Revised Estimates for the Number of Human and Bacteria Cells in the Body

Impact of gut microbiota in chronic kidney disease: natural polyphenols as beneficial regulators

Chronic kidney disease (CKD) poses a severe health risk with high morbidity and mortality, profoundly affecting patient quality of life and survival. Despite advancements in research, the pathophysiology of CKD remains incompletely understood. Growing evidence links CKD with shifts in gut microbiota function and composition. Natural compounds, particularly polyphenols, have shown promise in CKD treatment due to their antioxidant and anti-inflammatory properties and their ability to modulate gut microbiota. This review discusses recent progress in uncovering the connections between gut microbiota and CKD, including microbiota changes across different kidney diseases. We also examine metabolite alterations,such as trimethylamine-N-oxide, tryptophan derivatives, branched-chain amino acids, short-chain fatty acids, and bile acids,which contribute to CKD progression. Further, we outline the mechanisms through which polyphenols exert therapeutic effects on CKD, focusing on signaling pathways like nuclear factor kappa-B (NF-κB), mitogen-activated protein kinase (MAPK), mammalian target of rapamycin (mTOR), NOD-like receptor thermal protein domain associated protein 3 (NLRP3), phosphatidylin-ositol-3-kinase (PI3K)/protein kinase B (Akt), and toll like receptors (TLR), as well as their impact on gut microbiota. Lastly, we consider how dietary polyphenols could be harnessed as bioactive drugs to slow CKD progression. Future research should prioritize multi-omics approaches to identify patients who would benefit from polyphenolic interventions, enabling personalized treatment strategies to enhance therapeutic efficacy.

Alcaligenes faecalis promotes colitis to colorectal cancer transition through IgA+ B cell suppression and vinculin acetylation

Lymphoid tissue-resident commensal bacteria (LRC), a subtype of gut microbiota essential for inflammation-associated carcinogenesis, predominantly attribute to colorectal cancer(CRC), whereas its role was largely unknown. Herein, we found Alcaligenes faecalis (A. faecalis), the main LRC embedded in Peyer's patches, was abundantly enriched in colitis, adenoma, and stage-dependently observed in CRC tissues. Interestingly, A. faecalis alone can not affect intestinal homeostasis, while during colitis, A. faecalis significantly translocated from Peyer's patches to colon, remarkably attenuated immune response abilities of B cells, T cells, and DC cells in PPs, consequently impeded IgA+ B cells homing. Meanwhile, during colitis, the ectopia of A. faecalis in colon tissues, promoted vinculin acetylation by A. faecalis-derived metabolite acetic acid, which impeded intestinal barrier via hindering the binding of vinculin to β-catenin. Our study revealed A. faecalis not only suppress mucosal immune responses via reducing IgA+ B cells in Peyer's patches but also disrupt intestinal barrier via increasing vinculin acetylation, ultimately promoting inflammation-to-cancer transition in CRC.

Intestinal and esophageal microbiota in esophageal cancer development and treatment

Esophageal cancer (EC) is the eleventh most commonly diagnosed cancer, and its prognosis remains poor. Several challenges remain for improving the clinical outcomes of EC, and improving technologies for early detection, diversifying treatment options, and advancing personalized treatment are essential. Alterations in the intestinal and esophageal microbiota are associated with the pathogenesis and progression of EC; for instance, Fusobacterium nucleatum is important in the pathogenesis and progression of esophageal squamous cell carcinoma. Therefore, a novel diagnostic biomarker may be identified using the intestinal microbiota. Furthermore, targeting the intestinal and esophageal microbiota may help in the early detection of EC, use of a novel prognostic biomarker, and even the detection of a therapeutic target, resulting in a more individualized therapeutic approach for EC. In this review, we summarize the clinical research focused on the intestinal and esophageal microbiota in EC development and its treatment, and discuss the challenges in the clinical application of intestinal and esophageal microbiota.

Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut

In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.

Exploring the interaction between the gut microbiota and cyclic adenosine monophosphate-protein kinase A signaling pathway: a potential therapeutic approach for neurodegenerative diseases

The interaction between the gut microbiota and cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling pathway in the host's central nervous system plays a crucial role in neurological diseases and enhances communication along the gut-brain axis. The gut microbiota influences the cAMP-PKA signaling pathway through its metabolites, which activates the vagus nerve and modulates the immune and neuroendocrine systems. Conversely, alterations in the cAMP-PKA signaling pathway can affect the composition of the gut microbiota, creating a dynamic network of microbial-host interactions. This reciprocal regulation affects neurodevelopment, neurotransmitter control, and behavioral traits, thus playing a role in the modulation of neurological diseases. The coordinated activity of the gut microbiota and the cAMP-PKA signaling pathway regulates processes such as amyloid-β protein aggregation, mitochondrial dysfunction, abnormal energy metabolism, microglial activation, oxidative stress, and neurotransmitter release, which collectively influence the onset and progression of neurological diseases. This study explores the complex interplay between the gut microbiota and cAMP-PKA signaling pathway, along with its implications for potential therapeutic interventions in neurological diseases. Recent pharmacological research has shown that restoring the balance between gut flora and cAMP-PKA signaling pathway may improve outcomes in neurodegenerative diseases and emotional disorders. This can be achieved through various methods such as dietary modifications, probiotic supplements, Chinese herbal extracts, combinations of Chinese herbs, and innovative dosage forms. These findings suggest that regulating the gut microbiota and cAMP-PKA signaling pathway may provide valuable evidence for developing novel therapeutic approaches for neurodegenerative diseases.

Marine natural products as potential anti-Pseudomonas aeruginosa agents: challenges and advances

Antimicrobial resistance (AMR) has become a pressing need to address in the major global public health challenges, posing a serious threat to human health. Pseudomonas aeruginosa (PA) is one of the most concerning Gram-negative pathogens and is typically treated with broad-spectrum antibiotics. PA exhibits resistance to multiple antibiotics, multifactorial virulence, and dynamic hyperadaptation, which results in a particularly formidable challenge in eliminating PA from patients. The problem of drug resistance is becoming increasingly serious, and the development of new antibiotics is extremely lagging behind, resulting in no drug with a new structure and mechanism being approved for the treatment of infections caused by drug-resistant Gram-negative bacteria over the past half-century. Consequently, the development of new antibiotics is of utmost urgency and importance. Marine natural products (MNPs) have become an important source for developing new antibiotics due to their unique properties. So far, 44 potential molecules with significant anti-PA activity have been isolated from marine organisms, of which 19 have been reported as quorum-sensing system inhibitors (QSIs) with potential for further development. In this review, we provide a comprehensive summary of the current status of drug resistance, pathogenic mechanisms, and resistance mechanisms associated with PA infections. We also highlight the challenges and opportunities presented by MNPs in the development of anti-PA drugs, and offer recommendations to accelerate the antibiotic development process, thereby providing valuable insights for the study and exploitation of novel antibiotics.

Gut microbiota in melanoma: Effects and pathogeneses

The gut microbiota exhibits intricate connections with the body's immune system and holds significant implications for various diseases and cancers. Currently, accumulating evidence suggests a correlation between the composition of the gut microbiota and the development, treatment, and prognosis of melanoma. However, the underlying pathogenesis remains incompletely elucidated. In this comprehensive review, we present an in-depth review of the role played by gut microbiota in melanoma tumorigenesis, growth, metastasis, treatment response, and prognosis. Furthermore, we discuss the potential utility of gut microbiota as a promising prognostic marker. Lastly, we summarize three routes through which gut microbiota influences melanoma: immunity, aging, and the endocrine system. By modulating innate and adaptive immunity in patients with melanoma across different age groups and genders, the gut microbiota plays a crucial role in anti-tumor immune regulation from tumorigenesis to prognosis management, thereby impacting tumor growth and metastasis. This review also addresses current study limitations while highlighting future research prospects.

Interplay between gut microbiota and exosome dynamics in sleep apnea

Sleep-disordered breathing (SDB) is characterized by recurrent reductions or interruptions in airflow during sleep, termed hypopneas and apneas, respectively. SDB impairs sleep quality and is linked to substantive health issues including cardiovascular and metabolic disorders, as well as cognitive decline. Recent evidence suggests a link between gut microbiota (GM) composition and sleep apnea. Indeed, GM, a community of microorganisms residing in the gut, has emerged as a potential player in various diseases, and several studies have identified associations between sleep apnea and GM diversity along with shifts in bacterial populations. Additionally, the concept of "leaky gut," a compromised intestinal barrier with potentially increased inflammation, has emerged as another key player in the potential bidirectional relationship between GM and sleep apnea. One of the potential effectors could be extracellular vesicles (EVs) underlying gut-brain communication pathways that are relevant to sleep regulation and function. Thus, therapeutic implications afforded by targeting the GM or exosomes for sleep apnea management have surfaced as promising areas of research. This review explores current understanding of the relationship between GM, exosomes and sleep apnea, highlighting key research dynamics and potential mechanisms. A comprehensive review of the literature was conducted, focusing on studies investigating GM composition, intestinal barrier function and gut-brain communication in relation to sleep apnea.

Fecal microbiota transplantation in allergic diseases

Microorganisms such as bacteria, fungi, viruses, parasites living in the human intestine constitute the human intestinal microbiota. Dysbiosis refers to compositional and quantitative changes that negatively affect healthy gut microbiota. In recent years, with the demonstration that many diseases are associated with dysbiosis, treatment strategies targeting the correction of dysbiosis in the treatment of these diseases have begun to be investigated. Faecal microbiota transplantation (FMT) is the process of transferring faeces from a healthy donor to another recipient in order to restore the gut microbiota and provide a therapeutic benefit. FMT studies have gained popularity after probiotic, prebiotic, symbiotic studies in the treatment of dysbiosis and related diseases. FMT has emerged as a potential new therapy in the treatment of allergic diseases as it is associated with the maintenance of intestinal microbiota and immunological balance (T helper 1/T helper 2 cells) and thus suppression of allergic responses. In this article, the definition, application, safety and use of FMT in allergic diseases will be discussed with current data.

Nanoplastic exposure affects the intestinal microbiota of adult Drosophila flies

Micro- and nanoplastics (MNPLs) are emerging environmental pollutants that have garnered significant attention over the past few decades due to their detrimental effects on human health through various exposure pathways. This study investigates the impact of MNPLs on gut microbiota, utilizing Drosophila melanogaster as a model organism. Drosophila was selected for its microbiota's similarities to humans and its established role as an accessible and well-characterized model system. To analyze microbiota, full-length 16S rRNA gene sequencing was performed using the Nanopore sequencing platform, enabling comprehensive profiling of the microbial populations present in the samples. As models of MNPLs, two commercial polystyrene nanoplastics (PS-NPLs, 61.20 and 415.22 nm) and one lab-made polylactic acid nanoplastic (PLA-NPLs, 463.90 nm) were selected. As a positive control, zinc oxide nanoparticles (ZnO-NPs) were used. The observed findings revealed that exposure to MNPLs induced notable alterations in gut microbiota, including a reduction in bacterial abundance and shifts in species composition. These results suggest that MNPLs exposure can lead to microbial dysbiosis and potential gut health disruptions through its interaction, either with the gut epithelial barrier or directly with the resident microorganisms.

Causal association between gut microbiota and endometrial cancer in European and East Asian populations: a two-sample Mendelian randomization study

BACKGROUND

Endometrial cancer (EC) is a significant global health concern. While observational epidemiological studies suggest a potential link between gut microbiota dysbiosis and the development of EC, the direction and causality of this association remain uncertain.

METHODS

We performed Mendelian randomization (MR) analysis to investigate the causal relationship between gut microbiota and EC. Exposure data were obtained from the MiBioGen study consortium (N = 18,340), and outcome data were sourced from the IEU OpenGWAS database, specifically datasets "ebi-a-GCST006464" (N = 121,885) and "bbj-a-113" (N = 90,730). The inverse variance-weighted(IVW) method was applied to evaluate the association between gut microbiota composition and EC risk. Sensitivity analyses were conducted to ensure the robustness of the findings.

RESULTS

Our study identified several microbial taxa linked to EC risk. In Europeans, genera such as Marvinbryantia, RuminococcaceaeUCG014, and Dorea exhibited protective effects, while family Erysipelotrichaceae (OR:1.224) and FamilyXI (OR:1.090) were significantly correlated with high EC risk. In East Asians, genera Lachnospira (OR:3.561) and family Bifidobacteriaceae (OR:1.715) were found associated with EC risk. Genera Lachnoclostridium and ErysipelotrichaceaeUCG003, family Coriobacteriaceae positively served as protective factors. Sensitivity analyses confirmed the reliability of our results, and there was no evidence of pleiotropy or heterogeneity. Our analysis identified several microbial taxa associated with EC risk. In Europeans, genera such as Marvinbryantia, Ruminococcaceae UCG014, and Dorea demonstrated protective effects, while the families Erysipelotrichaceae (OR: 1.224) and FamilyXI (OR: 1.090) were significantly associated with increased EC risk. In East Asians, the genus Lachnospira (OR: 3.561) and the family Bifidobacteriaceae (OR: 1.715) were linked to higher EC risk, whereas the genera Lachnoclostridium and Erysipelotrichaceae UCG003 and the family Coriobacteriaceae were identified as protective factors. Sensitivity analyses confirmed the reliability of these results, with no evidence of pleiotropy or heterogeneity.

CONCLUSION

This study highlights a relationship between gut microbiota and EC, emphasizing the potential of gut microbiota as therapeutic targets and biomarkers for assessing EC prognosis and treatment efficacy. These findings provide novel insights into the role of gut microbiota in the development and progression of EC.

Repeated enema administration in rhesus macaques is not sufficient to promote bacterial dysbiosis or gastrointestinal dysfunction

Chronic gastrointestinal diseases are a significant global health burden that can require the use of gastrointestinal-cleansing regimens for diagnostics or therapeutic treatment. These regimens are beneficial for facilitating surgical preparation, drug delivery, colorectal cancer screenings, and personal use is common among proponents of natural health and among certain populations at high risk of HIV acquisition. It remains unclear, however, whether repeated clearance of the colonic microbiome induces persistent changes in the microbiome, intestinal immunity, and viral disease susceptibility. We addressed these parameters by repeatedly administering iso-osmolar enemas to rhesus macaques prior to low-dose intra-rectal challenge with simian immunodeficiency virus (SIV). Considering both longitudinal and cross-sectional analyses, we observed no consistent changes in the fecal microbiome or intestinal immune parameters of treated animals, nor were significant differences observed in susceptibility to SIV acquisition. Unexpectedly, enema-treated animals exhibited significantly lower setpoint viral loads after infection, although we were unable to clearly identify attributing causes. Our study demonstrates that repeated microbiome clearance using clinically administered iso-osmolar enemas is not sufficient to restructure the fecal microbiome, perturb intestinal immune parameters, or increase susceptibility to mucosal SIV challenge. This research framework serves as a model for the development of colonic-administered diagnostics and interventions.

Designing live bacterial therapeutics for cancer

Humans are home to a diverse community of bacteria, many of which form symbiotic relationships with their host. Notably, tumors can also harbor their own unique bacterial populations that can influence tumor growth and progression. These bacteria, which selectively colonize hypoxic and acidic tumor microenvironments, present a novel therapeutic strategy to combat cancer. Advancements in synthetic biology enable us to safely and efficiently program therapeutic drug production in bacteria, further enhancing their potential. This review provides a comprehensive guide to utilizing bacteria for cancer treatment. We discuss key considerations for selecting bacterial strains, emphasizing their colonization efficiency, the delicate balance between safety and anti-tumor efficacy, and the availability of tools for genetic engineering. We also delve into strategies for precise spatiotemporal control of drug delivery to minimize adverse effects and maximize therapeutic impact, exploring recent examples of engineered bacteria designed to combat tumors. Finally, we address the underlying challenges and future prospects of bacterial cancer therapy. This review underscores the versatility of bacterial therapies and outlines strategies to fully harness their potential in the fight against cancer.

The role of nutritional factors in exercise-induced bronchoconstriction: a narrative review

Exercise-induced bronchoconstriction (EIB) describes an acute narrowing of the airways that develops following vigorous physical activity. Clinical responses to current asthma therapy, such as leukotriene antagonists and corticosteroids, are heterogeneous, even with optimal treatment. Epidemiological studies indicate an increasing use of complementary and alternative medicine therapy in asthma patients due to the lack of efficacy of conventional treatment, concerns about potentially harmful side effects of pharmacological treatment, cost barriers to asthma care, and the accessibility of complementary and alternative medicine therapy. Plausible physiological mechanisms now exist for many nutrients as potential modifiers of EIB severity, primarily because of their role in inflammatory processes, airway smooth muscle function, and modulation of lung microvascular volume and pressure. Dietary supplementation as a treatment for EIB has generally shown evidence of significant yet incomplete inhibition of EIB with low-salt diets, omega-3 fatty acids, and vitamin C when supplemented for up to 3 weeks. However, larger, randomized, placebo-controlled, double-blinded trials are needed to clarify the effectiveness of nutritional intervention in individuals with EIB. Additionally, many studies have focused on nonathletes with EIB, and therefore, more studies are required to evaluate the efficacy of nutritional intervention on EIB in elite athletes. In conclusion, if dietary supplementation or restriction is prescribed, it should be seen as an option to lessen the reliance on pharmaceutical interventions and not as an alternative to established pharmacotherapies.

Molecular mimicry in the pathogenesis of autoimmune rheumatic diseases

Autoimmune rheumatic diseases (ARDs) are a heterogeneous group of conditions characterized by excessive and misdirected immune responses against the body's own musculoskeletal tissues. Their exact aetiology remains unclear, with genetic, demographic, behavioural and environmental factors implicated in disease onset. One prominent hypothesis for the initial breach of immune tolerance (leading to autoimmunity) is molecular mimicry, which describes structural or sequence similarities between human and microbial proteins (mimotopes). This similarity can lead to cross-reactive antibodies and T-cell receptors, resulting in an immune response against autoantigens. Both commensal microbes in the human microbiome and pathogens can trigger molecular mimicry, thereby potentially contributing to the onset of ARDs. In this review, we focus on the role of molecular mimicry in the onset of rheumatoid arthritis and systemic lupus erythematosus. Moreover, implications of molecular mimicry are also briefly discussed for ankylosing spondylitis, systemic sclerosis and myositis.

Actinomyces viscosus promotes neuroprotection in C. elegans models of Parkinson's disease

Parkinson's Disease is characterized by selective degeneration of dopaminergic neurons, primarily in the substantia nigra pars compacta, as well as accumulation of alpha-synuclein enriched protein aggregates within neurons. The pathogenesis of PD is still not completely understood, and no treatments exist that alter disease progression. Obvious genetic causes are detected in only a small number of PD patients (5-10 %), suggesting that environmental factors play a significant role the development of PD. Correlative studies suggest that the microbiota could be an important environmental modifier of neurodegeneration. We identified a microbiotal isolate, Actinomyces viscosus, that reduced neurodegeneration in C. elegans expressing a pathological mutant form (G2019S) of leucine-rich repeat kinase 2 (LRRK2) in dopaminergic neurons. A. viscosus also suppressed autophagic dysfunction in these animals and reduced alpha-synuclein aggregation in a synucleinopathy model. Global gene expression analysis revealed increased expression of aspartic cathepsins in response to A. viscosus. Consistent with the involvement of these proteins in neuroprotection, we found that reducing aspartic cathepsin function increased neurodegeneration in the LRRK2 transgenic model. Our findings contribute to the current understanding of how the gut microbiota may influence PD, elucidating one potential mechanism of microbiota-mediated neuroprotection.

The intestinal barrier: a pivotal role in health, inflammation, and cancer

The intestinal barrier serves as a boundary between the mucosal immune system in the lamina propria and the external environment of the intestinal lumen, which contains a diverse array of microorganisms and ingested environmental factors, including pathogens, food antigens, toxins, and other foreign substances. This barrier has a central role in regulating the controlled interaction between luminal factors and the intestinal immune system. Disruptions of intestinal epithelial cells, which serve as a physical barrier, or the antimicrobial peptides and mucins they produce, which act as a chemical barrier, can lead to a leaky gut. In this state, the intestinal wall is unable to efficiently separate the intestinal flora and luminal contents from the intestinal immune system. The subsequent activation of the immune system has an important role in the pathogenesis of inflammatory bowel disease, as well as in metabolic dysfunction-associated steatohepatitis, primary sclerosing cholangitis, and colorectal cancer. Dysregulated intestinal barrier integrity has also been described in patients with chronic inflammatory diseases outside the gastrointestinal tract, including rheumatoid arthritis and neurodegenerative disorders. Mechanistic studies of barrier dysfunction have revealed that the subsequent local activation and systemic circulation of activated immune cells and the cytokines they secrete, as well as extracellular vesicles, promote proinflammatory processes within and outside the gastrointestinal tract. In this Review, we summarise these findings and highlight several new therapeutic concepts currently being developed that attempt to control inflammatory processes via direct or indirect modulation of intestinal barrier function.

Gut microbe-skin axis on a chip for reproducing the inflammatory crosstalk

The gut-skin axis has emerged as a crucial mediator of skin diseases, with mounting evidence highlighting the influence of gut microbiota on skin health. However, investigating these mechanisms has been hindered by the lack of experimental systems that enable direct study of gut microbiota-skin interactions. Here, we present the gut microbe-skin chip (GMS chip), a novel microfluidic platform designed to model microbiome-gut-skin axis interactions. The GMS chip allows the coculture of intestinal epithelial cells (Caco-2), human epidermal keratinocytes (HEKa), and gut microbes with fluidic connection mimicking the blood flow. We validated that the gut compartment, with a self-sustaining oxygen gradient, enabled coculturing gut bacteria such as Escherichia coli (E. coli) and Lactobacillus rhamnosus GG (LGG), and the skin cells properly differentiated in the chip in the presence of fluid flow. Disruption of intestinal epithelial integrity by dextran sodium sulfate (DSS) combined with lipopolysaccharides (LPS) selectively decreased skin cell viability while sparing gut cells. Notably, pretreatment with LGG showed a protective effect against the skin cell damage by enhancing the intestinal barrier function. The GMS chip effectively recapitulates the influence of gut microbiota on skin health, representing a pivotal step forward in studying gut-skin axis mechanisms and the role of the gut microbiome in skin diseases.

Impact of antimicrobial exposure at delivery and siblings on early Bifidobacterium succession and allergy development up to 24 months of age

BACKGROUND

Allergic diseases such as asthma, eczema, and food allergies are rising globally. The infant gut microbiota, particularly the dominance of Bifidobacterium, shapes immune development and allergy risk. In Japan-where Bifidobacterium prevalence is notably high-longitudinal investigations focusing on the pre-weaning period, when external influences are relatively limited, remain scarce. Therefore, based on consistent hypotheses and findings from previous studies, we investigated how two important early factors-antibiotic exposure at birth and the presence of older siblings-influence the gut environment in early infancy and subsequent allergy development.

RESULTS

In a prospective cohort of 121 Japanese infants, stool samples were collected at seven time points from birth through 24 months. We quantified the relative abundances of Bifidobacterium, Bacteroides, Clostridium, and Faecalibacterium and recorded allergic outcomes at 2 years. Both antimicrobial exposure at delivery and sibling presence significantly altered gut microbiota composition and overall diversity in early infancy. Although the full cohort showed no consistent diversity or Bifidobacterium differences by allergic status, in several subgroups where these two factors were excluded, infants who had an allergy by 24 months exhibited marked shifts in early gut microbiota community structure-particularly in beta diversity-and reduced Bifidobacterium occupancy during the pre-weaning period (1-6 months) versus non-allergic peers. Moreover, infants whose gut microbiota was initially affected by these factors showed a recovery in diversity after weaning, a rebound more pronounced in non-allergic individuals.

CONCLUSIONS

These findings indicate that both the initial community configuration and its capacity to rebound after perturbation are critical determinants of allergy risk. By focusing on dynamic changes through weaning and adjusting for decisive confounders, this study refines insight beyond prior cross-sectional work. Early interventions that preserve or restore microbial diversity and Bifidobacterium dominance may therefore offer a promising strategy to mitigate allergic disease development.

Fecal 16S rRNA sequencing and metabolomics reveal abnormal metabolism activity in preterm infants with different gestational ages

Objective

This study aims to conduct a comprehensive analysis of the differences in gut microbiota and metabolomics in preterm infants stratified by gestational age.

Methods

Fresh fecal samples were collected from neonates within the first 3 days after birth. The gut microbiota composition and the changes in specific taxa abundance were analyzed using 16S rRNA sequencing. Metabolomic profiling was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Participants were categorized into four groups based on gestational age at birth: PreA group (34-36 weeks), PreB group (32-33 weeks), PreC group (28-31 weeks), and control group (37-42 weeks). Metabolic pathways were identified through metabolomics analysis, referencing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

Results

Notably, Principal Coordinates Analysis (PCoA) showed clear separation among samples from all groups, with significant differences noted in the PreC group when compared with the other three. We found a strong association between Escherichia-Shigella and Ureaplasma genera with infants born before 32 weeks of gestation, suggesting a higher risk of opportunistic infections for preterm infants under this gestational threshold. As gestational age increases, Megamonas and Prevotella gradually emerged, while Escherichia-Shigella and Ureaplasma progressively diminished. KEGG enrichment analysis indicated that Pyrimidine metabolism was a differentially regulated pathway between the PreA group and the control group. Interestingly, the only major differential metabolic pathway between the PreB group and the control group was Arachidonic acid metabolism. The bubble diagram revealed significant enrichment of differential metabolites in Pyrimidine and beta-Alanine metabolism pathways when comparing the PreC group with the control group.

Conclusion

Significant differences were observed in the fecal microbiome and metabolome between preterm and full-term infants, particularly in those born before 32 weeks of gestation. These findings suggested that the gut microbial system in preterm infants undergone progressive maturation, approaching a "healthy" state characteristic of full-term infants as gestational age increases.

A consortium of seven commensal bacteria promotes gut microbiota recovery and strengthens ecological barrier against vancomycin-resistant enterococci

BACKGROUND

Vancomycin-resistant enterococci (VRE) often originate from the gastrointestinal tract, where their proliferation precedes dissemination into the bloodstream, and can lead to systemic infection. Uncovering the actors and mechanisms reducing the intestinal colonisation by VRE is essential to control infection. We aimed to identify commensal bacteria that interfere with VRE gut colonisation or act as an ecological barrier.

RESULTS

We performed a 3-week longitudinal analysis of the gut microbiota composition and VRE carriage levels during microbiota recovery in mice colonised with VRE after antibiotic-induced dysbiosis. By combining biological data and mathematical modelling, we identified 15 molecular species (OTUs) that negatively correlated with VRE overgrowth. Six strains representative of these OTUs were collected, cultivated and used in mixture with a seventh strain (Mix7) in two different mouse lines challenged with VRE. Of the seven strains, three belonged to Lachnospiraceae, one to Muribaculaceae, one to Ruminococcaceae and two to Lactobacillaceae. We found that Mix7 led to a better recovery of the gut microbiota composition and reduced VRE carriage. Differences in the effect of Mix7 were observed between responder and non-responder mice. These differences were associated with variations in the composition of the initial microbiota and during recovery and represent potential biomarkers for predicting response to Mix7. In a mouse model of alternative stable state of dysbiosis, response to Mix7 was associated with higher concentrations of short-chain fatty acids (acetate, propionate, butyrate) and a range of metabolites including bile acids, reflecting the recovery of the microbiota back to initial state. Furthermore, Muribaculum intestinale strain was required to obtain the Mix7 effect on VRE reduction in vivo, but the presence of at least one of the other six strains was needed. None of the supernatant of the seven strains, alone or in combination, inhibited VRE growth in vitro. Interestingly, five strains belong to species shared among humans and mice, and the other two have human functional equivalents.

CONCLUSIONS

An innovative approach based on mathematical modelling of the microbiota composition permitted to identify a mixture of commensal bacterial strains, which improves the ecological barrier effect against VRE. The mechanisms are dependent on the recovery and initial composition of the microbiota. Ultimately, this work will enable a move towards a personalised medicine by targeting predisposed patients presenting a risk of infection, such as neutropenic or bone-marrow transplant patients, and likely to respond to supplementation with commensal strains, providing new live biotherapeutic products and biomarkers to predict response to supplementation. Video Abstract.

Genealogically bewildered individuals and forensic identification: a review of current and emerging solutions

The increasing use of assisted reproductive technologies (ART) with donor gametes is driven by rising infertility rates, delayed parenthood, and the need to prevent hereditary diseases. Greater social acceptance of diverse family structures, advancements in reproductive medicine, and improving success rates also contribute. Accessibility, affordability, and cross-border reproductive care further expand ART's reach, making donor gametes a preferred option for many individuals and couples worldwide. The widespread application of ART has led to an increasing number of donor-conceived individuals, many of whom are now reaching reproductive maturity. This demographic shift introduces significant challenges for traditional forensic genetic identification methods, which rely on biological reference samples from genetically related individuals. The absence of such samples complicates the identification process, particularly for individuals conceived via gamete donation or adoption, where biological and legal parentage are incongruent. Conventional forensic genetic analyses, including short tandem repeat (STR) and single nucleotide polymorphism (SNP) profiling of autosomal, Y-chromosome, X-chromosome, and mitochondrial DNA, exhibit limited efficacy in these scenarios. While these methods can sometimes identify individuals conceived using a single donor gamete, they are insufficient for cases involving dual donor gametes or mitochondrial replacement therapy. Emerging methodologies such as forensic genetic genealogy, DNA methylation profiling, and human microbiome analysis offer innovative approaches but necessitate further clinical validation and standardization.

Exploring bacterial cellulose as an engineered living and programmable biomaterial across disciplines through qualitative thematic analysis

Bacterial cellulose is an engineered living material which holds significant potential due to its material properties and broad applicability across scientific and design disciplines. However, challenges in interdisciplinary collaboration, scalability and commercialization have slowed its widespread adoption and integration into industry applications such as fashion and textiles. This study addresses the gap in understanding how bacterial cellulose is perceived, developed, and utilized across scientific and design disciplines. Through 20 semi-structured interviews with scientists and designers around the world, this paper explores the following themes: (1) the human-living material relationship spectrum, which highlights the distinct ways science and design stakeholders interact with bacterial cellulose as a living material; (2) perceptions of a living material made from bacteria; and (3) bacterial cellulose's potential as a programmable biomaterial. Additionally, we employ Bruno Latour's Actor-Network Theory to map the complex network of human and non-human actors shaping bacterial cellulose's trajectory, identifying critical factors such as consumer acceptance, interdisciplinary collaboration, and material culture. By bridging perspectives from science and design, this study offers actionable insights into bacterial cellulose's future as a sustainable and programmable engineered living material, guiding its responsible development and broader adoption across industries.

Menopause and gastrointestinal health and disease

Menopause has far-reaching effects on human physiology, including the gastrointestinal tract, and can negatively influence the quality of life of women who are affected. Menopause can have multiple effects on gastrointestinal function, including altering gut motility and changing the composition of the gut microbiota. As a result, some gastrointestinal and hepatic conditions are more common among individuals in peri- and postmenopause, and people with these conditions before menopause might also experience greater symptom severity and worse health-related quality of life during this time. The use of hormone replacement therapy to treat menopausal symptoms might also affect gastrointestinal health and well-being. Individuals in postmenopause are at risk for bone remodelling and osteoporosis due to ageing and loss of sex hormones. However, secondary osteoporosis can also occur due to medications used to treat gastrointestinal conditions (for example, glucocorticoids and other immunosuppressive medications) and the conditions themselves (for example, autoimmune disease or coeliac disease). Although all people who menstruate will eventually transition to menopause, there are relatively few studies evaluating the effect of menopause on gastrointestinal symptoms and quality of life. This Review aims to summarize available evidence and highlight areas where research is needed.

Insights from the 2024 pediatric rheumatology basic/translational years in review

BACKGROUND

Advances in Pediatric Rheumatology are driven by mechanistic insights from basic and translational science. We have selected and reviewed the most impactful basic/translational science from our "Year in Review (YIR)" presentations from the 2024 Pediatric Rheumatology European Society and American College of Rheumatology Convergence meetings (September and November 2024, respectively).

MAIN BODY

We drew from fundamental immunology, human genetics, animal models, and computational & "omic" manuscripts published in the year preceding these meetings. Avoiding overlap with other topics presented in this "Perspectives" series, summarized herein are the major themes we gleaned from that process. These include (1) innovative concepts and tools to study immune health, (2) new mechanistic insights into pediatric rheumatic diseases and (3) novel therapeutic targets and treatment approaches in rheumatic disease.

CONCLUSIONS

As part of a living relationship with the basic/translational literature that shapes our field and practice, we hope readers will be inspired to delve more deeply into the topics and manuscripts highlighted in this YIR summary.

Intestinal Microbes, Metabolites, and Hormones in Alcohol-Associated Liver Disease

Alcohol-associated liver disease (ALD)-encompassing conditions including steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma-refers to hepatic damage arising from excessive or hazardous alcohol consumption, and is now recognized as a significant global health burden. Although the mechanisms underlying ALD remain incompletely understood, several pathways have been substantiated over the last five decades, notably the involvement of intestinal microorganisms and the involvement of the gut-liver axis in alcohol metabolism and ALD pathogenesis. Ethanol intake disrupts the intestinal microbial balance and compromises the gut barrier, resulting in increased permeability to microbial products. The subsequent translocation of microbial metabolites and other antigenic substances to the liver activates hepatic immune responses, thereby contributing to liver injury. In addition, gastrointestinal hormones are also implicated in ALD progression through various mechanisms. Although no therapies for ALD have been approved by the Food and Drug Administration, various therapeutic strategies targeting the intestinal microbiota and gut barrier have been identified. In conclusion, this review discusses the role of the gut-liver axis in alcohol metabolism and ALD pathogenesis and explores the emerging therapeutic strategies.

Changing Gastrointestinal Transit Time Alters Microbiome Composition and Bile Acid Metabolism: A Cross-Over Study in Healthy Volunteers

BACKGROUND

The specific influence of whole gut transit time (WGTT) on microbiome dynamics and bile acid metabolism remains unclear, despite links between changes in WGTT and certain gastrointestinal disorders. Our investigation aimed to determine the impact of WGTT changes on the composition of the fecal microbiome and bile acid profile.

METHODS

Healthy volunteers (n = 18) received loperamide, to decrease bowel movement frequency, and senna, a laxative, each over a 6-day period, in a randomized sequence, with a minimum 16-day interval between each treatment. Stool samples were analyzed for microbiome by shotgun sequencing and bile acid composition determined with high-performance liquid chromatography coupled to tandem mass spectrometry. Sera were examined for markers of bile acid synthesis.

KEY RESULTS

Senna or loperamide decreased or increased WGTT, respectively. Treatment altered stool characteristics, bowel movement frequency, and stool weight. The senna-treated group had increased primary and secondary fecal bile acids; serum levels of fibroblast growth factor 19 were significantly reduced. Increasing WGTT with loperamide led to an increase in bile salt hydrolase genes, along with elevated bacterial species richness (p = 0.04). Thirty-six species exhibiting significant differences were identified, several of which have notable implications for gut health. WGTT displayed negative correlations with total primary (particularly chenodeoxycholic acid) and secondary bile acids (ursodeoxycholic acid and glycochenodeoxycholic acid). Treatment-induced changes in microbiome composition and bile acid metabolism reverted back to baseline within 16 days.

CONCLUSION

Whole gut transit time changes significantly affect fecal microbiome composition and function, as well as bile acid composition and synthesis in healthy subjects. This consideration is likely to have long-term implications.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.

Expression of Fluorescence Reporters and Natural Products in Native Gut Escherichia coli

Escherichia coli is a widely studied model organism and an integral component of the human gut microbiome, offering significant potential for bacteria-based therapeutic applications. Despite this promise, engineering native E. coli strains remains challenging. In this study, we employed the chassis-independent recombinase-assisted genome engineering (CRAGE) technique to genetically engineer the native gut strain E. coli EcAZ-1 and the probiotic strain E. coli Nissle 1917 (EcN). We successfully expressed a suite of heterologous genes, including the bioluminescent lux operon, green fluorescent protein (GFP), and oxygen-independent fluorescent protein IFP2.0, in both strains. Optimization of IFP2.0 fluorescence was achieved under both aerobic and anaerobic conditions by coexpressing a heme oxygenase gene and/or supplementing the chromophore biliverdin or hemin. Additionally, we engineered these strains to biosynthesize the bioactive compounds naringenin and mycosporine-like amino acids. This work highlights the potential of native E. coli strains as versatile platforms for synthetic biology, paving the way for innovative applications in biomedical research and therapeutic development.

The intestinal interferon system and specialized enterocytes as putative drivers of HIV latency

The barrier to HIV cure is the HIV reservoir, which is composed of latently infected CD4+ T cells and myeloid cells that carry stably integrated and replication-competent provirus. The gastrointestinal tract (GIT) contains a substantial part of the HIV reservoir and its immunophysiology could be especially conducive for HIV persistence and reactivation. However, the exact cellular microenvironment and molecular mechanisms that govern the renewal of provirus-harboring cells and proviral reactivation in the GIT remain unclear. In this review, we outline the evidence supporting an overarching hypothesis that interferon activity driven by specialized enterocytes creates a microenvironment that fosters proliferation of latently infected CD4+ T cells and sporadic HIV reactivation from these cells. First, we describe unique immunologic features of the gastrointestinal associated lymphoid tissue (GALT), specifically highlighting IFN activity in specialized enterocytes and potential interactions between these cells and neighboring HIV susceptible cells. Then, we will describe dysregulation of IFN signaling in HIV infection and how IFN dysregulation in the GALT may contribute to the persistence and reactivation of the latent HIV reservoir. Finally, we will speculate on the clinical implications of this hypothesis for HIV cure strategies and outline the next steps.

Engineered Tissue Models to Decode Host-Microbiota Interactions

A mutualistic co-evolution exists between the host and its associated microbiota in the human body. Bacteria establish ecological niches in various tissues of the body, locally influencing their physiology and functions, but also contributing to the well-being of the whole organism through systemic communication with other distant niches (axis). Emerging evidence indicates that when the composition of the microbiota inhabiting the niche changes toward a pathogenic state (dysbiosis) and interactions with the host become unbalanced, diseases may present. In addition, imbalances within a single niche can cause dysbiosis in distant organs. Current research efforts are focused on elucidating the mechanisms leading to dysbiosis, with the goal of restoring tissue homeostasis. In vitro models can provide critical experimental platforms to address this need, by reproducing the niche cyto-architecture and physiology with high fidelity. This review surveys current in in vitro host-microbiota research strategies and provides a roadmap that can guide the field in further developing physiologically relevant in vitro models of ecological niches, thus enabling investigation of the role of the microbiota in human health and diseases. Lastly, given the Food and Drug Administration Modernization Act 2.0, this review highlights emerging in vitro strategies to support the development and validation of new therapies on the market.

Nanomedicines as disruptors or inhibitors of biofilms: Opportunities in addressing antimicrobial resistance

The problem of antimicrobial resistance (AMR) has caused global concern due to its great threat to human health. Evidences are emerging for a critical role of biofilms, one of the natural protective mechanisms developed by bacteria during growth, in resisting commonly used clinical antibiotics. Advances in nanomedicines with tunable physicochemical properties and unique anti-biofilm mechanisms provide opportunities for solving AMR risks more effectively. In this review, we summarize the five "A" stages (adhesion, amplification, alienation, aging and allocation) of biofilm formation and mechanisms through which they protect the internal bacteria. Aimed at the characteristics of biofilms, we emphasize the design "THAT" principles (targeting, hacking, adhering and transport) of nanomedicines in their interactions with biofilms and internal bacteria. Furthermore, recent progresses in multimodal antibacterial nanomedicines, including biofilms disruption and bactericidal activity, and the types of currently available antibiofilm nanomedicines contained organic and inorganic nanomedicines are outlined and highlighted their potential applications in the development of preclinical research. Last but not least, we offer a perspective for the effectiveness of nanomedicines designed to address AMR and challenges associated with their clinical translation.

Associations of microbiome pathophysiology with social activity and behavior are mediated by epigenetic modulations: Avenues for designing innovative therapeutic strategies

A number of investigations have shown that gut microbiome influences humans' ability to communicate with others, and impairments in social interactions are linked to alterations in gut microbiome composition and diversity, via epigenetic mechanisms. This article reviews the links among gut microbiome, social behavior, and epigenetic shifts relevant to gut microbiome-derived metabolites. First, we discuss how different social determinants of health, such as socioeconomic status, diet, environmental chemicals, migration, ecological conditions, and seasonal changes may influence gut microbiome composition, diversity, and functionality, along with epigenetic alterations and thereby affect social behavior. Next, we consider how gut microbiome-derived metabolites, diet, probiotics, and fecal microbiome transplantation may reduce impairments in social interactions through the adjustment of epigenetic aberrations (e.g., DNA methylation, histone modifications, and microRNAs expression) which may suppress or increase gene expression patterns. Finally, we present the potential benefits and unresolved challenges with the use of gut microbiome-targeted therapeutics in reducing social deficits.

Universal Law for the Dispersal of Motile Microorganisms in Porous Media

Dispersal is essential to the plethora of motile microorganisms living in porous environments, yet how it relates to movement patterns and pore space structure remains largely unknown. Here we investigate numerically the long-time dispersal of a run-and-tumble microorganism that remains trapped at solid surfaces and escapes from them by tumbling. We find that dispersal and mean run time are connected by a universal relation, that applies for a variety of porous microstructures and swimming strategies. We explain how this generic dependence originates in the invariance of the mean free path with respect to the movement pattern, and we discuss the optimal strategy that maximizes dispersal. Finally, we extend our approach to microorganisms moving along the surface. Our results provide a general framework to quantify dispersal that works across the vast diversity of movement patterns and porous media.

Tiny but Mighty: Small RNAs-The Micromanagers of Bacterial Survival, Virulence, and Host-Pathogen Interactions

Bacterial pathogens have evolved diverse strategies to infect hosts, evade immune responses, and establish successful infections. While the role of transcription factors in bacterial virulence is well documented, emerging evidence highlights the significant contribution of small regulatory RNAs (sRNAs) in bacterial pathogenesis. These sRNAs function as posttranscriptional regulators that fine-tune gene expression, enabling bacteria to adapt rapidly to challenging environments. This review explores the multifaceted roles of bacterial sRNAs in host-pathogen interactions. Firstly, it examines how sRNAs regulate pathogenicity by modulating the expression of key virulence factors, including fimbriae, toxins, and secretion systems, followed by discussing the role of sRNAs in bacterial stress response mechanisms that counteract host immune defenses, such as oxidative and envelope stress. Additionally, this review investigates the involvement of sRNAs in antibiotic resistance by regulating efflux pumps, biofilm formation, and membrane modifications, which contribute to multi-drug resistance phenotypes. Lastly, this review highlights how sRNAs contribute to intra- and interspecies communication through quorum sensing, thereby coordinating bacterial behavior in response to environmental cues. Understanding these regulatory networks governed by sRNAs is essential for the development of innovative antimicrobial strategies. This review highlights the growing significance of sRNAs in bacterial pathogenicity and explores their potential as therapeutic targets for the treatment of bacterial infections.

Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis

Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.

The NRF2/HO- 1 Pathway: a Potential Regulatory Factor in Fluoride-Induced Colonic Injury under Estrogen Deficiency

Our previous studies have demonstrated that fluoride (F) overexposure is a risk factor for colonic microenvironment, yet its underlying mechanisms and the influencing factors remain poorly understood. Here, a rat model of F exposure (0, 25, 50, 100 mg/L in drinking water) combined with ovariectomy (OVX)-induced estrogen deficiency was established to investigate the roles of nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) pathway in F-induced colonic damage under the state of estrogen deficiency. Result showed that F exposure significantly reduced occludin and claudin-1 expression, further resulting in the colon's morphology impairment. Concurrently, F suppressed epithelial proliferation, decreased goblet cell numbers, and diminished short-chain fatty acid (SCFA) production. OVX-induced estrogen deficiency exacerbated F-induced colonic barrier damage and SCFA decreased. Mechanistically, estrogen deficiency aggravated F intestinal toxicity by further inhibiting the protein expression of Nrf2 and HO-1 and upregulating Keap1 protein expression, following downregulated Bcl-2 mRNA levels and upregulated Bax and caspase-3 mRNA levels, and promoting colonic epithelial cell apoptosis. These findings identify that Nrf2/HO-1 key protein disorders are involved in F-induced colonic barrier injury, and estrogen deficiency further aggravated F intestinal toxicity.

Nervous system-gut microbiota-immune system axis: future directions for preventing tumor

Tumor is one of the leading causes of death worldwide. The occurrence and development of tumors are related to multiple systems and factors such as the immune system, gut microbiota, and nervous system. The immune system plays a critical role in tumor development. Studies have also found that the gut microbiota can directly or indirectly affect tumorigenesis and tumor development. With increasing attention on the tumor microenvironment in recent years, the nervous system has emerged as a novel regulator of tumor development. Some tumor therapies based on the nervous system have also been tested in clinical trials. However, the nervous system can not only directly interact with tumor cells but also indirectly affect tumor development through the gut microbiota. The nervous system-mediated gut microbiota can regulate tumorigenesis, growth, invasion, and metastasis through the immune system. Here, we mainly explore the potential effects of the nervous system-gut microbiota-immune system axis on tumorigenesis and tumor development. The effects of the nervous system-gut microbiota-immune system axis on tumors involve the nervous system regulating immune cells through the gut microbiota, which can prevent tumor development. Meanwhile, the direct effects of the gut microbiota on tumors and the regulation of the immune system by the nervous system, which can affect tumor development, are also reviewed.

Assembling the jigsaw puzzle of life

The cell is a dynamic system where millions of molecules of thousands different kinds act within a complex network with numerous feedback loops. Because we cannot pursue many targets simultaneously, 'big data' rarely yield useful leads. Comprehensive models can place the snippets obtained in simplified experimental conditions into a coherent picture.

Red blood cell metabolism: a window on systems health towards clinical metabolomics

PURPOSE OF REVIEW

This review focuses on recent advances in the understanding of red blood cell (RBC) metabolism as a function of hypoxia and oxidant stress. In particular, we will focus on RBC metabolic alterations during storage in the blood bank, a medically relevant model of erythrocyte responses to energy and redox stress.

RECENT FINDINGS

Recent studies on over 13 000 healthy blood donors, as part of the Recipient Epidemiology and Donor Evaluation Study (REDS) III and IV-P RBC omics, and 525 diversity outbred mice have highlighted the impact on RBC metabolism of biological factors (age, BMI), genetics (sex, polymorphisms) and exposure (dietary, professional or recreational habits, drugs that are not grounds for blood donor deferral).

SUMMARY

We review RBC metabolism from basic biochemistry to storage biology, briefly discussing the impact of inborn errors of metabolism and genetic factors on RBC metabolism, as a window on systems metabolic health. Expanding on the concept of clinical chemistry towards clinical metabolomics, monitoring metabolism at scale in large populations (e.g., millions of blood donors) may thus provide insights into population health as a complementary tool to genetic screening and standard clinical measurements.

Harnessing Human Holobiome and Meta-Multi-Omics Analyses for Medical Applications

Next-generation sequencing technology has revolutionized all fields of living systems, and its applications almost reinvented some research areas including metagenomics. The microbiotas in our body, including those of the oral, nasal, ocular, alveolar, skin regions, and particularly gut microbiota, have close linkages with our health status. Maturation of experimental techniques for metagenomics has been followed by other related omics platforms, for example, metatranscriptomics, metaproteomics, and all possible metacounterparts of multiomics studies. Now, we are on the eve of a meta-multi-omics era for the analysis of human holobiome in medical research. This era will help buttress the current efforts for systems medicine by illuminating the relationships between human holobiome and health or all human diseases including not only cancers but also infectious diseases, autoimmune diseases, obesity, aging, genetic disorders, and psychiatric conditions. Equally important, meta-multi-omics era is also poised to inform the determinants of human health and, by extension, help build individually tailored precision medicine interventions.

An expanded metabolic pathway for androgen production by commensal bacteria

Commensal bacteria have been implicated in the modulation of steroid hormones, including circulating androgen levels in the host. However, the microbial genetic pathways involved in androgen production have not been fully characterized. Here we identify a microbial gene encoding an enzyme that catalyses the conversion of androstenedione to epitestosterone in the gut microbiome member Clostridium scindens and named this gene desF. We demonstrate that epitestosterone impacts androgen receptor-dependent prostate cancer cell proliferation in vitro. We also demonstrate that stool desF levels are elevated in patients with prostate cancer who are unresponsive to abiraterone/prednisone therapy. Bacterial isolates from urine or prostatectomy tissue produced androgens, and 17β-hydroxysteroid dehydrogenase activity encoded by the desG gene was detected in strains of the urinary tract bacterium Propionimicrobium lymphophilum. Furthermore, we demonstrate that urinary androgen-producing bacterial strains can promote prostate cancer cell growth through metabolism of cortisol and prednisone. Abiraterone, which targets host desmolase (CYP17A1), a rate-limiting enzyme in adrenal steroidogenesis, does not inhibit bacterial desmolase (DesAB), whereas the conversion of prednisone to androgens by DesAB, DesF and DesG drives androgen-receptor-dependent prostate cancer cell line proliferation in vitro. Our results are a significant advance in steroid microbiology and highlight a potentially important role for gut and urinary tract bacteria in host endocrine function and drug metabolism.

Interactions between the intestinal microbiota and drug metabolism - Clinical implications and future opportunities

The importance of the intestinal microbita in a multitude of physiological processes is well-evidenced. These include metabolism of nutrients and xenobiotics, biosynthesis of vitamin K and vitamin B12, immunomodulation, maintenance of the gut mucosal barrier integrity and protection against some pathogens. Interindividual differences in the intestinal microbiota composition have impacts on health. The bioavailability and activity of some pharmaceuticals are heavily influenced by interindividual variability in metabolism, which has a genetic basis. This variability, primarily occurring in the liver but also in the intestine, has been studied extensively. Despite the advancement of this field - pharmacogenetics - its integration into clinical practice remains limited for reasons discussed herein. This highlights the even greater challenge of applying emerging knowledge on variability in the gut microbiota to drug therapy. However, ignoring these opportunities would be a mistake. While clinical applications of microbiota-guided drug therapy are currently absent and the ideas in this article are largely theoretical, research is uncovering that in cases where a substantial portion of a drug or its metabolites reaches the colon, or where drugs are formulated for colonic delivery, the gut microbiota can significantly affect drug metabolism and activity. Greater focus should be placed on research into how interindividual variability in the intestinal microbiome can modify pharmaceutical bioavailability and activity. This article is deliberately speculative and exploratory but proposes that, though there are still no clinical examples of microbiome-guided drug therapy, these interactions could afford opportunities for improvements in personalised medicine and also for drug design.

Disinfection of outpatient ophthalmic devices: a critique of "semicritical" designation

Ophthalmic devices used in outpatient clinics are undergoing scrutiny by regulatory agencies and hospital infection control groups. Applying a nearly century-old classification for disinfection and sterilization of reusable devices and instruments, they are faulting ophthalmologists for not using high-level disinfection (HLD) listed in newer manufacturer instructions for use. By this classification, A-scan and B-scan ultrasound probes, fundus and laser contact lenses, and gonioscopy lenses are grouped with other "semicritical" devices, such as gastrointestinal endoscopes, laryngoscope blades, and anorectal manometers, and therefore require sterilization or HLD. HLD, however, varies by geographic region, compatibility with material, and disinfectant availability. Because HLD necessitates turnover time, clinics must buy more devices to maintain patient volume. Therefore, manufacturers have no incentive to develop sustainable or reusable devices. Most important, however, none of the ophthalmic devices in question has been associated with spread of infection. In short, the mandate for HLD seems to be arbitrary, reactive to perception of possible infection risk from classification of the eye as a "mucous membrane," and devoid of evidence that HLD decreases risk of infection transmission relative to current cleaning and disinfection methods. In the manner that the Ophthalmic Instrument Cleaning and Sterilization Task Force Regulatory raised concerns that regulatory agencies arbitrarily were imposing costly infection control measures for intraocular ophthalmic surgery without evidence that they improved patient safety, a similar task force is needed to address regulatory HLD mandates for clinic devices used in tens of millions of patient encounters for decades without infection transmission.

Pericyte Electrical Signalling and Brain Haemodynamics

Dynamic control of membrane potential lies at the nexus of a wide spectrum of biological processes, ranging from the control of individual cell secretions to the orchestration of complex thought and behaviour. Electrical signals in all vascular cell types (smooth muscle cells, endothelial cells and pericytes) contribute to the control of haemodynamics and energy delivery across spatiotemporal scales and throughout all tissues. Here, our goal is to review and synthesize key studies of electrical signalling within the brain vasculature and integrate these with recent data illustrating an important electrical signalling role for pericytes, in doing so attempting to work towards a holistic description of blood flow control in the brain by vascular electrical signalling. We use this as a framework for generating further questions that we believe are important to pursue. Drawing parallels with electrical signal integration in the nervous system may facilitate deeper insights into how signalling is organized within the vasculature and how it controls blood flow at the network level.

Erythrocyte Extracellular Vesicles Amalgamate into the Hair and Skin to Maintain Homeostasis

Erythrocytes are a major cell type in the circulation, numbering between 20 and 30 trillion. The function of erythrocytes is to bring oxygen to the tissues and release carbon dioxide to the lungs. Anaemic patients, who have low levels of erythrocytes, show significant symptoms affecting the hair and skin; however, the detailed relationship between erythrocytes and the integumentary system is not fully understood. Here, we show that erythrocyte extracellular vesicle (EV) can transfer haemoglobin, ABO antigens and keratin into the hair and promote hair regeneration through miR-20a-5p- and miR-22-3p-mediated upregulation of Wnt/β-catenin signalling in dermal papilla cells. Moreover, we show that local injection of autologous erythrocyte EVs ameliorates hair growth in androgenic alopecia (AGA) patients. Interestingly, we found that erythrocyte EVs exit the body from the hair/skin and their membranes contribute to the formation of the outer barrier of the skin. In summary, we identify a previously unknown role of erythrocytes in amalgamating into hair structures and reveal a new therapeutic approach using erythrocyte EVs to promote hair regeneration in AGA patients.

The heart, a secondary organ in the control of blood circulation

Circulation of the blood is a fundamental physiological function traditionally ascribed to the pressure-generating function of the heart. However, over the past century the 'cardiocentric' view has been challenged by August Krogh, Ernst Starling, Arthur Guyton and others, based on haemodynamic data obtained from isolated heart preparations and organ perfusion. Their research brought forth experimental evidence and phenomenological observations supporting the concept that cardiac output occurs primarily in response to the metabolic demands of the tissues. The basic tenets of Guyton's venous return model are presented and juxtaposed with their critiques. Developmental biology of the cardiovascular system shows that the blood circulates before the heart has achieved functional integrity and that its movement is intricately connected with the metabolic demands of the tissues. Long discovered, but as yet overlooked, negative interstitial pressure may play a role in assisting the flow returning to the heart. Based on these phenomena, an alternative circulation model has been proposed in which the heart functions like a hydraulic ram and maintains a dynamic equilibrium between the arterial (centrifugal) and venous (centripetal) forces which define the blood's circular movement. In this focused review we introduce some of the salient arguments in support of the proposed circulation model. Finally, we present evidence that exercising muscle blood flow is subject to local metabolic control which upholds optimal perfusion in the face of a substantive rise in muscle vascular conductance, thus lending further support to the permissive role of the heart in the overall control of blood circulation.

Gut microbiome in colorectal cancer: metagenomics from bench to bedside

Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approach.

The human microbiome: redefining cancer pathogenesis and therapy

The human microbiome has always been an important determinant of health and recently, its role has also been described in cancer. The altered microbiome could aid cancer progression, modulate chemoresistance and significantly alter drug efficacy. The broad implications of microbes in cancer have prompted researchers to investigate the microbe-cancer axis and identify whether modifying the microbiome could sensitize cancer cells for therapy and improve the survival outcome of cancer patients. The preclinical data has shown that enhancing the number of specific microbial species could restore the patients' response to cancer drugs and the microbial biomarkers may play a vital role in cancer diagnostics. The elucidation of detailed interactions of the human microbiota with cancer would not only help identify the novel drug targets but would also enhance the efficacy of existing drugs. The field exploring the emerging roles of microbiome in cancer is at a nascent stage and an in-depth scientific perspective on this topic would make it more accessible to a wider audience. In this review, we discuss the scientific evidence connecting the human microbiome to the origin and progression of cancer. We also discuss the potential mechanisms by which microbiota affects initiation of cancer, metastasis and chemoresistance. We highlight the significance of the microbiome in therapeutic outcome and evaluate the potential of microbe-based cancer therapy.

Oro-pharyngeal mucosal microbiome alternations causing immune system dysregulation in schizophrenia

Schizophrenia is a chronic and thoughtful psychological disorder that affects a person's thinking, feelings, and behaviours. Multi-factorial genetic, environmental, and neurological variables cause it. Recently, more research focused on the human microbiome, which alters the immune system and develops adverse health effects on the human body. The study discusses a possible relationship between the oropharyngeal microbiome and schizophrenia. According to recent studies, the oropharyngeal microbiome may alter the immune system in the human body and cause various psychiatric disorders, including schizophrenia. The oropharyngeal microbiome can cause schizophrenia either by affecting the genes, chromosomes, and immune system in the human body. Additionally, it examines the combined mechanism of how the oropharyngeal microbiome's alterations lead to genetic abnormalities and immune dysregulation in schizophrenia. By combining the various approaches, this chapter offers a comprehensive view of the oropharyngeal microbiome's role in schizophrenia and suggests that microbial alterations could serve as biomarkers or therapeutic targets for the disorder.