Commensal host-bacterial relationships in the gut

Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea

Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.

Causal link between gut microbiota and obsessive-compulsive disorder: A two-sample Mendelian randomization analysis

BACKGROUND

Previous studies have indicated a potential link between the gut microbiota and obsessive-compulsive disorder (OCD). However, the exact causal relationship remains uncertain. In this study, we employed a two-sample Mendelian randomization (MR) analysis to evaluate the causal connection between gut microbiota and OCD.

METHODS

We collected Genome-Wide Association Study (GWAS) summary data on gut microbiota (n = 18, 340) and OCD (n = 199, 169), using single nucleotide polymorphisms (SNPs) as the instrumental variable. SNPs with an F-statistic of <10 were deemed weak instrumental variables and subsequently excluded. The MR analysis was conducted using five methods: inverse variance weighting (IVW), MR Egger, weighted median, weighted mode, and simple mode. Heterogeneity and pleiotropy were assessed using Cochran's Q-test and MR Egger intercept test, while sensitivity analysis was performed using a leave-one-out approach.

RESULTS

The IVW analysis revealed that at the phylum level, Proteobacteria (OR = 0.545, 95%CI: 0.347-0.855, P = 0.008) served as a protective factor for OCD, whereas at the order level, Bacillales (OR = 1.327, 95%CI: 1.032-1.707, P = 0.027) was identified as a risk factor. At the family level, Ruminococcaceae (OR = 0.570, 95%CI: 0.354-0.918, P = 0.021) also acted as a protective factor. At the genus level, Bilophila (OR = 0.623, 95%CI: 0.425-0.911, P = 0.015) was a protective factor, while Eubacterium ruminantium group (OR = 1.347, 95%CI: 1.012-1.794, P = 0.041) and Lachnospiraceae UCG001 (OR = 1.384, 95%CI: 1.003-1.910, P = 0.048) were identified risk factors. Reverse MR analysis showed no significant causal relationship between OCD and the gut microbiota, with no significant heterogeneity or horizontal pleiotropy observed.

CONCLUSION

Our analysis suggested that specific gut microbiota might have a causal relationship with OCD, revealing potential intervention strategies for the prevention and treatment of this disorder.

Investigating the impact of fecal contamination on antibiotic resistance genes in urban environments using host-associated molecular indicators

Antibiotic resistome of gut microbiota can be transmitted into the urban ecosystems via fecal pollution, potentially leading to a public health crisis. It is essential to determine the primary sources of fecal contamination and accurately evaluate the health risks for the propagation of antibiotic resistance genes (ARGs) from the intestinal microbiota. In this research, the occurrence, sources and potential hosts of ARGs in urban environmental samples collected from a wastewater treatment plant (WWTP), natural water bodies, tap water and farmland soil were comprehensively investigated. Host-associated fecal indicators for general warm-blooded animals (BacGeneral), humans (crAssphage), and other animals (bovines and swine) were employed for reliable microbial source tracking (MST). Results showed that the fecal indicator BacGeneral was detected in 84.00 % of collected environmental samples, indicating the widespread fecal contamination in local water and farmland. The WWTP was the reservoir and main source of fecal contamination in local environment, harboring the highest total abundances of ARGs (3.85 ± 2.72 ARGs/16S rRNA) and mobile genetic elements (MGEs) (0.32 ± 0.12 MGEs/16S rRNA) from multiple animals and humans. Although the swine-associated indicator was undetected, fecal contamination from both bovines and humans was prevalent in collected samples, with detection rates of pollution indicators at 52.00 % for bovine and 28.00 % for human sources. The co-occurrence of ARGs, fecal indicators and MGEs was analyzed, and significant correlation (P < 0.01) between total ARG abundance and fecal indicator (BacGeneral) in contaminated environments demonstrated that fecal pollution exhibited a great influence on overall resistome in local environment. This research offers a comprehensive understanding of the sources and dissemination of ARGs in feces-polluted urban environments, providing data for the monitoring and prevention of ARG pollution.

Effect of a 24-week supervised concurrent exercise intervention on fecal microbiota diversity and composition in young sedentary adults: The ACTIBATE randomized controlled trial

BACKGROUND

Numerous physiological responses to exercise are observed in humans, yet the effects of long-term exercise and varying intensities on the diversity and composition of human fecal microbiota remain unclear. We investigated the effect of a 24-week supervised concurrent exercise intervention, at moderate and vigorous intensities, on fecal microbiota diversity and composition in young adults.

METHODS

This ancillary study was based on data from the ACTIBATE randomized controlled trial (ClinicalTrials.gov ID: NCT02365129), and included adults (aged 18-25 years, 70 % female) that were randomized to (i) a control group (CON: no exercise, n = 20), (ii) a moderate-intensity exercise group (MOD-EX, n = 21), and (iii) a vigorous-intensity exercise group (VIG-EX, n = 20). Fecal samples were collected before and after the 24-week exercise intervention, and the diversity and composition of the fecal microbiota were analyzed by 16S rRNA sequencing. Inferential functional profiling of the fecal microbiota was performed and correlations between microbial changes and cardiometabolic outcomes were assessed.

RESULTS

Exercise did not modify beta or alpha diversities regardless of the intensity (all P ≥ 0.062). The relative abundance of the Erysipelotrichaceae family (Bacillota phylum) (-0.3 ± 1.2 %; P = 0.031) was however reduced in the VIG-EX group. Coprococcus was the only genus showed a significant difference between MOD-EX and VIG-EX after the intervention, with its relative abundance increasing in MOD-EX (+0.4 ± 0.6 %; P = 0.005). None of these changes were related to the exercise-induced cardiometabolic benefits (all P ≥ 0.05).

CONCLUSIONS

In young adults, a 24-week supervised concurrent exercise program, at moderate and vigorous intensities, resulted in minor changes in fecal microbiota composition, while neither alpha nor beta diversities were affected.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov ID: NCT02365129.

Guava root exudate-driven rhizosphere microorganisms changes transmitted to foliar-feeding insects influence their feeding behaviour

The growth of different grafted guava was different as affected by grafting on different rootstock varieties, which also influenced the damage degree of Spodoptera litura larvae. The co-regulation of the pest gut by rhizosphere microorganisms and root exudates may contribute to this differential damage. In this study, the microorganisms of soil, plants, S. litura larvae and root exudates of guava grafted on different rootstock varieties were analysed and compared. The activities of superoxide dismutase, peroxidase and catalase in the midgut of S. litura larvae feeding on heterograft leaves of guava (where rootstock and scion are of the different variety) were significantly higher than those in the midgut of S. litura larvae feeding on homograft leaves of guava (where rootstock and scion are of the same variety), and glutathione s-transferase activity showed an opposite result. Enterococcus spp. and Escherichia spp. were the two bacterial genera with the greatest difference in abundance in the midgut of S. litura larvae and exhibited a negative correlation with each other. The root system of guava influenced the root structure, soil nutrients and the population structure and diversity of rhizosphere microorganisms by regulating the type and amount of root exudates. Root exudates also influenced the physiological and biochemical status of S. litura larvae by regulating the rhizosphere microorganisms driving the tritrophic interaction of plant-microbes-insects. Based on our results and the observed differences in pest occurrence among different grafted plants, improving varieties through grafting may become an effective strategy to reduce the impact of insect pests on guava.

Efficacy of yeast-mediated SeNPs on gastric ulcer healing and gut microbiota dysbiosis in male albino rats

BACKGROUND

Gastric ulcer is one of the most common gastrointestinal tract diseases with a higher extent in male patients to. Selenium nanoparticles (SeNPs) possess therapeutic benefits, including antimicrobial, antioxidant, anti-inflammatory, and anti-ulcerative agents. The study aimed to investigate the modulatory effect of yeast-mediated SeNPs on gastric ulcers and microbiota dysbiosis in a rat model.

METHOD

Twenty-four rats were randomly divided into four groups. Both the control and SeNPs-only groups received distilled water orally, and after 1 h, they received 2 % carboxymethyl cellulose (CMC). The ulcer model and SeNPs-treated groups received 99 % ethanol (5 ml/kg orally) for ulcer induction, followed by 2 % CMC after one hour. The SeNPs-treated group got SeNPs (60 mg/kg) suspended in 2 % CMC. We measured ulcer markers (ulcer index and gastric juice pH and volume and stomach tissue oxidative stress markers (malondialdehyde (MDA), glutathione (GSH), nitric oxide (NO), and catalase (CAT)), in addition to histopathological examination of gastric tissues stained with three different satins: hematoxylin-eosin (H&E), periodic acid-Schiff (PAS), and Masson's trichrome stains (many-color dye), and microbiological analysis of freshly collected fecal sample.

RESULTS

SeNPs treatment significantly decreased gastric volume, ulcer index, malondialdehyde, and increased glutathione levels. A macroscopic examination of the treated stomach revealed decreased ulcer lesion numbers. Furthermore, histopathological examination showed that SeNPs treatment repaired ulcerative gastric tissue through the regeneration of epithelial cells and reduction in damaged areas and collagen fibers. In the treated group, microbiological analysis of rat feces showed a significant increase in Leuconostoc pseudomesenteroides, Escherichia coli, and Enterococcus faecium counts.

CONCLUSION

This research suggests that SeNPs exhibit anti-ulcer activity and can accelerate ulcer healing via their antioxidant action. They also have a modulatory effect on gut microbiota dysbiosis associated with gastric ulcers. This is the first research studying the impact of safe yeast-mediated SeNPs on rat's gastric ulcer and gut microbiota.

Risk factors for catheter-associated urinary tract infection in an intensive care unit: a matched case-control study

OBJECTIVE

Catheter-associated urinary tract infections (CAUTIs) are common healthcare-related infections in intensive care units (ICUs). This study investigated the risk factors for CAUTIs in critically ill patients.

METHODS

This study was a single-centre, retrospective, matched case-control study of patients undergoing indwelling catheterization in the ICU from December 1, 2016, to October 31, 2021. Patients with catheterizations were matched 1:4 with controls that were hospitalized in the ICU during the same period (with a difference in admission time of no more than two months).

RESULTS

CAUTI occurred in 18 of 403 patients, with an infection rate of 3.7/per 1000 catheter days. Repeat catheterization of the urinary catheter (OR = 10.09) and days of antibiotic use (OR = 0.13) were independent risk factors for CAUTI (P < 0.05). A total of 31 pathogen strains were detected in urine samples from 18 CAUTI patients. The main pathogens were Gram-positive bacteria (n = 13, 41.9%), fungi (n = 10, 32.3%) and Gram-negative bacteria (n = 7, 22.6%). CAUTI was associated with an increase in hospitalization days by 26 days and an increase in total hospitalization cost of ¥160,000 (P < 0.001).

CONCLUSION

CAUTIs pose an economic and health burden for ICU patients. Repeat catheterization and longer use of antibiotics are to be avoided as much as possible.

Oral absorption mechanisms of polysaccharides and potential as carriers for the construction of nano-delivery systems: A review

Polysaccharides have garnered increasing attention in recent years for their potential in oral drug delivery within biomaterials and pharmaceuticals, owing to their excellent physicochemical properties, bioactivity, and low toxicity. However, the absorption of polysaccharides encounters multiple challenges posed by the biological, chemical, mechanical, and immune barriers of the intestinal mucosa. Therefore, elucidating the mechanisms by which polysaccharides traverse the intestinal mucosa for oral absorption is essential for their further development and application. Current studies have identified several polysaccharide absorption pathways, including transcellular transport, paracellular transport, M cell and Peyer's patches mediated transport, and intestinal flora mediated transport. Furthermore, numerous studies have demonstrated that polysaccharides can enhance the solubility, gastrointestinal stability, and permeability of small molecule components, which significantly improves their bioavailability. More importantly, nano-delivery systems utilizing polysaccharides as carriers have shown great promise in enhancing the targeting of small molecule components, thereby opening new avenues for drug delivery applications. We hope this review will provide theoretical support and inspiration for a deeper understanding of oral absorption mechanisms and the potential of polysaccharides in the development of nano-delivery systems.

Bacterial Infection Disrupts the Intestinal Bacterial Community and Facilitates the Enrichment of Pathogenic Bacteria in the Intestines of Penaeus vannamei

Pathogenic infections can reshape the intestinal microbiota of aquatic animals, thereby impacting their health status. In this study, we aimed to investigate whether Vibrio parahaemolyticus infection induces dysbiosis in the intestinal bacterial community of Penaeus vannamei and to assess the associated ecological risks. Our findings revealed the deterministic processes in intestinal bacterial community assembly during bacterial infections, indicating that host selection, i.e., host immune response post-infection, has a significant influence on intestinal microbes. More importantly, we found that bacterial infection reshaped the intestinal community by reducing the relative abundance of probiotic Ruegeria species (e.g., R. atlantica, R. lacuscaerulensis, R. conchae, R. profundi, R. arenilitoris, R. pomeroyi) and increasing the relative abundance of Vibrio species (V. harveyi, V. sinaloensis, V. coralliilyticus, and V. brasiliensis). Significant negative correlations were observed between the relative abundance of these Ruegeria species and the relative abundance of Vibrio species. Moreover, the control P. vannamei contained a substantially higher number of keystone species belonging to Ruegeria in the bacterial community network, whereas bacterial infection individuals had few or no keystone species belonging to Ruegeria, with keystone species belonging to Vibrio becoming more prominent. Thus, the significant increase in Vibrio species abundance in the P. vannamei intestine following bacterial infection was associated with the marked reduction in Ruegeria species. Our findings will provide valuable insights into the complex interactions among bacterial infection, intestinal microbiota, and host health, and they provide guidance for the development of probiotics in promoting the healthy culture of P. vannamei.

Ginsenoside CK modulates glucose metabolism via PPARγ to ameliorate SCOP-induced cognitive dysfunction

Ginsenoside compound K (CK) exhibits neuroprotective properties; however, the underlying mechanisms behind these effects have not been investigated thoroughly. CK is the primary active compound derived from ginseng and is metabolized in the gut. It enhances neuronal function by modulating the gut microflora. Therefore, the present study aimed to elucidate the mechanism through which CK enhances cognitive function, employing gut microbiome and microarray analyses. The results revealed that CK upregulated the expression of peroxisome proliferator-activated receptor gamma (PPARγ), suppressed amyloid-β (Aβ) aggregation in hippocampal neurons, and influenced the expression of cyclin-dependent kinase-5 (CDK5), (including insulin receptor substrate 2) IRS2, insulin-degrading enzyme (IDE), glycogen synthase kinase-3 beta (GSK-3β), glucose transporter type 1 (GLUT1), and glucose transporter type 3 (GLUT3) proteins. These proteins play crucial roles in regulating brain glucose metabolism, increasing neuronal energy, and reducing neuronal apoptosis, thereby ameliorating cognitive impairment in mice.

Gut microbiota regulates gut homeostasis, mucosal immunity and influences immune-related diseases

The intestinal microbiome constitutes a sophisticated and massive ecosystem pivotal for maintaining gastrointestinal equilibrium and mucosal immunity via diverse pathways. The gut microbiota is continuously reshaped by multiple environmental factors, thereby influencing overall wellbeing or predisposing individuals to disease state. Many observations reveal an altered microbiome composition in individuals with autoimmune conditions, coupled with shifts in metabolic profiles, which has spurred ongoing development of therapeutic interventions targeting the microbiome. This review delineates the microbial consortia of the intestine, their role in sustaining gastrointestinal stability, the association between the microbiome and immune-mediated pathologies, and therapeutic modalities focused on microbiome modulation. We emphasize the entire role of the intestinal microbiome in human health and recommend microbiome modulation as a viable strategy for disease prophylaxis and management. However, the application of gut microbiota modification for the treatment of immune-related diseases, such as fecal microbiota transplantation and probiotics, remain quite challenging. Therefore, more research is needed into the role and mechanisms of these therapeutics.

Activity-Based Protein Profiling Identifies an α-Amylase Family Protein Contributing to the Virulence of Methicillin-Resistant Staphylococcus aureus

In search of new putative antimicrobial drug targets in methicillin-resistant Staphylococcus aureus, we aimed to identify and characterize retaining glycosidase activities in this bacterial pathogen. Using activity-based protein profiling (ABPP), a panel of 7 fluorescent probes was screened to detect activities of diverse retaining glycosidase families. Based on this, a cocktail of 3 biotinylated probes (targeting α-glucosidases, β-galactosidases and α-fucosidases) was used for target enrichment and three glycoside hydrolase family proteins were identified by mass-spectrometry: 6-phospho-β-glucosidase (BglA), α-amylase family protein trehalase C (TreC), and autolysin (Atl). The physiological relevance of previously uncharacterized BglA and TreC was addressed in CRISPRi and inhibitor studies with the putative TreC inhibitor α-cyclophellitol-aziridine. Silencing of treC did not affect bacterial growth in rich media, but reduced biofilm formation in vitro, and attenuated virulence during Galleria mellonella infection, warranting future investigations into the biochemical function of this enzyme.

Antihypertensive effects of rice peptides involve intestinal microbiome alterations and intestinal inflammation alleviation in spontaneously hypertensive rats

Gut dysbiosis serves as an underlying risk factor for the development of hypertension. The resolution of this dysbiosis has emerged as a promising strategy in improving hypertension. Food-derived bioactive protein peptides have become increasingly more attractive in ameliorating hypertension, primarily due to their anti-inflammatory and anti-oxidant activities. However, the regulatory mechanisms linking rice peptides (RP), gut dysbiosis, and hypertension remain to be fully elucidated. In our study, male spontaneously hypertensive rats (SHR) were fed with chow diet and concomitantly treated with ddH2O (Ctrl) or varying doses of rice peptides (20, 100, or 500 mg (kg bw day)-1 designated as low-dose RP, LRP; medium-dose RP, MRP; high-dose RP, HAP) or captopril (Cap) by intragastric administration. Wistar-Kyoto (WKY) rats served as the normotensive control group and were orally administered with ddH2O. We observed beneficial effects of RP in lowering blood pressure and ameliorating cardiovascular risk profiles, as evidenced by improvements in glucolipid metabolic disorders, hepatic and renal damage, left ventricular hypertrophy and endothelial dysfunction in hypertensive rats. More importantly, we found that RP attenuated intestinal pathological damage, improved impaired intestinal barrier, and reduced intestinal inflammation by inhibiting the HMGB1-TLR4-NF-κB pathway. Notably, multi-omics integrative analyses have revealed that RP altered the composition and function of the gut microbiota. This is exemplified by the observed enrichment of beneficial bacterial constituents, such as g_Lactobacillus, g_Lactococcus, s_Lactobacillus_intestinalis, and Lactococcus lactis, and elevated production of microbiota-derived short-chain fatty acid metabolites. Collectively, these studies suggest that the hypotensive effects of RP may be associated with modulation of the gut microbiota and its short-chain fatty acids metabolites. This implicates the microbiota-gut-HMGB1-TLR4-NF-κB axis as a novel venue for the amelioration of hypertension and its complications.

The roles of functional bacterial amyloids in neurological physiology and pathophysiology: Pros and cons for neurodegeneration

Bacterial biofilms, which are complex communities of microorganisms encapsulated in a self-produced extracellular matrix, play critical roles in various diseases. Recent research has underscored the dualistic nature of amyloids, structural proteins within these biofilms, in human health, particularly highlighting the significant role in neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's disease (PD). These amyloids modulate the immune response by inducing the production of interleukin-10 (IL-10), which plays a role in anti-inflammatory processes. Additionally, they inhibit the aggregation of human amyloids and enhance the integrity of the intestinal barrier. Detrimentally, they exacerbate neuroinflammation by elevating inflammatory cytokines and promoting the aggregation of human amyloid proteins-amyloid-β (Aβ) in AD and α-synuclein (αS) in PD-through a process known as cross-seeding. Moreover, bacterial amyloids have also been shown to stimulate the production of anti-curli/DNA antibodies, which are implicated in the pathogenesis of autoimmune diseases. Given their dualistic nature, bacterial amyloids may, under specific conditions, function as beneficial proteins for human health. This understanding holds promise for the development of targeted therapeutic strategies aimed at modulating bacterial amyloids in the context of neurodegenerative diseases, such as AD and PD.

Droplet microfluidics: unveiling the hidden complexity of the human microbiome

The human body harbors diverse microbial communities essential for maintaining health and influencing disease processes. Droplet microfluidics, a precise and high-throughput platform for manipulating microscale droplets, has become vital in advancing microbiome research. This review introduces the foundational principles of droplet microfluidics, its operational capabilities, and wide-ranging applications. We emphasize its role in enhancing single-cell sequencing technologies, particularly genome and RNA sequencing, transforming our understanding of microbial diversity, gene expression, and community dynamics. We explore its critical function in isolating and cultivating traditionally unculturable microbes and investigating microbial activity and interactions, facilitating deeper insight into community behavior and metabolic functions. Lastly, we highlight its broader applications in microbial analysis and its potential to revolutionize human health research by driving innovations in diagnostics, therapeutic development, and personalized medicine. This review provides a comprehensive overview of droplet microfluidics' impact on microbiome research, underscoring its potential to transform our understanding of microbial dynamics and their relevance to health and disease.

Oral administration of Lactobacillus rhamnosus MP108 ameliorates hemolytic jaundice in rats

Accumulating evidence suggests that specific probiotic strains exert effects on hemolytic jaundice (HJ), and probiotic strains of Lactobacillus rhamnosus exhibit potential beneficial effects against HJ. This study aimed to determine the effects of L. rhamnosus MP108 (MP108) on rats with acetylphenylhydrazine (APH)-induced HJ. One week of oral MP108 administration (16 × 109 CFU/kg·day) significantly reversed the HJ-induced body-weight reduction and normalized serum levels of serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), total superoxide dismutase (T-SOD), glutathione peroxidase (GSH-PX), hydrogen peroxide (H2O2), and superoxide anion (O2-) in HJ rats. Furthermore, significant improvements were observed in the pathological changes of liver and intestinal tissues. 16S rRNA high-throughput sequencing of fecal samples demonstrated that MP108 altered gut microbiota composition by increasing Lacticaseibacillus spp. abundance, which correlated with the serum levels of ALT, AST, TBIL, T-SOD, GSH-PX, H2O2, and O2-. In summary, these results provide evidence that MP108 has the potential to improve HJ symptoms by alleviating hepatic impairment, which is associated with changes in gut microbiota composition. PRACTICAL APPLICATION: The study indicates that MP108 can modulate the gut microbiota, improve liver function, and thereby alleviate the symptoms of hemolytic jaundice (HJ). These findings suggest a promising therapeutic approach for HJ, offering potential benefits to patients with related conditions.

Probiotic potential of Bacillus Isolates from Polish Bee Pollen and Bee Bread

The main goal of this study was the evaluation of the probiotic potential of 10 Bacillus spp. strains isolated from 5 bee bread and 3 bee pollen samples. The antagonistic interaction with Staphylococcus aureus and Escherichia coli was a primary criterion for the preliminary selection of the isolates. Three out of ten strains-PY2.3 (isolated from pollen), BP20.15 and BB10.1 (both isolated from bee bread)-were found to be possible probiotic strains. All these strains are safe for humans (exhibiting γ -hemolytic activity) and meet all essential requirements for probiotics in terms of viability in the presence of bile salts and acid conditions, hydrophobicity, auto-aggregation, and co-aggregation with the cells of important human pathogenic bacteria. They also assimilate more than 30% of cholesterol after 24 h of incubation. These three isolates are resistant to penicillin but sensitive (or exhibit moderate resistance) to the other nine antibiotics tested herein. On the basis of whole-genome sequencing, BP20.15 and BB10.1 were classified as B. subtilis and PY2.3 as B. velezensis. Moreover, genomic analyses revealed that all these isolates are potential producers of different antimicrobial compounds, including bacteriocins and secondary metabolites. The outcomes of this study have proven that some of the Bacillus strains isolated from bee pollen or bee bread are potential probiotics.

Periodontitis increases the risk of gastrointestinal dysfunction: an update on the plausible pathogenic molecular mechanisms

Periodontitis is an immuno-inflammatory disease of the soft tissues surrounding the teeth. Periodontitis is linked to many communicable and non-communicable diseases such as diabetes, cardiovascular disease, rheumatoid arthritis, and cancers. The oral-systemic link between periodontal disease and systemic diseases is attributed to the spread of inflammation, microbial products and microbes to distant organ systems. Oral bacteria reach the gut via swallowed saliva, whereby they induce gut dysbiosis and gastrointestinal dysfunctions. Some periodontal pathogens like Porphyromonas. gingivalis, Klebsiella, Helicobacter. Pylori, Streptococcus, Veillonella, Parvimonas micra, Fusobacterium nucleatum, Peptostreptococcus, Haemophilus, Aggregatibacter actinomycetomcommitans and Streptococcus mutans can withstand the unfavorable acidic, survive in the gut and result in gut dysbiosis. Gut dysbiosis increases gut inflammation, and induce dysplastic changes that lead to gut dysfunction. Various studies have linked oral bacteria, and oral-gut axis to various GIT disorders like inflammatory bowel disease, liver diseases, hepatocellular and pancreatic ductal carcinoma, ulcerative colitis, and Crohn's disease. Although the correlation between periodontitis and GIT disorders is well established, the intricate molecular mechanisms by which oral microflora induce these changes have not been discussed extensively. This review comprehensively discusses the intricate and unique molecular and immunological mechanisms by which periodontal pathogens can induce gut dysbiosis and dysfunction.

Effects of Antimicrobial Peptides on Antioxidant Properties, Non-specific Immune Response and Gut Microbes of Tsinling Lenok Trout (Brachymystax lenok tsinlingensis)

Antimicrobial peptides (AMPs) are an important part of non-specific immunity and play a key role in the cellular host defense against pathogens and tissue injury infections. We investigated the effects of AMP supplementation on the antioxidant capacity, non-specific immunity, and gut microbiota of tsinling lenok trout. 240 fish were fed diets (CT, A120, A240 and A480) containing different amounts of AMP peptides (0, 120 mg kg-1, 240 mg kg-1, 480 mg kg-1) for 8 weeks. Our results showed that the activity of total antioxidant capacity (T-SOD) and glutathione peroxidase (GSH-Px), lysozyme (LZM), catalase (CAT) and acid phosphatase (ACP) in the A240 and A480 group were higher than that in the CT group (P < 0.05). The content of malondialdehyde (MDA) in AMP group was significantly lower than that in CT group (P < 0.05). Furthermore, we harvested the mid-gut and applied next-generation sequencing of 16S rDNA. The results showed that the abundance of Halomonas in AMP group was significantly lower than that in CT group. Functional analysis showed that the abundance of chloroalkane and chloroalkene degradation pathway increased significantly in AMP group. In conclusion, AMP enhanced the antioxidant capacity, non-specific immunity, and intestinal health of tsinling lenok trout.

Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts

Gut microbiome, the group of commensals residing within the intestinal tract, is closely associated with dietary patterns by interacting with food components. The gut microbiome is modifiable by the diet, and in turn, it utilizes the undigested food components as substrates and generates a group of small molecule-metabolites that addressed as "meta-metabolome" in this review. Profiling and mapping of meta-metabolome could yield insightful information at higher resolution and serve as functional readouts for precision nutrition and formation of personalized dietary strategies. For assessing the meta-metabolome, sample preparation is important, and it should aim for retrieval of gut microbial metabolites as intact as possible. The meta-metabolome can be investigated via untargeted and targeted meta-metabolomics with analytical platforms such as nuclear magnetic resonance spectroscopy and mass spectrometry. Employing flux analysis with meta-metabolomics using available database could further elucidate metabolic pathways that lead to biomarker discovery. In conclusion, integration of gut microbiome and meta-metabolomics is a promising supplementary approach to tailor precision dietary intervention. In this review, relationships among diet, gut microbiome, and meta-metabolome are elucidated, with an emphasis on recent advances in alternative analysis techniques proposed for nutritional research. We hope that this review will provide information for establishing pipelines complementary to traditional approaches for achieving precision dietary intervention.

A review on gut microbiota and miRNA crosstalk: implications for Alzheimer's disease

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and progressive neuronal damage. Recent research has highlighted the significant roles of the gut microbiota and microRNAs (miRNAs) in the pathogenesis of AD. This review explores the intricate interaction between gut microbiota and miRNAs, emphasizing their combined impact on Alzheimer's progression. First, we discuss the bidirectional communication within the gut-brain axis and how gut dysbiosis contributes to neuroinflammation and neurodegeneration in AD. Changes in gut microbiota composition in Alzheimer's patients have been linked to inflammation, which exacerbates disease progression. Next, we delve into the biology of miRNAs, focusing on their roles in gene regulation, neurodevelopment, and neurodegeneration. Dysregulated miRNAs are implicated in AD pathogenesis, influencing key processes like inflammation, tau pathology, and amyloid deposition. We then examine how the gut microbiota modulates miRNA expression, particularly in the brain, potentially altering neuroinflammatory responses and synaptic plasticity. The interplay between gut microbiota and miRNAs also affects blood-brain barrier integrity, further contributing to Alzheimer's pathology. Lastly, we explore therapeutic strategies targeting this gut microbiota-miRNA axis, including probiotics, prebiotics, and dietary interventions, aiming to modulate miRNA expression and improve AD outcomes. While promising, challenges remain in fully elucidating these interactions and translating them into effective therapies. This review highlights the importance of understanding the gut microbiota-miRNA relationship in AD, offering potential pathways for novel therapeutic approaches aimed at mitigating the disease's progression.

A Data-Driven Approach to Enhance the Prediction of Bacteria-Metabolite Interactions in the Human Gut Microbiome Using Enzyme Encodings and Metabolite Structural Embeddings

Background: The human gut microbiome is critical for host health by facilitating essential metabolic processes. Our study presents a data-driven analysis across 312 bacterial species and 154 unique metabolites to enhance the understanding of underlying metabolic processes in gut bacteria. The focus of the study was to create a strategy to generate a theoretical (negative) set for binary classification models to predict the consumption and production of metabolites in the human gut microbiome. Results: Our models achieved median balanced accuracies of 0.74 for consumption predictions and 0.95 for production predictions, highlighting the effectiveness of this approach in generating reliable negative sets. Additionally, we applied a kernel principal component analysis for dimensionality reduction. The consumption model with a polynomial kernel, and the production model with a radial basis function with 32 reduced features, showed median accuracies of 0.58 and 0.67, respectively. This demonstrates that biological information can still be captured, albeit with some loss, even after reducing the number of features. Furthermore, our models were validated on six previously unseen cases, achieving five correct predictions for consumption and four for production, demonstrating alignment with known biological outcomes. Conclusions: These findings highlight the potential of integrating data-driven approaches with machine learning techniques to enhance our understanding of gut microbiome metabolism. This work provides a foundation for creating bacteria-metabolite datasets to enhance machine learning-based predictive tools, with potential applications in developing therapeutic methods targeting gut microbes.

Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology

Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.

Toll-like receptor 13-mediated signaling protects against the development of colon cancer

Appropriate host-microbiota interactions are essential for maintaining intestinal homeostasis; hence, an imbalance in these interactions leads to inflammation-associated intestinal diseases. Toll-like receptors (TLRs) recognize microbial ligands and play a key role in host-microbe interactions in health and disease. TLR13 has a well-established function in enhancing host defenses against pathogenic bacteria. However, its role in maintaining intestinal homeostasis and controlling colitis-associated colon cancer (CAC) is largely unknown. This study aimed to investigate the involvement of TLR13-mediated signaling in intestinal homeostasis and colonic tumorigenesis using ex vivo cell and in vivo CAC animal model. Tlr13-deficient mice were prone to dextran sodium sulfate (DSS)-induced colitis. During the early stages of the CAC regimen (AOM/DSS-treated), Tlr13 deficiency led to severe ulcerative colitis. Moreover, Tlr13-deficient mice exhibited increased intestinal permeability, as evidenced by elevated levels of fluorescein isothiocyanate (FITC)-dextran, endotoxins, and bacterial translocation. Enhanced cell survival and proliferation of colonic intestinal cells were observed in Tlr13-deficient mice. A transcriptome analysis revealed that Tlr13 deficiency is associated with substantial changes in gene expression profile of colonic tumor tissue. Tlr13-deficient mice were more susceptible to CAC, with increased production of interleukin (IL)-6, IL-12, and TNF-α cytokines and enhanced STAT3, NF-κB, and MAPK signaling in colon tissues. These findings suggest that TLR13 plays a protective role in maintaining intestinal homeostasis and controlling CAC. Our study provides a novel perspective on intestinal health via TLR13-mediated signaling, which is crucial for deciphering the role of host-microbiota interactions in health and disease.

The human gut microbiome in health and disease: time for a new chapter?

The gut microbiome, composed of the colonic microbiota and their host environment, is important for many aspects of human health. A gut microbiome imbalance (gut dysbiosis) is associated with major causes of human morbidity and mortality. Despite the central part our gut microbiome plays in health and disease, mechanisms that maintain homeostasis and properties that demarcate dysbiosis remain largely undefined. Here we discuss that sorting taxa into meaningful ecological units reveals that the availability of respiratory electron acceptors, such as oxygen, in the host environment has a dominant influence on gut microbiome health. During homeostasis, host functions that limit the diffusion of oxygen into the colonic lumen shelter a microbial community dominated by primary fermenters from atmospheric oxygen. In turn, primary fermenters break down unabsorbed nutrients into fermentation products that support host nutrition. This symbiotic relationship is disrupted when host functions that limit the luminal availability of host-derived electron acceptors become weakened. The resulting changes in the host environment drive alterations in the microbiota composition, which feature an elevated abundance of facultatively anaerobic microbes. Thus, the part of the gut microbiome that becomes imbalanced during dysbiosis is the host environment, whereas changes in the microbiota composition are secondary to this underlying cause. This shift in our understanding of dysbiosis provides a novel starting point for therapeutic strategies to restore microbiome health. Such strategies can either target the microbes through metabolism-based editing or strengthen the host functions that control their environment.

Intestinal organ chips for disease modelling and personalized medicine

Alterations in intestinal structure, mechanics and physiology underlie acute and chronic intestinal conditions, many of which are influenced by dysregulation of microbiome, peristalsis, stroma or immune responses. Studying human intestinal physiology or pathophysiology is difficult in preclinical animal models because their microbiomes and immune systems differ from those of humans. Although advances in organoid culture partially overcome this challenge, intestinal organoids still lack crucial features that are necessary to study functions central to intestinal health and disease, such as digestion or fluid flow, as well as contributions from long-term effects of living microbiome, peristalsis and immune cells. Here, we review developments in organ-on-a-chip (organ chip) microfluidic culture models of the human intestine that are lined by epithelial cells and interfaced with other tissues (such as stroma or endothelium), which can experience both fluid flow and peristalsis-like motions. Organ chips offer powerful ways to model intestinal physiology and disease states for various human populations and individual patients, and can be used to gain new insight into underlying molecular and biophysical mechanisms of disease. They can also be used as preclinical tools to discover new drugs and then validate their therapeutic efficacy and safety in the same human-relevant model.

Salmonella re-engineers the intestinal environment to break colonization resistance in the presence of a compositionally intact microbiota

The gut microbiota prevents harmful microbes from entering the body, a function known as colonization resistance. The enteric pathogen Salmonella enterica serovar (S.) Typhimurium uses its virulence factors to break colonization resistance through unknown mechanisms. Using metabolite profiling and genetic analysis, we show that the initial rise in luminal pathogen abundance was powered by a combination of aerobic respiration and mixed acid fermentation of simple sugars, such as glucose, which resulted in their depletion from the metabolome. The initial rise in the abundance of the pathogen in the feces coincided with a reduction in the cecal concentrations of acetate and butyrate and an increase in epithelial oxygenation. Notably, these changes in the host environment preceded changes in the microbiota composition. We conclude that changes in the host environment can weaken colonization resistance even in the absence of overt compositional changes in the gut microbiota.

The Role of Geography, Diet, and Host Phylogeny on the Gut Microbiome in the Hawaiian Honeycreeper Radiation

The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phylosymbiosis studies have largely focused on clades that diverged tens of millions of years ago, and little is known about the degree of gut microbiome divergence in more recent species radiations. This study explores the drivers of microbiome variation across the unique and recent Hawaiian honeycreeper radiation (Fringillidae: Drepanidinae). Fecal samples were collected from 14 extant species spanning the main islands of the Hawaiian archipelago and were sequenced using three metabarcoding markers to characterize the gut microbiome, invertebrate diet, and plant diet of Hawaiian honeycreepers. We then used these metabarcoding data and the honeycreeper host phylogeny to evaluate their relative roles in shaping the gut microbiome. Microbiome variation across birds was highly individualized; however, source island had a small but significant effect on microbiome structure. The microbiomes did not recapitulate the host phylogenetic tree, indicating that evolutionary history does not strongly influence microbiome structure in the honeycreeper clade. These results expand our understanding of the roles of diet, geography, and phylogeny on avian microbiome structure, while also providing important ecological information about the diet and gut microbiota of wild Hawaiian honeycreepers.

Garlic-Induced Enhancement of Bifidobacterium: Enterotype-Specific Modulation of Gut Microbiota and Probiotic Populations

The gut microbiome is a dynamic ecosystem crucial for maintaining its host's health by regulating various immune and metabolic functions. Since diet plays a fundamental role in shaping the gut microbiome, understanding the relationship between food consumption and microbiome structure is essential. Although medicinal plants are widely recognized for their broad health benefits, their specific impact on the gut microbiome remains unclear. In this study, we investigated the effects of garlic (Allium sativum) on the gut microbiome using an in vitro human fecal incubation model. Our findings revealed that the impact of garlic on gut microbial structure varied depending on the dominant gut microbiome components (enterotypes). The Bacteroides-dominant enterotype exhibited significant changes in overall microbial diversity in response to garlic, while the Prevotella-dominant enterotype remained unaffected. Additionally, the garlic treatment led to specific alterations in microbiota composition, such as an increase in beneficial probiotics like Bifidobacterium. We validated garlic's prebiotic potential by promoting the growth of Bifidobacterium adolescentis under in vitro culture conditions. Our study highlights the importance of understanding enterotype-specific responses to diet and suggests that garlic may serve as a dietary supplement for modulating gut microbiota and promoting the growth of beneficial probiotics.

Gut microbiome in children undergoing hematopoietic stem cell transplantation

Hematopoietic stem cell transplantation (HSCT) is used in children as a treatment for various cancers, e.g. acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), or other diseases, e.g. severe congenital immunodeficiency, metabolic disorders, hence the patient population is quite diverse. There is an increasing interest on the role of the microbiome in peri-transplant period. In this review, concepts of HSCT with the focus on the importance of microbiome composition, its changes during treatment and possible microbiota oriented interventions will be discussed. This paper analyzes data in pediatric population, but in view of interesting results and absence of analogous data for pediatric patients, it also looks at studies performed on adult population and pre-clinical trials on animals discussing possible translation to children.

Appendix removal affects the subsequent cancer risk in Asian adults: A territory-wide population-based cohort study

Human appendix is critical for the maintenance of intestinal homeostasis. Appendicectomy has been the optimal treatment of acute appendicitis, yet the cancer incidence after appendix removal remains unclear. In this territory-wide retrospective cohort study, adult participants who underwent appendicectomy from 2000 to 2018 were retrieved from a population database (n = 43,983), while matched reference participants were retrieved as controls (n = 85,853). After appendicectomy, the overall cancer risk was significantly increased (subdistribution hazard ratio (SHR) = 1.124) compared to the non-appendicectomy group. Appendicectomy-treated males had higher cancer risk than males without appendicectomy (SHR = 1.197), while such difference was not observed in female participants. Significant increase in cancer risk was also observed in elder participants (age >60) with appendicectomy (SHR = 1.390). Appendicectomy was positively correlated with the risk of digestive tract and respiratory cancers including colon (SHR = 1.440), pancreas (SHR = 1.930), and trachea, bronchus, and lung (SHR = 1.394). In contrast, the risk of liver cancer was markedly decreased after appendicectomy (SHR = 0.713). In conclusion, we reported the association of appendicectomy with subsequent cancer incidence. These findings highlight the potential complication after appendix removal and the necessity of post-operative management to monitor and prevent long-term adverse events.

Genomic Exploration of a Chitinolytic Streptomyces albogriseolus PMB5 Strain from European mantis (Mantis religiosa)

The genus Streptomyces is renowned not only for its natural antibiotic production but also for its abundant chitinolytic enzymes, which break down stubborn chitin into chitooligosaccharides. Despite this, there have been limited studies utilizing whole-genome sequencing to explore the repertoire of chitin degradation and utilization genes in Streptomyces. A particularly compelling source of novel antimicrobials and enzymes lies in the microbiota of insects, where bacterial symbionts produce antimicrobials to protect against opportunistic pathogens and enzymes to adapt to the environment. In this study, we present the chitinolytic strain Streptomyces albogriseolus PMB5, isolated from the insectivorous Mantis religiosa (European mantis). Whole-genome sequencing revealed that PMB5 harbors a linear chromosome of 7,211,961 bp and a linear plasmid of 327,989 bp. The genome comprises 6683 genes, including 6592 protein-coding sequences and 91 RNA genes. Furthermore, genome analysis revealed 19 biosynthetic gene clusters covering polyketides, terpenes, and RiPPs, with 10 clusters showing significant gene similarity (>80%) to known clusters like antimycin, hopene, and geosmin. In the genome of S. albogriseolus PMB5, we were able to identify several antibiotic resistance genes; these included cml (resistance to phenicol), gimA (resistance to macrolides), parY (resistance to aminocoumarin), oleC/oleD (resistance to macrolides), novA (resistance to aminocoumarin) and bla/blc (resistance to beta-lactams). Additionally, three clusters displayed no similarity to known sequences, suggesting novel bioactive compound discovery potential. Remarkably, strain PMB5 is the first reported S. albogriseolus capable of thriving on a medium utilizing chitin as a carbon source, with over 50 chitin-utilizing genes identified, including five AA10 family LPMOs, five GH18 chitinases, and one GH19 chitinase. This study significantly enhances the genomic understanding of S. albogriseolus, a species previously underrepresented in research, paving the way to further exploration of the biotechnological potential of the species.

Cyclic Oligosaccharide-Induced Modulation of Immunoglobulin A Reactivity to Gut Bacteria Contributes to Alterations in the Bacterial Community Structure

Immunoglobulin A (IgA) is a major gut antibody that coats commensal gut bacteria and contributes to shaping a stable gut bacterial composition. Although previous studies have shown that cyclic oligosaccharides, including cyclic nigerosyl-1,6-nigerose (CNN) and cyclodextrins (CDs, including αCD, βCD, and γCD), alter the gut bacterial composition, it remains unclear whether cyclic oligosaccharides modify the IgA coating of gut bacteria, which relates to cyclic oligosaccharide-induced alteration of the gut bacterial composition. To address this issue, mice were maintained for 12 weeks on diets containing CNN, αCD, βCD, or γCD; the animals' feces were evaluated for their bacterial composition and the IgA coating index (ICI), a measure of the degree of IgA coating of bacteria. We observed that the intake of each cyclic oligosaccharide altered the gut bacterial composition, with changes in the ICI found at both the phylum and genus levels. The ICI for Bacillota, Lachnospiraceae NK4A136 group, UC Lachnospiraceae, and Tuzzerella were significantly and positively correlated with the relative abundance (RA) in total bacteria for these bacteria; in contrast, significant correlations were not seen for other phyla and genera. Our observations suggest that cyclic oligosaccharide-induced modulation of the IgA coating of gut bacteria may partly relate to changes in the community structure of the gut bacteria.

The regulatory effects of water probiotic supplementation on the blood physiology, reproductive performance, and its related genes in Red Tilapia (Oreochromis niloticus X O. mossambicus)

Probiotics are becoming increasingly popular as eco-friendly alternatives in aquaculture. However, there is limited research on their impacts on the reproductive efficiency of Red Tilapia (Oreochromis niloticus x O. mossambicus) broodstock. Therefore, this experiment aimed to explore the combined effects of selective probiotics Bacillus subtilis and B. licheniformis (BSL; 1:1) added to water on blood hematology, serum metabolites, gonadal histology, reproductive performance, and reproductive associated genes in Red Tilapia broodstock. Tilapia broodfish weighing 140-160 g were stocked in four treatment groups: control (T0), and the other three groups were added different levels of BSL to the water as follows: T1 (0.01 g/m3), T2 (0.02 g/m3), and T3 (0.03 g/m3), respectively. Results indicate that BSL administration significantly improved RBCs, hemoglobin, hematocrit, MCH, and MCHC, with the highest improvement seen in the T3 group (P < 0.05). BSL added to the fish water significantly enhanced serum protein fractions (total protein, albumin, and globulins), while AST, ALT, ALP, creatinine, uric acid, and glucose were significantly diminished in a dose-dependent way (P < 0.05). Adding 0.02-0.03 g/ m3 of BSL resulted in higher antioxidant status (superoxide dismutase and catalase) compared to other groups (P < 0.05). Testosterone levels were higher in T3 than in other groups (P < 0.05). All female hormones (LH, FSH, estradiol, and progesterone) were substantially augmented by the addition of BSL. Additionally, the BSL groups exhibited higher GSI, HSI, VSI (male only), egg diameter (mm), mean number of fry/fish, and mean fry weight (g) compared to the control group (P < 0.05). Expression of reproductive-associated genes (vasa, nanos1a, nanos2, dnd1, pum1, AMH, and vtg) were significantly up-regulated in the gonads of fish in the 0.03 g/m3 treatment. The histological gonadal structure exhibited that BSL improved gonad maturation in both genders of Tilapia fish. Overall, adding a mixture of B. subtilis and B. licheniformis (0.03 g/m3 water) can accelerate reproductive performance in Red Tilapia through up-regulation of reproductive genes and enhance the health profile.

The microbiome compositional and functional differences between rectal mucosa and feces

In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population.

IMPORTANCE

This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.

Kidney transplantation and gut microbiota

Kidney transplantation is an effective way to improve the condition of patients with end-stage renal disease. However, maintaining long-term graft function and improving patient survival remain a key challenge after kidney transplantation. Dysbiosis of intestinal flora has been reported to be associated with complications in renal transplant recipients. The commensal microbiota plays an important role in the immunomodulation of the transplant recipient responses. However, several processes, such as the use of perioperative antibiotics and high-dose immunosuppressants in renal transplant recipients, can lead to gut dysbiosis and disrupt the interaction between the microbiota and the host immune responses, which in turn can lead to complications such as infection and rejection in organ recipients. In this review, we summarize and discuss the changes in intestinal flora and their influencing factors in patients after renal transplantation as well as the evidence related to the impact of intestinal dysbiosis on the prognosis of renal transplantation from in vivo and clinical studies, and conclude with a discussion of the use of microbial therapy in the transplant population. Hopefully, a deeper understanding of the function and composition of the microbiota in patients after renal transplantation may assist in the development of clinical strategies to restore a normal microbiota and facilitate the clinical management of grafts in the future.

Intestinal Delivery of Probiotics: Materials, Strategies, and Applications

Probiotics with diverse and crucial properties and functions have attracted broad interest from many researchers, who adopt intestinal delivery of probiotics to modulate the gut microbiota. However, the major problems faced for the therapeutic applications of probiotics are the viability and colonization of probiotics during their processing, oral intake, and subsequent delivery to the gut. The challenges of simple oral delivery (stability, controllability, targeting, etc.) have greatly limited the use of probiotics in clinical therapies. Nanotechnology can endow the probiotics to be delivered to the intestine with improved survival rate and increased resistance to the adverse environment. Additionally, the progress in synthetic biology has created new opportunities for efficiently and purposefully designing and manipulating the probiotics. In this article, a brief overview of the types of probiotics for intestinal delivery, the current progress of different probiotic encapsulation strategies, including the chemical, physical, and genetic strategies and their combinations, and the emerging single-cell encapsulation strategies using nanocoating methods, is presented. The action mechanisms of probiotics that are responsible for eliciting beneficial effects are also briefly discussed. Finally, the therapeutic applications of engineered probiotics are discussed, and the future trends toward developing engineered probiotics with advanced features and improved health benefits are proposed.

Research progress on intestinal microbiota regulating cognitive function through the gut-brain axis

The intestinal microbiota community is a fundamental component of the human body and plays a significant regulatory role in maintaining overall health and in the management disease states.The intestinal microbiota-gut-brain axis represents a vital connection in the cognitive regulation of the central nervous system by the intestinal microbiota.The impact of intestinal microbiota on cognitive function is hypothesized to manifest through both the nervous system and circulatory system. Imbalances in intestinal microbiota during the perioperative period could potentially contribute to perioperative neurocognitive dysfunction. This article concentrates on a review of existing literature to explore the potential influence of intestinal microbiota on brain and cognitive functions via the nervous and circulatory systems.Additionally, it summarizes recent findings on the impact of perioperative intestinal dysbacteriosis on perioperative neurocognitive dysfunction and suggests novel approaches for prevention and treatment of this condition.

Contemporary Perspectives on the Role of Vitamin D in Enhancing Gut Health and Its Implications for Preventing and Managing Intestinal Diseases

Vitamin D, a crucial fat-soluble vitamin, is primarily synthesized in the skin upon exposure to ultraviolet radiation and is widely recognized as a bone-associated hormone. However, recent scientific advancements have unveiled its intricate association with gut health. The intestinal barrier serves as a vital component, safeguarding the intestinal milieu and maintaining overall homeostasis. Deficiencies in vitamin D have been implicated in altering the gut microbiome composition, compromising the integrity of the intestinal mucosal barrier, and predisposing individuals to various intestinal pathologies. Vitamin D exerts its regulatory function by binding to vitamin D receptors (VDR) present in immune cells, thereby modulating the production of pro-inflammatory cytokines and influencing the intestinal barrier function. Notably, numerous studies have reported lower serum vitamin D levels among patients suffering from intestinal diseases, including inflammatory bowel disease, irritable bowel syndrome, and celiac disease, highlighting the growing significance of vitamin D in gut health maintenance. This comprehensive review delves into the latest advancements in understanding the mechanistic role of vitamin D in modulating the gut microbiome and intestinal barrier function, emphasizing its pivotal role in immune regulation. Furthermore, we consolidate and present relevant findings pertaining to the therapeutic potential of vitamin D in the management of intestinal diseases.

Inter-kingdom communication and the sympoietic way of life

Organisms are now seen as holobionts, consortia of several species that interact metabolically such that they sustain and scaffold each other's existence and propagation. Sympoiesis, the development of the symbiotic relationships that form holobionts, is critical for our understanding the origins and maintenance of biodiversity. Rather than being the read-out of a single genome, development has been found to be sympoietic, based on multigenomic interactions between zygote-derived cells and symbiotic microbes. These symbiotic and sympoietic interactions are predicated on the ability of cells from different kingdoms of life (e.g., bacteria and animals) to communicate with one another and to have their chemical signals interpreted in a manner that facilitates development. Sympoiesis, the creation of an entity by the interactions of other entities, is commonly seen in embryogenesis (e.g., the creation of lenses and retinas through the interaction of brain and epidermal compartments). In holobiont sympoiesis, interactions between partners of different domains of life interact to form organs and biofilms, wherein each of these domains acts as the environment for the other. If evolution is forged by changes in development, and if symbionts are routinely involved in our development, then changes in sympoiesis can constitute an important factor in evolution.

Equol: a metabolite of gut microbiota with potential antitumor effects

An increasing number of studies have shown that the consumption of soybeans and soybeans products is beneficial to human health, and the biological activity of soy products may be attributed to the presence of Soy Isoflavones (SI) in soybeans. In the intestinal tracts of humans and animals, certain specific bacteria can metabolize soy isoflavones into equol. Equol has a similar chemical structure to endogenous estradiol in the human body, which can bind with estrogen receptors and exert weak estrogen effects. Therefore, equol plays an important role in the occurrence and development of a variety of hormone-dependent malignancies such as breast cancer and prostate cancer. Despite the numerous health benefits of equol for humans, only 30-50% of the population can metabolize soy isoflavones into equol, with individual variation in gut microbiota being the main reason. This article provides an overview of the relevant gut microbiota involved in the synthesis of equol and its anti-tumor effects in various types of cancer. It also summarizes the molecular mechanisms underlying its anti-tumor properties, aiming to provide a more reliable theoretical basis for the rational utilization of equol in the field of cancer treatment.

Surface-mediated fluorescent sensor array for identification of gut microbiota and monitoring of colorectal cancer

The development of efficient, accurate, and high-throughput technology for gut microbiota sensing holds great promise in the maintenance of health and the treatment of diseases. Herein, we developed a rapid fluorescent sensor array based on surface-engineered silver nanoparticles (AgNPs) and vancomycin-modified gold nanoclusters (AuNCs@Van) for gut microbiota sensing. By controlling the surface of AgNPs, the recognition ability of the sensor can be effectively improved. The sensor array was used to successfully discriminate six gut-derived bacteria, including probiotics, neutral, and pathogenic bacteria and even their mixtures. Significantly, the sensing system has also been successfully applied to classify healthy individuals and colorectal cancer (CRC) patients rapidly and accurately within 30 min, demonstrating its clinically relevant specificity.

Gut-Liver-Pancreas Axis Crosstalk in Health and Disease: From the Role of Microbial Metabolites to Innovative Microbiota Manipulating Strategies

The functions of the gut are closely related to those of many other organs in the human body. Indeed, the gut microbiota (GM) metabolize several nutrients and compounds that, once released in the bloodstream, can reach distant organs, thus influencing the metabolic and inflammatory tone of the host. The main microbiota-derived metabolites responsible for the modulation of endocrine responses are short-chain fatty acids (SCFAs), bile acids and glucagon-like peptide 1 (GLP-1). These molecules can (i) regulate the pancreatic hormones (insulin and glucagon), (ii) increase glycogen synthesis in the liver, and (iii) boost energy expenditure, especially in skeletal muscles and brown adipose tissue. In other words, they are critical in maintaining glucose and lipid homeostasis. In GM dysbiosis, the imbalance of microbiota-related products can affect the proper endocrine and metabolic functions, including those related to the gut-liver-pancreas axis (GLPA). In addition, the dysbiosis can contribute to the onset of some diseases such as non-alcoholic steatohepatitis (NASH)/non-alcoholic fatty liver disease (NAFLD), hepatocellular carcinoma (HCC), and type 2 diabetes (T2D). In this review, we explored the roles of the gut microbiota-derived metabolites and their involvement in onset and progression of these diseases. In addition, we detailed the main microbiota-modulating strategies that could improve the diseases' development by restoring the healthy balance of the GLPA.

Recent progress on engineered micro/nanomaterials mediated modulation of gut microbiota for treating inflammatory bowel disease

Inflammatory bowel disease (IBD) is a type of chronic recurrent inflammation disease that mainly includes Crohn's disease and ulcerative colitis. Currently, the treatments for IBD remain highly challenging, with clinical treatment drugs showing limited efficacy and adverse side effects. Thus, developing drug candidates with comprehensive therapeutic effects, high efficiency, and low toxicity is urgently needed. Recently, micro/nanomaterials have attracted considerable interest because of their bioavailability, multitarget and efficient effects on IBD. In addition, gut modulation plays a substantial role in restoring intestinal homeostasis. Therefore, efficient microbiota-based strategies modulating gut microenvironment have great potential in remarkably treating IBD. With the development of micro- and nanomaterials for the treatment of IBD and more in-depth studies of their therapeutic mechanisms, it has been found that these treatments also have a tendency to positively regulate the intestinal flora, resulting in an increase in the beneficial flora and a decrease in the level of pathogenic bacteria, thus regulating the composition of the intestinal flora to a normal state. In this review, we first present the interactions among the immune system, intestinal barrier, and gut microbiome. In addition, recent advances in administration routes and methods that positively arouse the regulation of intestinal flora for IBD using probiotics, prebiotics, and redox-active micro/nanomaterials have been reviewed. Finally, the key challenges and critical perspectives of gut microbiota-based micro/nanomaterial treatment are also discussed.

The ArgR-Regulated ADI Pathway Facilitates the Survival of Vibrio fluvialis under Acidic Conditions

Vibrio fluvialis is an emerging foodborne pathogenic bacterium that can cause severe cholera-like diarrhea and various extraintestinal infections, posing challenges to public health and food safety worldwide. The arginine deiminase (ADI) pathway plays an important role in bacterial environmental adaptation and pathogenicity. However, the biological functions and regulatory mechanisms of the pathway in V. fluvialis remain unclear. In this study, we demonstrate that L-arginine upregulates the expression of the ADI gene cluster and promotes the growth of V. fluvialis. The ADI gene cluster, which we proved to be comprised of two operons, arcD and arcACB, significantly enhances the survival of V. fluvialis in acidic environments both in vitro (in culture medium and in macrophage) and in vivo (in mice). The mRNA level and reporter gene fusion analyses revealed that ArgR, a transcriptional factor, is necessary for the activation of both arcD and arcACB transcriptions. Bioinformatic analysis predicted the existence of multiple potential ArgR binding sites at the arcD and arcACB promoter regions that were further confirmed by electrophoretic mobility shift assay, DNase I footprinting, or point mutation analyses. Together, our study provides insights into the important role of the ArgR-ADI pathway in the survival of V. fluvialis under acidic conditions and the detailed molecular mechanism. These findings will deepen our understanding of how environmental changes and gene expression interact to facilitate bacterial adaptations and virulence.

Acetate Alleviates Gut Microbiota Depletion-Induced Retardation of Skeletal Muscle Growth and Development in Young Mice

The normal growth and development of skeletal muscle is essential for the health of the body. The regulation of skeletal muscle by intestinal microorganisms and their metabolites has been continuously demonstrated. Acetate is the predominant short-chain fatty acids synthesized by gut microbiota through the fermentation of dietary fiber; however, the underlying molecular mechanisms governing the interaction between acetate and skeletal muscle during the rapid growth stage remains to be further elucidated. Herein, specific pathogen-free (SPF) mice, germ-free (GF) mice, and germ-free mice supplemented with sodium acetate (GS) were used to evaluate the effects of acetate on the skeletal muscle growth and development of young mice with gut microbiota deficiency. We found that the concentration of serum acetate, body mass gain, succinate dehydrogenase activity, and expression of the myogenesis maker gene of skeletal muscle in the GS group were higher than those in the GF group, following sodium acetate supplementation. Furthermore, the transcriptome analysis revealed that acetate activated the biological processes that regulate skeletal muscle growth and development in the GF group, which are otherwise inhibited due to a gut microbiota deficiency. The in vitro experiment showed that acetate up-regulated Gm16062 to promote skeletal muscle cell differentiation. Overall, our findings proved that acetate promotes skeletal muscle growth and development in young mice via increasing Gm16062 expression.

Small Intestinal Bacterial Overgrowth (SIBO) and Twelve Groups of Related Diseases-Current State of Knowledge

The human gut microbiota creates a complex microbial ecosystem, characterized by its high population density, wide diversity, and complex interactions. Any imbalance of the intestinal microbiome, whether qualitative or quantitative, may have serious consequences for human health, including small intestinal bacterial overgrowth (SIBO). SIBO is defined as an increase in the number of bacteria (103-105 CFU/mL), an alteration in the bacterial composition, or both in the small intestine. The PubMed, Science Direct, Web of Science, EMBASE, and Medline databases were searched for studies on SIBO and related diseases. These diseases were divided into 12 groups: (1) gastrointestinal disorders; (2) autoimmune disease; (3) cardiovascular system disease; (4) metabolic disease; (5) endocrine disorders; (6) nephrological disorders; (7) dermatological diseases; (8) neurological diseases (9); developmental disorders; (10) mental disorders; (11) genetic diseases; and (12) gastrointestinal cancer. The purpose of this comprehensive review is to present the current state of knowledge on the relationships between SIBO and these 12 disease groups, taking into account risk factors and the causal context. This review fills the evidence gap on SIBO and presents a biological-medical approach to the problem, clearly showing the groups and diseases having a proven relationship with SIBO, as well as indicating groups within which research should continue to be expanded.

Microflora structure and functional capacity in Tibetan kefir grains and selenium-enriched Tibetan kefir grains: A metagenomic analysis

Tibetan kefir grains (TKGs) are a complex protein-lipid-polysaccharide matrix composed of various microorganisms. Microorganisms have the benefit of being effective, secure, and controllable when used for selenium enrichment. In this study, selenium-enriched Tibetan kefir grains (Se-TKGs) were made, and the microbiology composition was analyzed through a metagenomic analysis, to explore the influence of selenium enrichment. The microbial composition of TKGs and Se-TKGs, as well as the probiotic species, quorum sensing system (QS) and functional genes were compared and evaluated. Lactobacillus kefiranofaciens was the most abundant microbial species in both communities. Compared with TKGs, Se-TKGs had a much higher relative abundance of acetic acid bacteria. Lactobacillus helveticus was the most common probiotic species both in TKGs and Se-TKGs. Probiotics with antibacterial and anti-inflammatory properties were more abundant in Se-TKGs. QS analysis revealed that Se-TKGs contained more QS system-associated genes than TKGs. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the pathway for human disease ko01501 had the greatest relative abundance in both TKGs and Se-TKGs. Compared with TKGs, Se-TKGs demonstrated a greater relative abundance of different drug resistance-related metabolic pathways. Additionally, linear discriminant analysis effect size was used to examine the biomarkers responsible for the difference between the two groups. In this study, we focused on the microbiological structure of TKGs and Se-TKGs, with the aim of establishing a foundation for a more thorough investigation of Se-TKGs and providing a basis for exploring potential future use.

Influence of Maqian essential oil on gut microbiota and immunoresponses in type 1 diabetes: In silico study

Diversity and homeostasis of gut bacterial composition is highly associated with the pathogenesis of insulin dysfunction and type 1 diabetes melittus (T1D), hence emerged in parallel with the activation of autoimmunity. We aimed to study the bioactive potential of essential oil from Zanthoxylum myriacanthum var. pubescens Huang (Maqian) through computational approaches. Twelve chemical constituents derived from Maqian essential oil were docked with selected proteins (i.e., 3pig, 1kho, 7dmq, 4m4d, 2z65, 4glp, and 3fxi) in which are involved in gut microbiota modulation in T1D. Subsequently, the prediction of bioavailability properties of the small molecules were evaluated. Among all chemical constituents, the post-docking interaction analysis demonstrated that α-phellandrene exhibits the strongest binding affinity and induces gut microbiota modulation with β-fructofuranosidase from Bifidobacterium longum. The current result revealed the potential of 3-Carene and α-Pinene in inducing specific changes in gut microbiota downregulating Clostridium perfringens and quenching Leptotrichia shahii respectively. β-Pinene possess exceptionally strong binding affinity that effectively disrupt the interaction between lipopolysaccharide and its cognate receptors, while α-Phellandrene was exhibited the uppermost binding affinity with TLR4/MD2 and could likely target TLR4 stimulating lipopolysaccharide. Our results are the first to report on the gut microbiota modulation effects of α-Phellandrene and β-Phellandrene via actions on LPS binding to CD14 and the TLR4 co-receptor signaling. In conclusion, our findings based on computational approaches, small molecules from Maqian present as promising agents which could regulate inflammatory response and modulate gut microbiota in type 1 diabetes mellitus.

Castration alters the ileum microbiota of Holstein bulls and promotes beef flavor compounds

BACKGROUND

In the beef industry, bull calves are usually castrated to improve flavor and meat quality; however, this can reduce their growth and slaughter performance. The gut microbiota is known to exert a significant influence on growth and slaughter performance. However, there is a paucity of research investigating the impact of castration on gut microbiota composition and its subsequent effects on slaughter performance and meat flavor.

RESULT

The objective of this study was to examine the processes via which castration hinders slaughter productivity and enhances meat quality. Bull and castrated calves were maintained under the same management conditions, and at slaughter, meat quality was assessed, and ileum and epithelial tissue samples were obtained. The research employed metagenomic sequencing and non-targeted metabolomics techniques to investigate the makeup of the microbiota and identify differential metabolites. The findings of this study revealed the Carcass weight and eye muscle area /carcass weight in the bull group were significantly higher than those in the steer group. There were no significant differences in the length, width, and crypt depth of the ileum villi between the two groups. A total of 53 flavor compounds were identified in the two groups of beef, of which 16 were significantly higher in the steer group than in the bull group, and 5 were significantly higher in the bull group than in the steer group. In addition, bacteria, Eukaryota, and virus species were significantly separated between the two groups. The lipid metabolism pathways of α-linolenic acid, linoleic acid, and unsaturated fatty acids were significantly enriched in the Steers group. Compared with the steer group, the organic system pathway is significantly enriched in the bull group. The study also found that five metabolites (LPC (0:0/20:3), LPC (20:3/0:0), LPE (0:0/22:5), LPE (22:5/0:0), D-Mannosamine), and three species (s_Cloning_vector_Hsp70_LexA-HP1, s_Bacteroides_Coprophilus_CAG: 333, and s_Clostridium_nexile-CAG: 348) interfere with each other and collectively have a positive impact on the flavor compounds of beef.

CONCLUSIONS

These findings provide a basic understanding that under the same management conditions, castration does indeed reduce the slaughter performance of bulls and improve the flavor of beef. Microorganisms and metabolites contribute to these changes through interactions.