, genomics, proteomics, and enzyme assays, we point to the possibility that these bacteria solve this problem by oxidizing ferredoxin and reducing NAD with Rnf [ferredoxin-NAD+ oxidoreductase (Na+-transporting)]. Genomic and phenotypic data suggest many bacteria may use Rnf similarly. This work shows the ferredoxin:NAD+ oxidoreductase activity of Rnf is important to propionate formation in Prevotella species and other bacteria from the environment, and it provides fundamental knowledge for manipulating fermentative propionate production.

Characterization of gut microbiota profile in Iranian patients with bipolar disorder compared to healthy controls

Introduction

The human gut microbiota plays a crucial role in mental health through the gut-brain axis, impacting central nervous system functions, behavior, mood, and anxiety. Consequently, it is implicated in the development of neuropsychiatric disorders. This study aimed to assess and compare the gut microbiota profiles and populations of individuals with bipolar disorder and healthy individuals in Iran.

Methods

Fecal samples were collected from 60 participants, including 30 bipolar patients (BPs) and 30 healthy controls (HCs), following rigorous entry criteria. Real-time quantitative PCR was utilized to evaluate the abundance of 10 bacterial genera/species and five bacterial phyla.

Results

Notably, Actinobacteria and Lactobacillus exhibited the greatest fold change in BPs compared to HCs at the phylum and genus level, respectively, among the bacteria with significant population differences. Ruminococcus emerged as the most abundant genus in both groups, while Proteobacteria and Bacteroidetes showed the highest abundance in BPs and HCs, respectively, at the phylum level. Importantly, our investigation revealed a lower Firmicutes/Bacteroidetes ratio, potentially serving as a health indicator, in HCs compared to BPs.

Conclusion

This study marks the first examination of an Iranian population and provides compelling evidence of significant differences in gut microbiota composition between BPs and HCs, suggesting a potential link between brain functions and the gut microbial profile and population.

The Interaction between the Host Genome, Epigenome, and the Gut-Skin Axis Microbiome in Atopic Dermatitis

Atopic dermatitis (AD) is a chronic inflammatory skin disease that occurs in genetically predisposed individuals. It involves complex interactions among the host immune system, environmental factors (such as skin barrier dysfunction), and microbial dysbiosis. Genome-wide association studies (GWAS) have identified AD risk alleles; however, the associated environmental factors remain largely unknown. Recent evidence suggests that altered microbiota composition (dysbiosis) in the skin and gut may contribute to the pathogenesis of AD. Examples of environmental factors that contribute to skin barrier dysfunction and microbial dysbiosis in AD include allergens, irritants, pollution, and microbial exposure. Studies have reported alterations in the gut microbiome structure in patients with AD compared to control subjects, characterized by increased abundance of Clostridium difficile and decreased abundance of short-chain fatty acid (SCFA)-producing bacteria such as Bifidobacterium. SCFAs play a critical role in maintaining host health, and reduced SCFA production may lead to intestinal inflammation in AD patients. The specific mechanisms through which dysbiotic bacteria and their metabolites interact with the host genome and epigenome to cause autoimmunity in AD are still unknown. By understanding the combination of environmental factors, such as gut microbiota, the genetic and epigenetic determinants that are associated with the development of autoantibodies may help unravel the pathophysiology of the disease. This review aims to elucidate the interactions between the immune system, susceptibility genes, epigenetic factors, and the gut microbiome in the development of AD.

Fucose modifies short chain fatty acid and H2S formation through alterations of microbial cross-feeding activities

Algae are a rich but unexplored source of fibers with the potential to contribute to the next generation of prebiotics. The sulfated brown algae polysaccharide, fucoidan, is mainly composed of the deoxy-hexose L-fucose, which can be metabolized to 1,2-propanediol (1,2-PD) or lactate by gut microbes as precursors of propionate and butyrate. It was the aim of this study to investigate the impact of fucoidan on the fermentation capacity of the fecal microbiota and to compare to fucose. In batch fermentations of fecal microbiota collected from 17 donor samples, fucose promoted the production of propionate while no consistent effect was observed for commercial fucoidan and Fucus vesiculosus extract prepared in this study containing laminarin and fucoidan. H2S production was detected under all tested conditions, and levels were significantly lower in the presence of fucose in a dose-dependent manner. The addition of high fucose levels led to higher relative abundance of microbial 1,2-PD and lactate cross-feeders. Our results highlight that fucose and not fucoidan addition impacted fermentation capacity and increased the proportions of propionate and butyrate, which allows for precise modulation of intestinal microbiota activity.

The impact of microbiota-derived short-chain fatty acids on macrophage activities in disease: Mechanisms and therapeutic potentials

Short-chain fatty acids (SCFAs) derived from the fermentation of carbohydrates by gut microbiota play a crucial role in regulating host physiology. Among them, acetate, propionate, and butyrate are key players in various biological processes. Recent research has revealed their significant functions in immune and inflammatory responses. For instance, butyrate reduces the development of interferon-gamma (IFN-γ) generating cells while promoting the development of regulatory T (Treg) cells. Propionate inhibits the initiation of a Th2 immune response by dendritic cells (DCs). Notably, SCFAs have an inhibitory impact on the polarization of M2 macrophages, emphasizing their immunomodulatory properties and potential for therapeutics. In animal models of asthma, both butyrate and propionate suppress the M2 polarization pathway, thus reducing allergic airway inflammation. Moreover, dysbiosis of gut microbiota leading to altered SCFA production has been implicated in prostate cancer progression. SCFAs trigger autophagy in cancer cells and promote M2 polarization in macrophages, accelerating tumor advancement. Manipulating microbiota- producing SCFAs holds promise for cancer treatment. Additionally, SCFAs enhance the expression of hypoxia-inducible factor 1 (HIF-1) by blocking histone deacetylase, resulting in increased production of antibacterial effectors and improved macrophage-mediated elimination of microorganisms. This highlights the antimicrobial potential of SCFAs and their role in host defense mechanisms. This comprehensive review provides an in-depth analysis of the latest research on the functional aspects and underlying mechanisms of SCFAs in relation to macrophage activities in a wide range of diseases, including infectious diseases and cancers. By elucidating the intricate interplay between SCFAs and macrophage functions, this review aims to contribute to the understanding of their therapeutic potential and pave the way for future interventions targeting SCFAs in disease management.

The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary Lactobacillus

Gut microbiota and their secreted metabolites have an influence on the initiation and progression of colon cancer. Probiotics are extensively perceived as a potential microbiota-modulation strategy to promote the health of the host, while the effectiveness of preventing colon cancer based on microbiota therapy has not been confirmed, and antitumor mechanisms influenced by microbiota and their metabolites with the intervention of probiotics remain to be further investigated. In vitro, Lactobacillus (JY300-8 and JMR-01) significantly inhibited the proliferation of CT26, HT29, and HCT116 cells. Moreover, we studied the prevention and therapy efficiency of Lactobacillus and its underlying antitumor mechanism through the alteration of gut microbiota and their metabolites regulated by Lactobacillus in colon cancer models in mice. We demonstrated that the pre-administration of Lactobacillus (JY300-8 and JMR-01) for 20 days before establishing tumor models resulted in an 86.21% reduction in tumor formation rate compared to tumor control group. Subsequently, continuous oral administration of living Lactobacillus significantly suppresses tumor growth, and tumor volumes decrease by 65.2%. Microbiome and metabolome analyses reveal that Lactobacillus suppresses colonic tumorigenesis and progression through the modulation of gut microbiota homeostasis and metabolites, including the down-regulation of secondary bile acids, sphingosine 1-phosphate (S1P), and pyrimidine metabolism, as well as the production of anticarcinogenic compounds in tumor-bearing mice. Additionally, metabolome analyses of Lactobacillus (JY300-8 and JMR-01) indicate that living Lactobacillus could reduce the relative abundance of alanine and L-serine to suppress tumor progression by regulating the tumor microenvironment, including down-regulation of pyrimidine metabolism and S1P signaling in cancer. These findings provide a potential prevention strategy and therapeutic target for colon cancer through the intervention of dietary Lactobacillus. IMPORTANCE The modulation of gut microbiota and metabolites has a significant influence on the progression of colon cancer. Our research indicated that the intervention of probiotics is a potentially feasible strategy for preventing colon cancer. We have also revealed the underlying antitumor mechanism through the alteration of gut microbiota and their metabolites, which could lead to broader biomedical impacts on the prevention and therapy of colon cancer with microbiota-based therapy regulated by probiotics.

Spontaneous episodic inflammation in the intestines of mice lacking HNF4A is driven by microbiota and associated with early life microbiota alterations

The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals who mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. Whereas IBD clinical presentation is well described, how interactions between microbiota and host genotype impact early subclinical stages of the disease remains unclear. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IECs) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 mo of age. Here, we tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodic elevated fecal lipocalin 2 (Lcn2) and loose stools beginning by 4-5 wk of age. Lifetime cumulative Lcn2 levels correlated with histopathological features of colitis at 12 mo. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4aΔIEC mice were dependent on microbiota. Fecal 16S rRNA gene sequencing in SPF Hnf4aΔIEC and control mice disclosed that genotype significantly contributed to differences in microbiota composition by 12 mo, and longitudinal analysis of the Hnf4aΔIEC mice with the highest lifetime cumulative Lcn2 revealed that microbial community differences emerged early in life when elevated fecal Lcn2 was first detected. These microbiota differences included enrichment of a novel phylogroup of Akkermansia muciniphila in Hnf4aΔIEC mice. We conclude that HNF4A functions in IEC to shape composition of the gut microbiota and protect against episodic inflammation induced by microbiota throughout the lifespan. IMPORTANCE The inflammatory bowel diseases (IBD), characterized by chronic inflammation of the intestine, affect millions of people around the world. Although significant advances have been made in the clinical management of IBD, the early subclinical stages of IBD are not well defined and are difficult to study in humans. This work explores the subclinical stages of disease in mice lacking the IBD-associated transcription factor HNF4A in the intestinal epithelium. Whereas these mice do not develop overt disease until late in adulthood, we find that they display episodic intestinal inflammation, loose stools, and microbiota changes beginning in very early life stages. Using germ-free and antibiotic-treatment experiments, we reveal that intestinal inflammation in these mice was dependent on the presence of microbiota. These results suggest that interactions between host genotype and microbiota can drive early subclinical pathologies that precede the overt onset of IBD and describe a mouse model to explore those important processes.

Structural characteristics and in vitro fermentation patterns of polysaccharides from Boletus mushrooms

The aim of this study was to investigate the structural characteristics and in vitro fermentation patterns of polysaccharides from Boletus mushrooms. Polysaccharides were solubilized from fruit bodies of selected mushrooms Boletus auripes, B. bicolor, and B. griseus using subcritical water extraction. Boletus polysaccharides were characterized for their general physicochemical pattern, constituent monosaccharides and molecular weight. A simulated in vitro fermentation model was used to study the utilization of Boletus polysaccharides by the gut microbiota and their consequent modulation of microbial communities. Results showed that the main constituent monosaccharides of Boletus polysaccharides were glucose, galactose and mannose, followed by fucose, xylose and rhamnose, with glucose being the most abundant. The polysaccharides from B. bicolor and B. griseus exhibited a relatively high proportion of galactose and mannose, respectively. Boletus polysaccharides exhibited a wide range of molecular weights (5 kDa to 2000 kDa), which covered multiple polysaccharide populations, but the proportions of these populations varied among the samples. Boletus polysaccharides were gradually utilized by the human fecal microbiota, promoting the production of SCFAs. Boletus polysaccharides contributed to a healthier gut microbiota composition by increasing the relative abundance of beneficial bacterial genera such as Bacteroides and Faecalibacterium and reducing the relative abundance of harmful bacterial genera such as Sutterella and Escherichia-Shigella. B. bicolor polysaccharides showed better fermentability and prebiotic effects than the other Boletus polysaccharide groups. Therefore, the consumption of select Boletus mushrooms, particularly B. bicolor, could be a potential approach to obtain polysaccharides for microbiota modulation and to support gut health.

Neuroactive Steroid-Gut Microbiota Interaction in T2DM Diabetic Encephalopathy

The pathological consequences of type 2 diabetes mellitus (T2DM) also involve the central nervous system; indeed, T2DM patients suffer from learning and memory disabilities with a higher risk of developing dementia. Although several factors have been proposed as possible contributors, how neuroactive steroids and the gut microbiome impact brain pathophysiology in T2DM remain unexplored. On this basis, in male Zucker diabetic fatty (ZDF) rats, we studied whether T2DM alters memory abilities using the novel object recognition test, neuroactive steroid levels by liquid chromatography-tandem mass spectrometry, hippocampal parameters using molecular assessments, and gut microbiome composition using 16S next-generation sequencing. Results obtained reveal that T2DM worsens memory abilities and that these are correlated with increased levels of corticosterone in plasma and with a decrease in allopregnanolone in the hippocampus, where neuroinflammation, oxidative stress, and mitochondrial dysfunction were reported. Interestingly, our analysis highlighted a small group of taxa strictly related to both memory impairment and neuroactive steroid levels. Overall, the data underline an interesting role for allopregnanolone and microbiota that may represent candidates for the development of therapeutic strategies.

Concentrate supplementation improves cold-season environmental fitness of grazing yaks: responsive changes in the rumen microbiota and metabolome

Yak (Bos grunniens) is an important economic animal species on the Qinghai-Tibet Plateau. Yaks grazed in the cold season often suffer from nutritional stress, resulting in low production performance. This situation can be improved by properly feeding the grazing yaks in the cold season; however, there is still little information about the effect of different feeding levels on the intestinal microflora and metabolites of yaks. Therefore, this study aimed to explore the effect of feeding different doses of concentrate supplements on rumen bacterial communities and metabolites in grazing yaks during the cold season. Feed concentrate supplementation significantly improved the production performance and rumen fermentation status of grazing yaks during the cold season, and switched the type of ruminal fermentation from acetic acid fermentation to propionic acid fermentation. Ruminal fermentation parameters and ruminal bacterial abundance correlated strongly. At the phylum level, the abundance of Firmicutes increased with increasing concentrate supplementation, while the opposite was true for Bacteroidota. At the genus level, the abundance of Christensenellaceae_R-7_group, NK4A214_group, Ruminococcus, norank_f__Eubacterium_coprostanoligenes_group, norank_f__norank_o__ Clostridia_UCG-014, Lachnospiraceae_NK3A20_group, Acetitomaculum, and Family_XIII_AD3011_group increased with increasing concentrate supplementation, while the abundance of Rikenellaceae_RC9_gut_ group decreased. Dietary concentrate supplementation altered the concentration and metabolic mode of metabolites in the rumen, significantly affecting the concentration of metabolites involved in amino acid and derivative metabolism (e.g., L-aspartic acid, L-glutamate, and L-histidine), purine metabolism (e.g., guanine, guanosine, and hypoxanthine), and glycerophospholipid metabolism (e.g., phosphatidate, phosphatidylcholine, and phosphocholine), and other metabolic pathways. The strong correlation between yak rumen microorganisms and metabolites provided a more comprehensive understanding of microbial community composition and function. This study showed significant changes in the composition and abundance of bacteria and metabolites in the rumen of cool season grazing yaks fed with concentrate supplements. Changes in ruminal fermentation parameters and metabolite concentration also showed a strong correlation with ruminal bacterial communities. These findings will be helpful to formulate supplementary feeding strategies for grazing yaks in the cold season from the perspective of intestinal microorganisms.

Short-chain fatty acids in diseases

Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of dietary fibre in the gastrointestinal tract. The absorption of SCFAs is mediated by substrate transporters, such as monocarboxylate transporter 1 and sodium-coupled monocarboxylate transporter 1, which promote cellular metabolism. An increasing number of studies have implicated metabolites produced by microorganisms as crucial executors of diet-based microbial influence on the host. SCFAs are important fuels for intestinal epithelial cells (IECs) and represent a major carbon flux from the diet, that is decomposed by the gut microbiota. SCFAs play a vital role in multiple molecular biological processes, such as promoting the secretion of glucagon-like peptide-1 by IECs to inhibit the elevation of blood glucose, increasing the expression of G protein-coupled receptors such as GPR41 and GPR43, and inhibiting histone deacetylases, which participate in the regulation of the proliferation, differentiation, and function of IECs. SCFAs affect intestinal motility, barrier function, and host metabolism. Furthermore, SCFAs play important regulatory roles in local, intermediate, and peripheral metabolisms. Acetate, propionate, and butyrate are the major SCFAs, they are involved in the regulation of immunity, apoptosis, inflammation, and lipid metabolism. Herein, we review the diverse functional roles of this major class of bacterial metabolites and reflect on their ability to affect intestine, metabolic, and other diseases. Video Abstract.

Lactiplantibacillus plantarum, lactiplantibacillus pentosus and inulin meal inclusion boost the metagenomic function of broiler chickens

BACKGROUND

The inclusion of alternative ingredients in poultry feed is foreseen to impact poultry gut microbiota. New feeding strategies (probiotics/prebiotics) must be adopted to allow sustainable productions. Therefore, the current study aimed to use metagenomics approaches to determine how dietary inclusion of prebiotic (inulin) plus a multi-strain probiotic mixture of Lactiplantibacillus plantarum and Lactiplantibacillus pentosus affected microbiota composition and functions of the gastro-intestinal tract of the broilers during production. Fecal samples were collected at the beginning of the trial and after 5, 11 and 32 days for metataxonomic analysis. At the end of the trial, broilers were submitted to anatomo-pathological investigations and caecal content was subjected to volatilome analysis and DNAseq.

RESULTS

Probiotic plus prebiotic inclusion did not significantly influence bird performance and did not produce histopathological alterations or changes in blood measurements, which indicates that the probiotic did not impair the overall health status of the birds. The multi-strain probiotic plus inulin inclusion in broilers increased the abundance of Blautia, Faecalibacterium and Lachnospiraceae and as a consequence an increased level of butyric acid was observed. In addition, the administration of probiotics plus inulin modified the gut microbiota composition also at strain level since probiotics alone or in combination with inulin select specific Faecalibacterium prausnitzi strain populations. The metagenomic analysis showed in probiotic plus prebiotic fed broilers a higher number of genes required for branched-chain amino acid biosynthesis belonging to selected F. prausnitzi strains, which are crucial in increasing immune function resistance to pathogens. In the presence of the probiotic/prebiotic a reduction in the occurrence of antibiotic resistance genes belonging to aminoglycoside, beta-lactamase and lincosamide family was observed.

CONCLUSIONS

The positive microbiome modulation observed is particularly relevant, since the use of these alternative ingredients could promote a healthier status of the broiler's gut.

Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization

The human gut microbiota can restrict the growth of pathogens to prevent them from colonizing the intestine ('colonization resistance'). However, antibiotic treatment can kill members of the gut microbiota ('gut commensals') and reduce competition for nutrients, making these nutrients available to support the growth of pathogens. This disturbance can lead to the growth and expansion of pathogens within the intestine (including antibiotic-resistant pathogens), where these pathogens can exploit the absence of competitors and the nutrient-enriched gut environment. In this review, we discuss nutrient competition between the gut microbiota and pathogens. We also provide an overview of how nutrient competition can be harnessed to support the design of next-generation microbiome therapeutics to restrict the growth of pathogens and prevent the development of invasive infections.

In vitro simulated fecal fermentation of mixed grains on short-chain fatty acid generation and its metabolized mechanism

In vitro simulated digestion and fecal fermentation were performed to investigate the influence of mixed grains on gut microbes. In addition, the key metabolic pathways and enzymes associated with short-chain fatty acids (SCFAs) were explored. The mixed grains exhibited an observable regulatory effect on the composition and metabolism of intestinal microorganisms, especially in probiotics, such as Bifidobacterium spp., Lactobacillus spp., and Faecalibacterium spp. WR (wheat + rye), WB (wheat + highland barley) and WO (wheat + oats) tended to generate lactate and acetate, which are related to Sutterella, Staphylococcus, etc. WQ (wheat + quinoa) induced high propionate and butyrate accumulation by consuming lactate and acetate, mainly through Roseburia inulinivorans, Coprococcus catus and Anaerostipes sp., etc. Moreover, bacteria enriched in different mixed grain groups regulated the expression of pivotal enzymes in metabolic pathways and then affected the generation of SCFAs. These results provide new knowledge on the characteristics of intestinal microbial metabolism in different mixed grain substrates.

Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach

This study is conducted to identify the microbial architecture and its functional capacity in the Asian population via the whole metagenomics approach. A brief comparison of the Asian countries namely Malaysia, India, China, and Thailand, was conducted, giving a total of 916 taxa under observation. Results show a close representation of the taxonomic diversity in the gut microbiota of Malaysia, India, and China, where Bacteroidetes, Firmicutes, and Actinobacteria were more predominant compared to other phyla. Mainly due to the multi-racial population in Malaysia, which also consists of Malays, Indian, and Chinese, the population tend to share similar dietary preferences, culture, and lifestyle, which are major influences that shapes the structure of the gut microbiota. Moreover, Thailand showed a more distinct diversity in the gut microbiota which was highly dominated by Firmicutes. Meanwhile, functional profiles show 1034 gene families that are common between the four countries. The Malaysia samples are having the most unique gene families with a total of 67,517 gene families, and 51 unique KEGG Orthologs, mainly dominated by the metabolic pathways, followed by microbial metabolism in diverse environments. In conclusion, this study provides some general overview on the structure of the Asian gut microbiota, with some additional highlights on the Malaysian population.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03671-3.

Effects of Fumarate and Nitroglycerin on In Vitro Rumen Fermentation, Methane and Hydrogen Production, and on Microbiota

This study aimed to investigate the effects of fumarate and nitroglycerin on rumen fermentation, methane and hydrogen production, and microbiota. In vitro rumen fermentation was used in this study with four treatment groups: control (CON), fumarate (FA), nitroglycerin (NG) and fumarate plus nitroglycerin (FN). Real-time PCR and 16S rRNA gene sequencing were used to analyze microbiota. The results showed that nitroglycerin completely inhibited methane production and that this resulted in hydrogen accumulation. Fumarate decreased the hydrogen accumulation and improved the rumen fermentation parameters. Fumarate increased the concentration of propionate and microbial crude protein, and decreased the ratio of acetate to propionate in FN. Fumarate, nitroglycerin and their combination did not affect the abundance of bacteria, protozoa and anaerobic fungi, but altered archaea. The PCoA showed that the bacterial (Anosim, R = 0.747, p = 0.001) and archaeal communities (Anosim, R = 0.410, p = 0.005) were different among the four treatments. Compared with CON, fumarate restored Bacteroidetes, Firmicutes, Spirochaetae, Actinobacteria, Unclassified Ruminococcaceae, Streptococcus, Treponema and Bifidobacterium in relative abundance in FN, but did not affect Succinivibrio, Ruminobacter and archaeal taxa. The results indicated that fumarate alleviated the depressed rumen fermentation caused by the inhibition of methanogenesis by nitroglycerin. This may potentially provide an alternative way to use these chemicals to mitigate methane emission in ruminants.

Extracellular Succinate: A Physiological Messenger and a Pathological Trigger

When tissues are under physiological stresses, such as vigorous exercise and cold exposure, skeletal muscle cells secrete succinate into the extracellular space for adaptation and survival. By contrast, environmental toxins and injurious agents induce cellular secretion of succinate to damage tissues, trigger inflammation, and induce tissue fibrosis. Extracellular succinate induces cellular changes and tissue adaptation or damage by ligating cell surface succinate receptor-1 (SUCNR-1) and activating downstream signaling pathways and transcriptional programs. Since SUCNR-1 mediates not only pathological processes but also physiological functions, targeting it for drug development is hampered by incomplete knowledge about the characteristics of its physiological vs. pathological actions. This review summarizes the current status of extracellular succinate in health and disease and discusses the underlying mechanisms and therapeutic implications.

Effect of Red-Beetroot-Supplemented Diet on Gut Microbiota Composition and Metabolite Profile of Weaned Pigs-A Pilot Study

Red beetroot is a well-recognized and established source of bioactive compounds (e.g., betalains and polyphenols) with anti-inflammatory and antimicrobial properties. It is proposed as a potential alternative to zinc oxide with a focus on gut microbiota modulation and metabolite production. In this study, weaned pigs aged 28 days were fed either a control diet, a diet supplemented with zinc oxide (3000 mg/kg), or 2% and 4% pulverized whole red beetroot (CON, ZNO, RB2, and RB4; respectively) for 14 days. After pigs were euthanized, blood and digesta samples were collected for microbial composition and metabolite analyses. The results showed that the diet supplemented with red beetroot at 2% improved the gut microbial richness relative to other diets but marginally influenced the cecal microbial diversity compared to a zinc-oxide-supplemented diet. A further increase in red beetroot levels (4%-RB4) led to loss in cecal diversity and decreased short chain fatty acids and secondary bile acid concentrations. Also, an increased Proteobacteria abundance, presumably due to increased lactate/lactic-acid-producing bacteria was observed. In summary, red beetroot contains several components conceived to improve the gut microbiota and metabolite output of weaned pigs. Future studies investigating individual components of red beetroot will better elucidate their contributions to gut microbiota modulation and pig health.

Gut microbial metabolites and its impact on human health

One of the primary methods by which the gut microbiome interacts with its host is through the interactions that occur through the production of the metabolites produced, either directly, or indirectly, through microbial metabolism. Decades of research has demonstrated that these metabolic products play a vital role in human health, either for its benefit or detriment. This review article highlights the main metabolites produced by the interactions between diet and the gut microbiome, bile acids and the gut microbiome, and products produced by the gut microbiome alone. Additionally, this article reviews the literature on the effects that these metabolites play on human health.

Phage Targeting Neonatal Meningitis E. coli K1 In Vitro in the Intestinal Microbiota of Pregnant Donors and Impact on Bacterial Populations

Escherichia coli K1 is a leading cause of neonatal meningitis. The asymptomatic carriage of these strains in the maternal intestinal microbiota constitutes a risk of vertical transmission to the infant at birth. The aim of this work was to evaluate the efficacy of phage therapy against E. coli K1 in an intestinal environment and its impact on the intestinal microbiota. For this purpose, three independent experiments were conducted on the SHIME® system, the first one with only the phage vB_EcoP_K1_ULINTec4, the second experiment with only E. coli K1 and the last experiment with both E. coli K1 and the phage. Microbiota monitoring was performed using metagenetics, qPCR, SCFA analysis and the induction of AhR. The results showed that phage vB_EcoP_K1_ULINTec4, inoculated alone, was progressively cleared by the system and replicates in the presence of its host. E. coli K1 persisted in the microbiota but decreased in the presence of the phage. The impact on the microbiota was revealed to be donor dependent, and the bacterial populations were not dramatically affected by vB_K1_ULINTec4, either alone or with its host. In conclusion, these experiments showed that the phage was able to infect the E. coli K1 in the system but did not completely eliminate the bacterial load.

In vivo evaluation of an innovative synbiotics on stage IIIb-IV chronic kidney disease patients

Background

Microbiota unbalance has been proven to affect chronic kidney disease (CKD) patients and, noteworthy, microbiota composition and activity are implicated in CKD worsening. The progression of kidney failure implies an exceeding accumulation of waste compounds deriving from the nitrogenous metabolism in the intestinal milieu. Therefore, in the presence of an altered intestinal permeability, gut-derived uremic toxins, i.e., indoxyl sulfate (IS) and p-cresyl sulfate (PCS), can accumulate in the blood.

Methods

In a scenario facing the nutritional management as adjuvant therapy, the present study assessed the effectiveness of an innovative synbiotics for its ability to modulate the patient gut microbiota and metabolome by setting a randomized, single-blind, placebo-controlled, pilot trial accounting for IIIb-IV stage CKD patients and healthy controls. Metataxonomic fecal microbiota and fecal volatilome were analyzed at the run-in, after 2 months of treatment, and after 1 month of wash out.

Results

Significant changes in microbiota profile, as well as an increase of the saccharolytic metabolism, in feces were found for those CKD patients that were allocated in the synbiotics arm.

Conclusions

Noteworthy, the here analyzed data emphasized a selective efficacy of the present synbiotics on a stage IIIb-IV CKD patients. Nonetheless, a further validation of this trial accounting for an increased patient number should be considered.

Clinical trial registration

https://clinicaltrials.gov/, identifier NCT03815786.

Altered gut microbiota as potential biomarker biomarkers for autism spectrum disorder in early childhood

Gastrointestinal (GI) disorders are widely recorded in autism spectrum disorder (ASD), and ASD with GI symptoms is a vital subtype of this disease. Growing evidence suggests altered gut microbiota biomarkers in ASD, but little is known about the gut microbiota of individuals with ASD with GI Symptoms, particularly in early childhood. In our study, the gut microbiota of 36 individuals with ASD along with GI symptoms and 40 typically developing (TD) children were compared using 16S rRNA gene sequencing. The microbial diversity and composition were found to differ between the two groups. Compared to TD, the gut microbiota of ASD patients with GI symptoms exhibited decreased alpha diversity and depletion of butyrate-producing bacteria (e.g., Faecalibacterium and Coprococcus). In addition, microbial functional analysis showed abnormality in several gut metabolic models and gut brain models of ASD with GI symptoms, including SCFAshort-chain fatty acid (SCFA) synthesis/degradation and neurotoxin-related p-cresol degradation, which are closely associated with ASD-related behaviors in animal models. Furthermore, we constructed a Support Vector Machine classification model, which robustly discriminated individuals with ASD and GI symptoms from TD individuals in a validation set (AUC = 0.88). Our findings provide a deep insight into the roles of the disturbed gut ecosystem in individuals with ASD and GI symptoms aged 3-6 years. Our classification model supports gut microbiota as a potential biomarker for the early identification of ASD and interventions targeting particular gut-beneficial microbiota.

Role of microbiota short-chain fatty acid chains in the pathogenesis of autoimmune diseases

There is emerging evidence that microbiota and its metabolites play an important role in helath and diseases. In this regard, gut microbiota has been found as a crucial component that influences immune responses as well as immune-related disorders such as autoimmune diseases. Gut bacterial dysbiosis has been shown to cause disease and altered microbiota metabolite synthesis, leading to immunological and metabolic dysregulation. Of note, microbiota in the gut produce short-chain fatty acids (SCFAs) such as acetate, butyrate, and propionate, and remodeling in these microbiota metabolites has been linked to the pathophysiology of a number of autoimmune disorders such as type 1 diabetes, multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis, celiac disease, and systemic lupus erythematosus. In this review, we will address the most recent findings from the most noteworthy studies investigating the impact of microbiota SCFAs on various autoimmune diseases.

Fucosylated Human Milk Oligosaccharides Drive Structure-Specific Syntrophy between Bifidobacterium infantis and Eubacterium hallii within a Modeled Infant Gut Microbiome

SCOPE

Fucosylated human milk oligosaccharides (fHMOs) are metabolized by Bifidobacterium infantis and promote syntrophic interactions between microbiota that colonize the infant gut. The role of fHMO structure on syntrophic interactions and net microbiome function is not yet fully understood.

METHODS AND RESULTS

Metabolite production and microbial populations are tracked during mono- and co-culture fermentations of 2'fucosyllactose (2'FL) and difucosyllactose (DFL) by two B. infantis strains and Eubacterium hallii. This is also conducted in an in vitro modeled microbiome supplemented by B. infantis and/or E. hallii. Metabolites are quantified by high performance liquid chromatography. Total B. infantis and E. hallii populations are quantified through qRT-PCR and community composition through 16S amplicon sequencing. Differential metabolism of 2'FL and DFL by B. infantis strains gives rise to strain- and fHMO structure-specific syntrophy with E. hallii. Within the modeled microbial community, fHMO structure does not strongly alter metabolite production in aggregate, potentially due to functional redundancy within the modeled community. In contrast, community composition is dependent on fHMO structure.

CONCLUSION

Whereas short chain fatty acid production is not significantly altered by the specific fHMO structure introduced to the modeled community, specific fHMO structure influences the composition of the gut microbiome.

Pulsatilla chinensis saponins improve SCFAs regulating GPR43-NLRP3 signaling pathway in the treatment of ulcerative colitis

ETHNOPHARMACOLOGICAL RELEVANCE

Pulsatilla decoction has been extensively used to treat ulcerative colitis (UC) in recent years. Pulsatilla chinensis saponin (PRS), the active ingredient of its monarch medicine Pulsatilla chinensis (Bunge) Regel, plays a crucial role in the treatment of UC, but its specific mechanism of action has not been fully elucidated.

AIM OF THE STUDY

This study aims to investigate the protective effect and possible mechanism of PRS on DSS-induced ulcerative colitis in rats.

MATERIALS AND METHODS

In this study, the DSS-induced colitis model was used to explore the metabolism and absorption of PRS under UC, detect the content of short-chain fatty acids (SCFAs) in colon tissue, the expression of receptor G Protein-Coupled Receptor 43 (GPR43) protein and inflammasome NLRP3, and observe the expression level of IL-1β, IL-6 and TNF-α in colon tissue. The protective effect of the PRS was also observed.

RESULTS

It was found that in the UC group, the absorption rate and extent of drugs increased, and the elimination was accelerated. Compared with the control group, PRS increased the content of short-chain fatty acids (SCFAs) in colon tissue, promoted the expression of SCFAs receptor GPR43 protein, inhibited the activation of the NLRP3 inflammasome, and decreased the content of IL-1β, IL-6 and TNF-α. PRS protects the colon in DSS-induced inflammatory bowel disease by increasing the content of SCFAs, promoting the expression of GPR43 protein, inhibiting the activation of the NLRP3 inflammasome, and reversing the increase in IL-1β, IL-6 and TNF-α levels.

CONCLUSIONS

PRS can increase the content of colonic SCFAs, activate the GPR43-NLRP3 signaling pathway, and reduce the levels of pro-inflammatory cytokines, thereby improving the symptoms of DSS-induced colitis.

Probiotics and Commensal Bacteria Metabolites Trigger Epigenetic Changes in the Gut and Influence Beneficial Mood Dispositions

The effect of the intestinal microbiome on the gut-brain axis has received considerable attention, strengthening the evidence that intestinal bacteria influence emotions and behavior. The colonic microbiome is important to health and the pattern of composition and concentration varies extensively in complexity from birth to adulthood. That is, host genetics and environmental factors are complicit in shaping the development of the intestinal microbiome to achieve immunological tolerance and metabolic homeostasis from birth. Given that the intestinal microbiome perseveres to maintain gut homeostasis throughout the life cycle, epigenetic actions may determine the effect on the gut-brain axis and the beneficial outcomes on mood. Probiotics are postulated to exhibit a range of positive health benefits including immunomodulating capabilities. Lactobacillus and Bifidobacterium are genera of bacteria found in the intestines and so far, the benefits afforded by ingesting bacteria such as these as probiotics to people with mood disorders have varied in efficacy. Most likely, the efficacy of probiotic bacteria at improving mood has a multifactorial dependency, relying namely on several factors that include the agents used, the dose, the pattern of dosing, the pharmacotherapy used, the characteristics of the host and the underlying luminal microbial environment (e.g., gut dysbiosis). Clarifying the pathways linking probiotics with improvements in mood may help identify the factors that efficacy is dependent upon. Adjunctive therapies with probiotics for mood disorders could, through DNA methylation molecular mechanisms, augment the intestinal microbial active cohort and endow its mammalian host with important and critical co-evolutionary redox signaling metabolic interactions, that are embedded in bacterial genomes, and that in turn can enhance beneficial mood dispositions.

Microbiome analysis of thai traditional fermented soybeans reveals short-chain fatty acid-associated bacterial taxa

Thua Nao is a Thai traditional fermented soybean food and low-cost protein supplement. This study aimed to evaluate the bacterial community in Thua Nao from northern Thailand and assess potentially active short-chain fatty acids (SCFAs)-related bacteria. Sixty-five Thua Nao consisting of 30 wet and 35 dried samples were collected from six provinces: Chiang Rai, Chiang Mai, Mae Hong Son, Lampang, Lamphun, and Phayao. Bacterial diversity was significantly higher in the wet samples than in the dried samples. The dominant phyla were Firmicutes (92.7%), Proteobacteria (6.7%), Actinobacteriota (0.42%), and Bacteroidota (0.26%). The genus Bacillus (67%) was the most represented in all samples. Lactobacillus, Enterococcus, and Globicatella were enriched in the wet samples. Assessment of the SCFA-microbiota relationships revealed that high butyrate and propionate concentrations were associated with an increased Clostridiales abundance, and high acetate concentrations were associated with an increased Weissella abundance. Wet products contained more SCFAs, including acetate (P = 2.8e-08), propionate (P = 0.0044), butyrate (P = 0.0021), and isovalerate (P = 0.017), than the dried products. These results provide insight into SCFA-microbiota associations in Thua Nao, which may enable the development of starter cultures for SCFA-enriched Thua Nao production.

Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota

Short-chain fatty acids (SCFAs) play a key role in health and disease, as they regulate gut homeostasis and their deficiency is involved in the pathogenesis of several disorders, including inflammatory bowel diseases, colorectal cancer, and cardiometabolic disorders. SCFAs are metabolites of specific bacterial taxa of the human gut microbiota, and their production is influenced by specific foods or food supplements, mainly prebiotics, by the direct fostering of these taxa. This Review provides an overview of SCFAs' roles and functions, and of SCFA-producing bacteria, from their microbiological characteristics and taxonomy to the biochemical process that lead to the release of SCFAs. Moreover, we will describe the potential therapeutic approaches to boost the levels of SCFAs in the human gut and treat different related diseases.

Regulation of short-chain fatty acids in the immune system

A growing body of research suggests that short-chain fatty acids (SCFAs), metabolites produced by intestinal symbiotic bacteria that ferment dietary fibers (DFs), play a crucial role in the health status of symbiotes. SCFAs act on a variety of cell types to regulate important biological processes, including host metabolism, intestinal function, and immune function. SCFAs also affect the function and fate of immune cells. This finding provides a new concept in immune metabolism and a better understanding of the regulatory role of SCFAs in the immune system, which impacts the prevention and treatment of disease. The mechanism by which SCFAs induce or regulate the immune response is becoming increasingly clear. This review summarizes the different mechanisms through which SCFAs act in cells. According to the latest research, the regulatory role of SCFAs in the innate immune system, including in NLRP3 inflammasomes, receptors of TLR family members, neutrophils, macrophages, natural killer cells, eosinophils, basophils and innate lymphocyte subsets, is emphasized. The regulatory role of SCFAs in the adaptive immune system, including in T-cell subsets, B cells, and plasma cells, is also highlighted. In addition, we discuss the role that SCFAs play in regulating allergic airway inflammation, colitis, and osteoporosis by influencing the immune system. These findings provide evidence for determining treatment options based on metabolic regulation.

Microbiota-related metabolites fueling the understanding of ischemic heart disease

Up-to-date knowledge of gut microbial taxa associated with ischemic heart disease (IHD). Microbial metabolites for mechanistic dissection of IHD pathology. Microbiome-based therapies in IHD prevention and treatment.

Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health

A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.

Feeding an unsalable carrot total-mixed ration altered bacterial amino acid degradation in the rumen of lambs

The objective of this study was to determine the influence of a total-mixed ration including unsalable carrots at 45% DM on the rumen microbiome; and the plasma, rumen and liver metabolomes. Carrots discarded at processing were investigated as an energy-dense substitute for barley grain in a conventional feedlot diet, and improved feed conversion efficiency by 25%. Here, rumen fluid was collected from 34 Merino lambs at slaughter (n = 16 control; n = 18 carrot) after a feeding period of 11-weeks. The V4 region of the 16S rRNA gene was sequenced to profile archaeal and bacterial microbe communities. Further, a comprehensive, targeted profile of known metabolites was constructed for blood plasma, rumen fluid and biopsied liver metabolites using a gas chromatography mass spectrometry (GC-MS) metabolomics approach. An in vitro batch culture was used to characterise ruminal fermentation including gas and methane (CH₄) production. In vivo rumen microbial community structure of carrot fed lambs was dissimilar (P < 0.01; PERMANOVA), and all measures of alpha diversity were greater (P < 0.01), compared to those fed the control diet. Unclassified genera in Bacteroidales (15.9 ± 6.74% relative abundance; RA) were more abundant (P < 0.01) in the rumen fluid of carrot-fed lambs, while unclassified taxa in the Succinivibrionaceae family (11.1 ± 3.85% RA) were greater (P < 0.01) in the control. The carrot diet improved in vitro ruminal fermentation evidenced as an 8% increase (P < 0.01) in DM digestibility and a 13.8% reduction (P = 0.01) in CH₄ on a mg/ g DM basis, while the control diet increased (P = 0.04) percentage of propionate within total VFA by 20%. Fourteen rumen fluid metabolites and 27 liver metabolites were influenced (P ≤ 0.05) by diet, while no effect (P ≥ 0.05) was observed in plasma metabolites. The carrot diet enriched (impact value = 0.13; P = 0.01) the tyrosine metabolism pathway (acetoacetic acid, dopamine and pyruvate), while the control diet enriched (impact value = 0.42; P ≤ 0.02) starch and sucrose metabolism (trehalose and glucose) in rumen fluid. This study demonstrated that feeding 45% DM unsalable carrots diversified bacterial communities in the rumen. These dietary changes influenced pathways of tyrosine degradation, such that previous improvements in feed conversion efficiency in lambs could be explained.

High Antioxidant Capacity of Lacticaseibacillus paracasei TDM-2 and Pediococcus pentosaceus TCM-3 from Qinghai Tibetan Plateau and Their Function towards Gut Modulation

Probiotic supplementation is a key therapeutic strategy for promoting gut health and maintaining gut homeostasis by modulating functional microbiota. In this study, we isolated two lactic acid bacteria (LAB) strains, Pediococcus pentosaceus TCM-3 and Lacticaseibacillus paracasei TDM-2, from Qinghai-Tibetan plateau, and evaluated their probiotic properties and antioxidant bioactivity. In which, TDM-2 had higher T-AOC activity than either TCM-3 or LGG (4.10 μmol/mL vs. 3.68 and 3.53 μmol/mL, respectively, p < 0.05). These strains have shown high antioxidant activity compared to the LAB strains and were found to be acid and bile salt tolerant, confronting the safety issues of antibiotic resistance and the capability of surviving in simulated gastric and intestinal juices. In vitro fermentation experiments with human gut microbiota revealed significant differences in microbial community composition between samples supplemented with TCM-3 and TDM-2 and those without. The addition of these two strains resulted in an enrichment of beneficial taxa, such as the Pediococcus, Lactobacillus, and Clostridium_sensu_strictos at the genus level, and Firmicutes and Proteobacteria at the phylum level. Notably, the TCM-3 group exhibited higher short-chain fatty acid production than the TDM-2 group and untreated controls (acetic acid at 12 h: 4.54 mmol L^-1 vs. 4.06 mmol L^-1 and 4.00 mmol L^-1; acetic acid at 24 h: 4.99 mmol L^-1 vs. 4.90 mmol L^-1 and 4.82 mmol L^-1, p < 0.05). These findings demonstrate that LAB supplementation with high antioxidant capacity and probiotic properties can promote gut health by modulating functional microbiota and is enriching for beneficial taxa. Our study provides guidance for therapeutic strategies that use novel LAB strains to maintain gut homeostasis and functional microbiota modulation.

Understanding the ADHD-Gut Axis by Metabolic Network Analysis

Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder diagnosed with hyperactivity, impulsivity, and a lack of attention inconsistent with the patient's development level. The fact that people with ADHD frequently experience gastrointestinal (GI) dysfunction highlights the possibility that the gut microbiome may play a role in this condition. The proposed research aims to determine a biomarker for ADHD by reconstructing a model of the gut-microbial community. Genome-scale metabolic models (GEM) considering the relationship between gene-protein-reaction associations are used to simulate metabolic activities in organisms of gut. The production rates of dopamine and serotonin precursors and the key short chain fatty acids which affect the health status are determined under three diets (Western, Atkins', Vegan) and compared with those of healthy people. Elasticities are calculated to understand the sensitivity of exchange fluxes to changes in diet and bacterial abundance at the species level. The presence of Bacillota (genus Coprococcus and Subdoligranulum), Actinobacteria (genus Collinsella), Bacteroidetes (genus Bacteroides), and Bacteroidota (genus Alistipes) may be possible gut microbiota indicators of ADHD. This type of modeling approach taking microbial genome-environment interactions into account helps us understand the gastrointestinal mechanisms behind ADHD, and establish a path to improve the quality of life of ADHD patients.

Molecular weight and gut microbiota determine the bioavailability of orally administered hyaluronic acid

The ability of hyaluronan as a dietary supplement to increase skin moisture and relieve knee pain has been demonstrated in several clinical studies. To understand the mechanism of action, determining hyaluronan's bioavailability and in vivo fate is crucial. Here, we used ¹³C-hyaluronan combined with LC-MS analysis to compare the absorption and metabolism of oral hyaluronan in germ-free and conventional wild-type mice. The presence of Bacteroides spp. in the gut was crucial for hyaluronan absorption. Specific microorganisms cleave hyaluronan into unsaturated oligosaccharides (<3 kDa) which are partially absorbed through the intestinal wall. The remaining hyaluronan fragments are metabolized into short-chain fatty acids, which are only metabolites available to the host. The poor bioavailability (~0.2 %) of oral hyaluronan indicates that the mechanism of action is the result of the systematic regulatory function of hyaluronan or its metabolites rather than the direct effects of hyaluronan at distal sites of action (skin, joints).

Poultry gut health and beyond

Intestinal health is critically important for the digestion and absorption of nutrients and thus is a key factor in determining performance. Intestinal health issues are very common in high performing poultry lines due to the high feed intake, which puts pressure on the physiology of the digestive system. Excess nutrients which are not digested and absorbed in the small intestine may trigger dysbiosis, i.e. a shift in the microbiota composition in the intestinal tract. Dysbiosis as well as other stressors elicit an inflammatory response and loss of integrity of the tight junctions between the epithelial cells, leading to gut leakage. In this paper, key factors determining intestinal health and the most important nutritional tools which are available to support intestinal health are reviewed.

Microbial production of odd-chain fatty acids

Odd-chain fatty acids (OcFAs) and their derivatives have attracted much attention due to their beneficial physiological effects and their potential to be alternatives to advanced fuels. However, cells naturally produce even-chain fatty acids (EcFAs) with negligible OcFAs. In the process of biosynthesis of fatty acids (FAs), the acetyl-CoA serves as the starter unit for EcFAs, and propionyl-CoA works as the starter unit for OcFAs. The lack of sufficient propionyl-CoA, the precursor, is usually regarded as the main restriction for large-scale bioproduction of OcFAs. In recent years, synthetic biology strategies have been used to modify several microorganisms to produce more propionyl-CoA that would enable an efficient biosynthesis of OcFAs. This review discusses several reported and potential metabolic pathways for propionyl-CoA biosynthesis, followed by advances in engineering several cell factories for OcFAs production. Finally, trends and challenges of synthetic biology driven OcFAs production are discussed.

HMOs Exert Marked Bifidogenic Effects on Children’s Gut Microbiota Ex Vivo, Due to Age-Related Bifidobacterium Species Composition

Prebiotics are substrates that are selectively utilized by host microorganisms, thus conferring a health benefit. There is a growing awareness that interpersonal and age-dependent differences in gut microbiota composition impact prebiotic effects. Due to the interest in using human milk oligosaccharides (HMOs) beyond infancy, this study evaluated how HMOs [2’Fucosyllactose (2’FL), Lacto-N-neotetraose (LNnT), 3’Sialyllactose (3’SL), 6’Sialyllactose (6’SL)] and blends thereof affect the microbiota of 6-year-old children (n = 6) and adults (n = 6), compared to prebiotics inulin (IN) and fructooligosaccharides (FOS). The ex vivo SIFR® technology was used, given its demonstrated predictivity in clinical findings. First, HMOs and HMO blends seemed to maintain a higher α-diversity compared to FOS/IN. Further, while 2′FL/LNnT were bifidogenic for both age groups, 3′SL/6′SL and FOS/IN were exclusively bifidogenic for children and adults, respectively. This originated from age-related differences in microbiota composition because while 3′SL/6′SL stimulated B. pseudocatenulatum (abundant in children), FOS/IN enhanced B. adolescentis (abundant in adults). Moreover, all treatments significantly increased acetate, propionate and butyrate (only in adults) with product- and age-dependent differences. Among the HMOs, 6′SL specifically stimulated propionate (linked to Bacteroides fragilis in children and Phocaeicola massiliensis in adults), while LNnT stimulated butyrate (linked to Anaerobutyricum hallii in adults). Indole-3-lactic acid and 3-phenyllactic acid (linked to immune health) and gamma-aminobutyric acid (linked to gut-brain axis) were most profoundly stimulated by 2′FL and HMO blends in both children and adults, correlating with specific Bifidobacteriaceae. Finally, 2′FL/LNnT increased melatonin in children, while 3′SL remarkably increased folic acid in adults. Overall, age-dependent differences in microbiota composition greatly impacted prebiotic outcomes, advocating for the development of age-specific nutritional supplements. HMOs were shown to be promising modulators in the adult, and particularly the children’s microbiota. The observed HMO-specific effects, likely originating from their structural heterogeneity, suggest that blends of different HMOs could maximize treatment effects.

Interaction between β-glucans and gut microbiota: a comprehensive review

Gut microbiota (GMB) in humans plays a crucial role in health and diseases. Diet can regulate the composition and function of GMB which are associated with different human diseases. Dietary fibers can induce different health benefits through stimulation of beneficial GMB. β-glucans (BGs) as dietary fibers have gained much interest due to their various functional properties. They can have therapeutic roles on gut health based on modulation of GMB, intestinal fermentation, production of different metabolites, and so on. There is an increasing interest in food industries in commercial application of BG as a bioactive substance into food formulations. The aim of this review is considering the metabolizing of BGs by GMB, effects of BGs on the variation of GMB population, influence of BGs on the gut infections, prebiotic effects of BGs in the gut, in vivo and in vitro fermentation of BGs and effects of processing on BG fermentability.

Benefits of Biotics for Cardiovascular Diseases

Cardiovascular diseases are the main cause of death in many countries, and the better prevention and prediction of these diseases would be of great importance for individuals and society. Nutrition, the gut microbiota, and metabolism have raised much interest in the field of cardiovascular disease research in the search for the main mechanisms that promote cardiovascular diseases. Understanding the interactions between dietary nutrient intake and the gut microbiota-mediated metabolism may provide clinical insight in order to identify individuals at risk of cardiometabolic disease progression, as well as other potential therapeutic targets to mitigate the risk of cardiometabolic disease progression. The development of cardiometabolic diseases can be modulated by specific beneficial metabolites derived from bacteria. Therefore, it is very important to investigate the impact of these metabolites on human health and the possibilities of modulating their production with dietary supplements called biotics.