The oral microbiota is an essential microbial community within the human body, playing a vital role in maintaining health. In older adults, age-related changes in the oral microbiota are linked to both systemic and oral health impairments. The use of various medications for systemic diseases in the elderly can also contribute to the development of oral diseases. Oral microbiota dysbiosis refers to an imbalance in the composition of oral microbial communities. This imbalance, along with disruptions in the host immune response and prolonged inflammation, is closely associated with the onset and progression of several diseases. It contributes to oral conditions such as dental caries, periodontal disease, and halitosis. It is also linked to systemic diseases, including Alzheimer's disease, type 2 diabetes mellitus, rheumatoid arthritis, atherosclerotic cardiovascular disease, and aspiration pneumonia. This review aims to explore how oral microbiota influences specific health outcomes in older individuals, focusing on Alzheimer's disease, type 2 diabetes mellitus, rheumatoid arthritis, atherosclerotic cardiovascular disease, and aspiration pneumonia. The oral microbiota holds promise as a diagnostic tool, therapeutic target, and prognostic biomarker for managing cardiovascular disease, metabolic diseases, infectious diseases and autoimmune diseases. Emphasizing proper oral health care and instilling an understanding of how drugs prescribed for systemic disease impact the oral microbiome, is anticipated to emerge as a key strategy for promoting the general health of older adults.

The main source of microorganisms in the blood is the intestinal and oral microflora through the route of atopobiosis. It is clear that the blood microbiome undergoes significant changes in response to various pathological conditions within the human body. In this review, we summarized data from studies of the human blood microbiome in diseases of the nervous system and cardiovascular, respiratory, liver, kidney, and metabolite disorders. Links between the blood microbiome and the above mentioned diseases are demonstrated. In support of this understanding, it is evident that analogous alterations in microbiome composition occur across various disease categories; however, the microbial signatures associated with the blood microbiome exhibit specificity. For instance, an elevated abundancy of Proteobacteria has been identified in cardiovascular, renal, and metabolic disorders. Conversely, while Firmicutes are found to be abundant in renal and metabolic conditions, their levels are diminished in cardiovascular diseases. Additionally, patients suffering from respiratory and liver ailments typically show a heightened presence of Bacteroidetes; notably, Flavobacterium is prevalent in respiratory diseases, whereas Enterobacteriaceae is associated with liver diseases. Hence, the human blood microbiome could be considered as a potential biomarker in certain diseases.

Biliary tract cancers (BTCs), a group of rare aggressive malignancies, posed significant clinical challenges due to late diagnosis and limited therapies. While gut microbiota had been extensively studied in gastrointestinal cancers, the role of oral microbiota-a primary microbial reservoir entering the digestive system-remained poorly understood. Emerging evidence indicated that oral bacteria might affect biliary carcinogenesis through direct colonization, immune modulation, and metabolic interactions via the oral-gut-liver axis. This narrative review analyzed current research connecting oral microbial imbalance with BTCs. It explored how bacterial translocation, inflammatory metabolites, and immune alterations could promote cancer development. Established BTC risk factors-including gallstones, primary sclerosing cholangitis, cirrhosis, and H. pylori infection-were evaluated for their associations with oral microbiota changes. Epidemiological studies revealed that periodontal disease and poor oral hygiene elevated BTC risk. Sequencing analyses identified oral-origin bacteria (Prevotella, Fusobacterium, Streptococcus) in bile and tumor tissues, suggesting microbial migration through swallowing or bloodstream. Mechanistic investigations showed microbial components (e.g., lipopolysaccharides, membrane vesicles) activated inflammatory pathways (TLR4/NF-κB, STAT3) and modified immune checkpoints, while metabolites potentially altered biliary cell metabolism. Different studies have found variable changes in oral microbiota in the presence of BTCs, thus a novel "biphasic dysbiosis" hypothesis was proposed to explain differing oral microbial diversity patterns across BTC subtypes. Despite progress, critical knowledge gaps persisted regarding causality, spatial microbial variations, and functional impacts of metabolites in BTCs. Future research was recommended to employ multi-omics approaches, single-cell analysis, and AI tools to enhance early detection and prevention strategies.

Foodborne outbreaks have raised concern about the microbial safety of fresh produce. Comprehensive data on key bacterial pathogens in these products remains scarce. This study explores the prevalence of foodborne pathogens in unprocessed fruits and vegetables, focusing on the variability according to a temporal scale, the geographical origin, and the product type. A total of 12 808 fresh produce samples were collected over a period of ten years (2013-2022), and analyzed for Salmonella spp., Shiga-toxin producing E. coli (STEC), L. monocytogenes, presumptive B. cereus, and coagulase-positive staphylococci. Overall, L. monocytogenes was the main pathogen detected (1.37%; 95% CI: 1.16-1.57%; n = 12 227), although only one sample exceeded the unsatisfactory threshold limit of 100 CFU/g. Enteric pathogens were less often detected, with a prevalence of 0.11% (95% CI: 0.05-0.17%; n = 11 538) and 0.02% (95% CI: 0.00-0.05%; n = 12 601) for STEC and Salmonella spp., respectively. Elevated levels (> 100 000 CFU/g) of presumptive B. cereus were found in 0.34% (95% CI: 0.18-0.51%; n = 4954) of cases, while coagulase-positive staphylococci were detected (> 100 CFU/g) in 0.26% (95% CI: 0.11-0.42%; n = 4169) of samples, with a maximum concentration of 190 CFU/g. The prevalence of L. monocytogenes fluctuated over time, varying from a minimum of 0.69% in 2022 to a maximum of 2.03% in 2017 and showing a seasonal effect, with an increased prevalence in June and from September to December. The major produce-pathogen combinations were L. monocytogenes and mushrooms (10.19%; 95% CI: 6.89-13.48%; n = 324) and head brassica (6.85%; 95% CI: 4.15-9.55%; n = 336); as well as STEC and legumes (0.47%; 95% CI: 0.00-1.39%; n = 213) and leafy brassica (0.40%; 95% CI: 0.00-1.17%; n = 252). This study provides valuable information for stakeholders, including farmers, distributors, retailers, and policymakers to be used in risk assessment.

While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.

The study of the microbiome has rapidly progressed over the past few decades, capturing the interest of both scientists and the general public. Nevertheless, there is still no widely agreed-upon definition for the term "microbiome" despite tremendous advances in our knowledge. The international scientific literature consistently underscores the difference between the human microbiome and human microbiota. Recent research has emphasized the importance of the female reproductive tract microbiome in fertility, impacting natural conception and assisted reproductive technologies (ARTs). This review explores the relationship between infertility and the microbiota of the female reproductive tract through a thorough evaluation of research papers and large-scale studies published up to 2024. The objective of this review is to critically assess current evidence on the role of the reproductive tract microbiome in female infertility and ART outcomes. Relevant papers were identified and analyzed through the electronic medical databases PubMed/MEDLINE and Scopus. A comprehensive synthesis of data from 36 original studies was performed, including observational, case-control, cohort, and randomized trials. By focusing on the vagina, cervix, and endometrium, this study offers a comprehensive overview of the microbiome throughout the female reproductive tract. RIF and poor reproductive outcomes are strongly linked to dysbiosis, which is characterized by a reduction in Lactobacillus species. Lactobacillus crispatus, in particular, plays a significant role in protecting against bacterial vaginosis and infertility. A thorough understanding of how the microbiome impacts fertility and the development of clinical strategies to improve reproductive outcomes requires standardized microbiome investigation techniques and larger, randomized trials that account for diverse patient characteristics.

High salt conditions negatively affect the fermentation efficiency of soy sauce and human health. This study aimed to construct a synthetic microbial community based on dominant functional microorganisms for salt-reduced soy sauce fermentation by investigating the succession and function of the microbial community during factory soy sauce fermentation. The findings revealed that the interplay between salinity and microorganisms influenced the dynamic changes of microbial communities. Furthermore, Aspergillus, Wickerhamomyces, Zygosaccharomyces, Staphylococcus, Weissella, and Tetragenococcus were analyzed to play key roles during soy sauce fermentation. Subsequently, the core strains were isolated and their strains and metabolic characteristics were evaluated. Finally, six strains (Aspergillus oryzae JQ09, Wickerhamomyces anomalus HJ07, Zygosaccharomyces rouxii JZ11, Staphylococcus carnosus QJ26, Weissella paramesenteroides ZJ19, and Tetragenococcus halophilus GY03) were employed to reconstruct the synthetic microbial community and conduct salt-reduced soy sauce fermentation. Biofortification increased the accumulation of metabolites in salt-reduced soy sauce. When the salt content was reduced to 14%, the sensory characteristics of soy sauce were closest to those of traditional soy sauce. Overall, this research presents a bottom-up approach to establish a simplified microbial community model with desired functions through deconstructing and reconstructing microbial structure and function. It has the potential to enhance the fermentation efficiency and realize the fermentation of salt-reduced traditional fermented food.

Insect farming represents a sustainable loop that recycles organic wastes back to the food chain while requiring minimal inputs such as land and water. Insect products are not only low in environment footprint, but also nutrient-dense and contain health-promoting bioactives. Black soldier fly larvae meal (BSFLM) stands out as an excellent source of protein and chitin, and the latter is a polysaccharide associated with promoting gut health. A 20-week feeding trial evaluated the effects of three dietary inclusion levels of BSFLM (0%, 6.5%, and 13%), with and without protease enzyme (Concentrase-P) supplementation, on two commercial laying hen strains: Lohmann Brown-Lite (brown hens) and Lohmann LSL-Lite White (white hens). The two strains of 52-week-old hens (mean weight = 2.2 kg) were housed in one production room, with each strain distributed across 36 conventional cages (5 birds per cage). Each treatment was randomly assigned to six cages (n = 6). At the end of the trial, cecal microbiome, SCFA production and excreta composition were studied.

White hens exhibited a distinct cecal microbiome compared to brown hens (p < 0.05), characterized by enhanced diversity, increased relative abundance of Actinobacteriota, and an altered cecal SCFA profile with increased butyric acid and reduced acetic acid levels (p < 0.05). Independent from strain, both 6.5% and 13% BSFLM inclusion promoted cecal microbial richness and evenness, shifting the community to produce more acetic acid and less butyric acid (p < 0.05). Excreta analysis showed significantly higher concentrations and daily excretion of nitrogen, ammoniacal nitrogen and non-ammoniacal nitrogen in both strains on the 13% BSFLM diet. Concentrase-P supplementation effectively ameliorated the elevated nitrogen and ammoniacal nitrogen excretion linked to the 13% BSFLM diet, despite having minimal effects on the cecal microbiome and SCFA production.

Our study provides a novel perspective on the enhanced cecal microbiome diversity in laying hens fed high levels of BSFLM, linking it to suboptimal protein digestion and an undesired increase in protein fermentation, which we have demonstrated can be partially addressed by protease supplementation. Our findings highlight the need to consider interactions between host nutrition, gut microbiome, and sustainability when evaluating novel feed ingredients.

The plant immune response plays a central role in maintaining a well-balanced and healthy microbiome for plant health. However, insights into how the fruit immune response and the fruit microbiome influence fruit health after harvest are limited. We investigated the temporal dynamics of the fruit microbiota and host defense gene expression patterns during postharvest storage of apple fruits at room temperature. Our results demonstrate a temporal dynamic shift in both bacterial and fungal community composition during postharvest storage that coincides with a steep-decline in host defense response gene expression associated with pattern-triggered immunity. We observed the gradual appearance of putative pathogenic/spoilage microbes belonging to genera Alternaria (fungi) and Gluconobacter and Acetobacter (bacteria) at the expense of Sporobolomyces and other genera, which have been suggested to be beneficial for plant hosts. Moreover, artificial induction of pattern-triggered immunity in apple fruit with the flg22 peptide delayed the onset of fruit rot caused by the fungal pathogen Penicillium expansum. Our results suggest that the fruit immune response helps to orchestrate a microbiome and that the collapse of the immunity results in the proliferation of spoilage microbes and fruit rot. These findings hold implications for the development of strategies to increase fruit quality and prolong shelf life in fruits and vegetables.

Male tract infections (MTIs) are a common clinical condition, often presenting without any signs nor symptoms of disease. As advised by the European Urology Guidelines dealing with this topic, patients are typically treated with antibiotics alone. Nevertheless, in between 40% and 50% of cases, antibiotic therapy is not effective in eradicating the semen infection. Therefore, persistent semen infection is frequently found upon semen culture evaluation following antibiotic therapy. In this study, we aimed to analyze the fecal microbiota of male infertile patients with persistent MTI in order to verify the prevalence of gut dysbiosis in these patients. We therefore enrolled 20 infertile patients with persistent MTIs after a proper cycle of antibiotic treatment. All patients performed the study for gut microbiota analysis after about 30 days after the last dose of antibiotic treatment. Gut microbiota analysis revealed that 50% of patients with persistent MTI presented a reduction in microbial biodiversity. Indeed, a situation of gut dysbiosis was reported in 75% of patients. In details, the Firmicutes-Bacteroidetes ratio was reduced in 70% of such patients, including 40% of patients where a severe reduction was observed due to an elevated abundance of Bacteroidetes (putrefactive dysbiosis). The most frequent enterotype was Prevotella-dominant (43%). We demonstrated for the first time that patients with recurrent MTIs have enterotypes associated with increased gut permeability and systemic inflammation. Further studies are required to analyze the molecular machinery by which gut dysbiosis exerts its role in patients with MTIs, in particular persistent MTIs, and how supplementation with probiotics might impact in terms of restoring eubiosis, in terms of eradicating the infection, and reducing prostate inflammation and eventually in terms of improving semen evaluation in male infertile patients.

There is an increase in the adoption of biological solutions for plant production as a means of attaining sustainable agriculture. A detailed understanding of the influence of specific bioinoculants and their volatile metabolites on native soil and plant microbiomes can improve future microbiome management practices.

Here, we examined the effect of bacterial inoculants and volatile compounds as individual and combined treatments on apple plant and soil microbiome. The study used specially designed microcosms that facilitated the separation of the different plant compartments. A compartment- and soil-specific effect of treatments on the native soil and plant microbiome was observed. The live bacterial inoculants as compared to their volatiles had a stronger effect on the plant and soil microbiome, particularly the root microbial community. The combined effect of bacterial inoculants was higher compared to volatiles (R2 = 5% vs. 3%). Treatment-specific effects were observed, like the influence of 2-butanone on the phyllosphere bacterial diversity, and an increase in fungal richness in Serratia-treated soils.

Among the examined treatments, inoculation with bacteria compared to volatile metabolites induced more significant shifts within the plant and soil microbiome. This observation has implications regarding the merits of applying living microorganisms. The findings highlight the potential of microbiome management approaches for enhancing microbiota functions.

Non-Hodgkin lymphomas (NHLs) encompass a diverse group of neoplasms arising from the clonal proliferation of B-cell progenitors, T-cell progenitors, mature B-cells, mature T-cells, and natural killer (NK) cells. These malignancies account for over 90% of lymphoid neoplasms. The link between the gut microbiome and neoplasms has been extensively studied in recent years. Growing evidence suggests that the gut microbiome may be involved not only in the development of the disease, but also in modulating the efficacy of implemented therapies. In this review, we summarize the current knowledge on the potential involvement of the gut microbiome in the development of diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), mucosa-associated lymphoid tissue (MALT) lymphoma, and NK/T-cell lymphoma, including cutaneous T-cell lymphoma (CTCL). Moreover, we discuss the relationship between gut microbiome changes before and after treatment and their association with treatment outcomes, focusing on chemotherapy and CAR T-cell therapy.

Flavanones, a key subclass of flavonoids, exhibit a wide range of biological activities, including antioxidant, anti-inflammatory, and neuroprotective properties. Predominantly found in citrus fruits, they occur in both aglycone and glycosylated forms, undergoing extensive metabolic transformation upon ingestion. Recent evidence suggests that flavanones, such as naringenin and hesperidin, influence gut microbiota composition, fostering a balance between beneficial and pathogenic bacterial populations. The gut microbiota plays a pivotal role in regulating the gut-brain axis, impacting cognitive function through the production of short-chain fatty acids (SCFAs), neurotransmitters, and anti-inflammatory cytokines. The modulation of the gut microbiome by flavanones has been associated with improvements in cognitive performance and a reduced risk of neurodegenerative disorders. This review provides a comprehensive analysis of the characteristics of major flavanones, their metabolic pathways, and their impact on gut microbiota and cognitive function. It covers the fundamental mechanisms through which flavanones exert their effects, as well as their potential therapeutic applications for brain health and neuroprotection. Despite promising findings, further research is needed to determine optimal dosages, strategies to enhance bioavailability, and long-term safety profiles.

Pediatric asthma is a common chronic airway inflammatory disease that begins in childhood and its impact persists throughout all age stages of patients. With the continuous progress of detection technologies, numerous studies have firmly demonstrated that gut microbiota and respiratory microbiota are closely related to the occurrence and development of asthma, and related research is increasing day by day. This article elaborates in detail on the characteristics, composition of normal gut microbiota and lung microbiota at different ages and in different sites, as well as the connection of the gut-lung axis. Subsequently, it deeply analyzes various factors influencing microbiota colonization, including host factor, delivery mode, maternal dietary and infant feeding patterns, environmental microbial exposure and pollutants, and the use of antibiotics in early life. These factors are highly likely to play a crucial role in the onset process and disease progression of asthma. Research shows that obvious changes have occurred in the respiratory and gut microbiota of asthma patients, and these microbiomes exhibit different characteristics according to the phenotypes and endotypes of asthma. Finally, the article summarizes the microbiota-related treatment approaches for asthma carried out in recent years, including the application of probiotics, nutritional interventions, and fecal microbiota transplantation. These treatment modalities are expected to become new directions for future asthma treatment and bring new hope for solving the problem of childhood asthma.

Algae-associated microbiomes are underexplored, limiting our understanding of their influence on the large-scale microalgae reactors. Over two 8-month periods, microbial dynamics were monitored three times per week in two microalgae raceways inoculated with Desmodesmus armatus. One reactor received wastewater, while the other used clean water and fertilizers. The sampled culture volume was filtered into pico and nano size fractions before DNA extraction. Metabarcoding of the 18S and 16S rRNA genes revealed a high microbial diversity across the two time series and a complex eukaryotic and prokaryotic community growing alongside the microalga. Chlorophyta and Fungi were the dominant eukaryotic groups, while Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Bacteroidia dominated the prokaryotic communities. Contrasting Amplicon Sequence Variants (ASVs) were found between healthy (D. armatus abundance > 70 %) and unhealthy (D. armatus abundance 10-20 %) conditions across reactors and time series. Network analysis identified up to 10 potential ecological interactions among D. armatus and its microbiome, predominantly positive. Specific ASVs associated with a healthy condition were positively correlated with D. armatus, while other ASVs linked to an unhealthy condition were negatively correlated. Potentially pathogenic bacteria included Mycobacterium and Flavobacterium, whereas potentially beneficial taxa included Geminocystis, Thiocapsa, Ahniella, and Bosea. Several fungal ASVs showed context-specific associations, whereas specific fungi such as Paraphelidium tribonemae, Aphelidium parallelum, Aphelidium desmodesmi, Aphelidiomycota sp., Rozellomycota sp., and Rhizophidium sp, were identified as potentially harmful. This study reveals the striking diversity and complexity of microalgae-associated microbiomes within raceways, providing valuable insights for optimizing industrial production processes, particularly for wastewater treatment and sustainable green biomass generation.

Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.

We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.

The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.

Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.

The gut microbiome influences physiological responses to exercise by modulating inflammatory markers and metabolite production. Athletes typically exhibit greater microbial diversity, which may be associated with improved performance, but the mechanisms linking different exercise modalities to the gut microbiome are not fully understood. In this study, blood and stool samples were collected from endurance athletes, strength athletes, and non-athletic controls performing two maximal exercise tests (the anaerobic Wingate test and the aerobic Bruce Treadmill Test) to integrate serum biomarker data with gut bacterial metagenomic profiles. While most biochemical markers showed similar post-exercise trends across groups, SPARC (secreted protein acidic and rich in cysteine) and adiponectin levels showed modality-specific responses. Strength-trained participants showed unique microbiome-biomarker associations after the Wingate test. In addition, baseline enrichment of certain bacterial taxa, including Clostridium phoceensis and Catenibacterium spp., correlated with reduced Bruce Treadmill test response in strength-trained individuals. These findings, while requiring further validation, indicate the complex interplay between exercise type, training background, and the gut microbiome, and suggest that specific microbial species may help shape recovery and adaptation.

This review provides an overview of research evidence focused on the microbial components essential to clinical cancer care, called the oncobiota (the interaction of human microbiota and cancer cells). It specifically examines the oncobiota in central nervous system cancer,breast cancer, pancreatic cancer, liver cancer, lung cancer, and cervical cancer. The literature review reveals insufficient knowledge about the oncobiota of organs once considered sterile. Many studies on oncobiota focus on small, geographically specific patient groups, and the absence of a reference (control) group complicates the development of microbial profiles for selected cancers. Consequently, this review aims to analyze the literature data and reports on the role of oncobiota in selected "sterile" organs and the resulting therapeutic or preventive implications. All relevant publications on oncobiota in patients with the selected cancers were considered to provide the most thorough analysis possible. Understanding the significance and role of oncobiota in the pathomechanisms of carcinogenesis may pave the way for targeted cancer prevention methods. Furthermore, therapeutic strategies based on oncobiota could represent a novel area of ​​personalized cancer treatment. Additionally, oncobiota may serve as an additional diagnostic tool in oncology.

Critically ill patients frequently experience alterations in gut microbiota, known as dysbiosis, which has been associated with unfavorable clinical outcomes. The use of probiotics is one approach to modulating gut microbiota.

This study aimed to evaluate the effects of probiotic supplementation combined with enteral nutrition (EN) in critically ill patients on infectious, gastrointestinal complications, and clinical outcomes.

This is a randomized, blinded, placebo-controlled clinical trial conducted with 70 individuals aged ≥18 years, receiving enteral nutrition, and admitted to the emergency intensive care unit (ICU) of a tertiary hospital. The intervention consisted of Lactobacillus paracasei SD 5275, Lactobacillus rhamnosus SD 5675, Lactobacillus acidophilus SD 5221, and Bifidobacterium lactis SD 5674 (109 Colony Forming Units (CFU) of each bacterium/sachet, two sachets per day were used), administered via EN once daily for at least 5 days until ICU discharge, death, or initiation of an oral diet. The primary outcomes were the occurrence of infections and gastrointestinal symptoms. Secondary outcomes included the use of antibiotics, laxatives, prokinetics, duration of mechanical ventilation (MV), ICU stay, and mortality.

There was no significant difference in the occurrence of any type of infection or gastrointestinal symptoms between the groups (p ≥ 0.05). The use of antibiotics and laxatives was similar between the groups (p = 1.000 and 0.917, respectively). The average duration of prokinetic use was shorter in the intervention group (2.80 ± 1.52 vs. 6.08 ± 5.58 days, 95 % Confidence interval (CI) -1.39; -0.0594, p = 0.011). Although the number of days on mechanical ventilation, ICU stay, and mortality were lower in the patients who received probiotics, no significant differences were observed between the groups (p ≥ 0.05).

It is concluded that ICU patients supplemented with probiotics have a shorter duration of prokinetic use. However, supplementation does not directly impact gastrointestinal symptoms, infections, antibiotic use, laxative use, duration of mechanical ventilation, ICU stay, or mortality.

Brazilian Clinical Trials Registry (ReBEC) under the number: ID RBR-2kqnj2t. SITE: https://ensaiosclinicos.gov.br/welcome.

In recent years, there has been significant progress in understanding bladder disorders and their connection to the bladder microbiome. Emerging evidence suggests that the bladder microbiome, which is unique to each individual, plays a pivotal role in maintaining bladder health. Disruptions to the normal microbiome composition have been associated with various pathological conditions such as recurrent urinary tract infections, interstitial cystitis, and chronic recalcitrant cystitis.

We completed a focused literature review to collect studies that evaluated the use of antibiotics for long-term treatment (more than 28 days) of infectious/inflammatory disturbed bladder microbiome DBM disorders.  RESULTS: This article reviews current literature on the composition of the bladder microbiome, describes the disorders associated with DBM, explores the utility of long-term antibiotics in managing DBM, and foresees future venues for DBM disorders research.

This review has demonstrated encouraging outcomes regarding the use of long-term antibiotics in managing infectious disorders of DBM, such as recurrent urinary tract infections and chronic recalcitrant cystitis, while no benefit was seen in interstitial cystitis patients. The studies showed that long-term cephalexin, fluoroquinolones, and fosfomycin are well-tolerated and effective options, with cephalexin being favored given its low side-effect profile.

Recent evidence underscores a reciprocal relationship between the gut microbiota and prostate cancer (PCa). Dysbiosis, often driven by Western dietary habits and antibiotic use, can heighten systemic inflammation and hinder antitumor immunity, thereby fostering PCa onset and progression. Conversely, certain gut microbes and their metabolites may protect against tumor growth by modulating immune and hormonal pathways that impact therapeutic responses, including androgen deprivation therapy (ADT). Emerging evidence links gut microbial shifts to PCa aggressiveness, potentially sustaining local androgen production and promoting resistance. In this review, we explore current understanding of the gut-PCa interplay, highlighting key knowledge gaps and the need for further research to clarify how targeting the microbiome might influence PCa outcomes.

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.

This chapter examines how human biology and microbial "secondary genomes" have co-evolved to shape neurodevelopment through the gut-brain axis. Microbial communities generate metabolites that cross blood-brain and placental barriers, influencing synaptogenesis, immune responses, and neural circuit formation. Simultaneously, Human Accelerated Regions (HARs) and Endogenous Retroviruses (ERVs) modulate gene expression and immune pathways, determining which microbes thrive in the gut and impacting brain maturation. These factors converge to form a dynamic host-microbe dialogue with significant consequences for neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and schizophrenia. Building on evolutionary perspectives, the chapter elucidates how genetic and immune mechanisms orchestrate beneficial and pathological host-microbe interactions in early brain development. It then explores therapeutic strategies, such as probiotics, prebiotics, fecal microbiota transplantation, and CRISPR-driven microbial engineering, targeting gut dysbiosis to mitigate or prevent neurodevelopmental dysfunctions. Furthermore, innovative organ-on-chip models reveal mechanistic insights under physiologically relevant conditions, offering a translational bridge between in vitro experiments and clinical applications. As the field continues to evolve, this work underscores the translational potential of manipulating the microbiome to optimize neurological outcomes. It enriches our understanding of the intricate evolutionary interplay between host genomes and the microbial world.

Dysbiosis, characterized by a microbial imbalance, particularly within the gut microbiota, has emerged as a significant health concern linked to various diseases. This study analyzed 8097 patent documents from The Lens database (2005-2024) to examine global innovation trends in dysbiosis management. The patent filings showed exponential growth, peaking at 1222 documents in 2022, with the United States leading in publications (4361 documents). The analysis revealed three primary innovation clusters: bacterial-based therapeutics (44.8% of patents), specific therapeutic applications (27.6%), and diagnostic methods (15.9%). The disease associations predominantly included inflammatory conditions, infections, and cancer. The patent classifications highlighted a significant focus on probiotic development and microbiota modulation. The surge in patent activity since 2014 correlates with advances in DNA sequencing technology and the growing recognition of dysbiosis's role in human health. This analysis provides valuable insights into the evolving landscape of microbiome therapeutics and future directions for dysbiosis management.

Chinese distillers' grains (CDGs), a byproduct of liquor production, have low protein, high fiber, and elevated alcohol/lactic acid levels, limiting their use as animal feed. This study utilised a synthetic microbiome composed of Candida utilis (protein enhancement), Trichoderma viride (fiber reduction), Bacillus subtilis (detoxification), and Lactobacillus casei (functional enhancement) for solid-state fermentation. The results showed that crude protein content increased to 23.61 %, and true protein content to 20.45 %. Crude fiber, ethanol, lactic acid, and acetic acid contents decreased by 22.31 %, 77.25 %, 85.08 %, and 73.89 %, respectively. Amino acid content increased by 23.80 %, and flavour compounds rose by 140.76 %. Mycotoxins like aflatoxin B1 (AFB1) and ochratoxin A (OTA) were undetectable, while vomitoxin (DON) remained below EU limits. In vitro digestibility of dry matter increased by 98.36 %. Pilot-scale trials showed a 1.42-fold increase in crude protein and a 1.34-fold increase in true protein, contributing to more efficient CDG utilisation and reduced agricultural costs.

The gut microbiome comprises trillions of microorganisms and profoundly influences human health by modulating metabolism, immune responses and neuronal functions. Disruption in gut microbiome composition is implicated in various inflammatory conditions, metabolic disorders and neurodegenerative diseases. However, determining the underlying mechanisms and establishing cause and effect is extremely difficult. Preclinical models offer crucial insights into the role of the gut microbiome in diseases and help identify potential therapeutic interventions. The Human Microbiome Action Consortium initiated a Delphi survey to assess the utility of preclinical models, including animal and cell-based models, in elucidating the causal role of the gut microbiome in these diseases. The Delphi survey aimed to address the complexity of selecting appropriate preclinical models to investigate disease causality and to study host-microbiome interactions effectively. We adopted a structured approach encompassing a literature review, expert workshops and the Delphi questionnaire to gather insights from a diverse range of stakeholders. Experts were requested to evaluate the strengths, limitations, and suitability of these models in addressing the causal relationship between the gut microbiome and disease pathogenesis. The resulting consensus statements and recommendations provide valuable insights for selecting preclinical models in future studies of gut microbiome-related diseases.

To illustrate and explore associations between the gut microbiome and spinal cord injury (SCI) characteristics, physical training, dietary intake, body composition, and blood biomarkers of elite Swiss athletes.

Baseline data analysis of athletes with SCI who participated in a pilot trial (NCT04659408) in the Swiss Paraplegic Center, Nottwil, Switzerland.

Elite athletes, five males, and six females, with SCI who competed internationally.

We conducted a differential abundance analysis and measured the alpha and beta diversity of the gut microbiome.

The athletes' median age was 34.5 years. Six had traumatic SCI and five had a spina bifida. The athletes competed in para-cycling (5), wheelchair athletics (3), and wheelchair tennis (3). A higher duration of training per week was positively associated with Akkermansia and Akkermansiaceae but negatively associated with Prevotellaceae. Muribaculaceae was negatively associated with the average number of trainings per week. Waist circumference is negatively associated with Butyricimonas. Significant differences in the alpha diversity were found with sex, gastrointestinal quality of life index (GIQLI) scores, total caloric intake, total fat intake, total carbohydrate intake, and high-sensitivity C-reactive protein (hs-CRP). Beta diversity differences were found with impairment of the sympathetic nervous system of the gut at the genus level and HbA1c at the family level.

This study provides insight into the gut microbiome of athletes with SCI. Our results were similar to those found in athletes without SCI. Further replication is needed to confirm the relationships of organisms observed in the gut of athletes with SCI.

This review summarizes and discusses key recent findings suggesting that microbiomes can play a role in the development and progression of osteoarthritis. Evidence supporting a gut microbiome-joint connection derived from human and animal studies is enumerated and discussed, with particular attention on the microbial and molecular basis for the development of therapeutic interventions that involve targeting the gut. Additionally, clinical data supporting the concept of a living microbiome within a diarthrodial joint are summarized. A discussion of key limitations in the current data and important technical considerations for firmly establishing the existence of a synovial joint microbial community is included.

Although various prebiotics, probiotics, and postbiotics are available, their safety and efficacy in combination are unknown.

We investigated the safety and functionality of a newly developed supplement, previously unreported in pet animals, containing 26 types of biotic material bacteria (2 prebiotics, 1 probiotic, and 23 postbiotics) in cats and dogs. The biotic materials included were selected based on current evidence from cats and dogs.

A new supplement developed using species tested in cats and dogs was administered. One-way analysis was used for data obtained from 3 cats (7 days of treatment and 7 days of nontreatment), and a parallel, controlled study was performed in 20 dogs (n = 10 each in control and test groups, for 27 days).

In cats, no abnormal values were observed in complete blood count or blood chemistry tests, whereas significant decreases in blood glucose and total cholesterol were confirmed (p < 0.05 each). In the feline lymphocyte subset test, significant increases were observed in T and B cells (p < 0.05). A significant difference in fecal pH was observed in the test group (p < 0.01). In addition, 60% (9/15) of the test group had an increase in total organic acids. In dogs, only indole showed a consistent decrease among putrefactive products (p = 0.055). Regarding analyses of intestinal flora from feces using a gene sequencer at the genus level, no changes were observed in cats. Conversely, Lachnospira and Anaeroplasma genera tended to be decreased in the control group but increased by 23.1% and 45%, respectively, in the test group. In addition, Escherichia-Shigella and Tyzzerella genera showed slight increases or changes in the control group but significant decreases in the test group. Regarding the Firmicutes/Bacteroidetes ratio, an increase in the control group and a decrease in the test group were observed in all cats, whereas no differences were observed in dogs.

The supplement is safe for both cats and dogs. Results of comprehensive analyses suggested that the supplement improved the intestinal environment by regulating the gastrointestinal microbiota.

There is accumulating evidence linking the microbiome and cardiovascular diseases. Nevertheless, no existing studies have been conducted on atrial fibrillation (AF) and the oral microbiome.

We collected and sequenced 245 AF tongue-coating samples and 26 AF samples after catheter ablation from Zhengzhou and Guangshan, China. We characterized tongue coating microbiome, constructed microbial classifiers in the discovery cohort, and verified their diagnostic potential in a cross-regional cohort.

Tongue coating microbial richness and diversity were significantly increased in the AF group compared to the control group, indicating increased bacterial colonization. The classifiers based on four optimal tongue coating microbial markers achieved good diagnostic efficiency in AF cohorts, with area under the curve (AUC) of 99.10 and 98.62% in the discovery and validation cohorts, respectively, and 97.97% in the cross-regional cohort. Paroxysmal AF and persistent AF shared similar taxonomic features, but some specific differential bacteria acted in the AF progression. Moreover, the outcomes revealed that catheter ablation contributed to rehabilitating oral bacterial disorders.

This was the first cross-sectional and longitudinal research of oral microbiome in AF patients and the alternations after catheter ablation, which offers promising new perspectives for AF clinical diagnosis and management.

The potential of phosphate-solubilizing microbes (PSMs) to enhance plant phosphorus uptake and reduce fertilizer dependency remains underutilized. This is partially attributable to frequent biofertilizer-farming system misalignments that reduce efficacy, and an incomplete understanding of underlying mechanisms. This study explored the seed microbiomes of nine Australian lucerne cultivars to identify and characterize high-efficiency PSMs. From a library of 223 isolates, 94 (42%) exhibited phosphate solubilization activity on Pikovskaya agar, with 15 showing high efficiency (PSI > 1.5). Genomic analysis revealed that the "high-efficiency" phosphate-solubilizing microbes belonged to four genera (Curtobacterium, Pseudomonas, Paenibacillus, Pantoea), including novel strains and species. However, key canonical genes, such as pqq operon and gcd, did not reliably predict phenotype, highlighting the limitations of in silico predictions. Mutagenesis of the high-efficiency isolate Pantoea rara Lu_Sq_004 generated mutants with enhanced and null solubilization phenotypes, revealing the potential role of "auxiliary" genes in downstream function of solubilization pathways. Inoculation studies with lucerne seedlings demonstrated a significant increase in shoot length (p < 0.05) following treatment with the enhanced-solubilization mutant, indicating a promising plant growth-promotion effect. These findings highlight the potential of more personalized "system-appropriate" biofertilizers and underscore the importance of integrating genomic, phenotypic, and in planta analyses to validate function. Further research is required to investigate links between genomic markers and functional outcomes to optimize the development of sustainable agricultural inputs.

Metaproteomics, an emerging field among the omic techniques, holds great promise for unraveling the function of microbiomes in host health and our environment. Metaproteomics can also be a valuable addition to multiomics studies of the microbiome, complementing genome-resolved metagenomics, metatranscriptomics, and metabolomics. The potential advancements from metaproteomics and multiomics research touch a breadth of disciplines, including ecology, biochemistry, immunology, medical microbiology, cell physiology, and medicine, and could lead to both fundamental and applied discoveries. However, there are significant roadblocks to widespread adoption of metaproteomics among microbiome researchers. In this Viewpoint article, we highlight the pivotal role of metaproteomics in microbiome research by showcasing its advantages, exploring opportunities to overcome challenges, and paving the way for its broader adoption as a mainstream technique. We hope that the recommendations provided in this Viewpoint article will inspire new, beneficial collaborations between proteomics experts, algorithm and infrastructure developers, biochemists, cell biologists, and microbiologists, enabling the construction of a knowledge base of microbiome function that can have an immediate and direct impact on host health and the environment.

The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .

The gut microbiome plays a vital role in human health, functioning as a metabolic organ that influences nutrient absorption and overall well-being. With growing evidence that dietary interventions can modulate the microbiome and improve health, this review examines whether healthcare systems should prioritize personalized microbiome-targeted therapies, such as probiotics, prebiotics, and microbiota transplants, over traditional pharmaceutical treatments for chronic diseases like obesity, diabetes, cardiovascular risk, and inflammatory conditions. A systematic review using Web of Science and Scopus databases was conducted, followed by a scientometric analysis. Key metabolic pathways, such as dietary fiber fermentation and short-chain fatty acid production, were explored, focusing on their impact on lipid and glucose metabolism. The interactions between microbial metabolites and the immune system were also investigated. Dietary interventions, including increased fiber and probiotic intake, show potential for addressing dysbiosis linked to conditions, such as type 2 diabetes, obesity, and autoimmune diseases. The review emphasizes the need to incorporate microbiome modulation strategies into clinical practice and research, calling for a multidisciplinary approach that integrates nutrition, microbiology, and biochemistry to better understand the gut microbiome's complex role in health.

The invasive nature of sample collection for studying the small intestinal (SI) microbiome often results in its poor characterization. This study evaluated a novel ingestible medical device (MD) for SI luminal sample collection. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics and culturomics assessed the MD's effectiveness in characterizing the healthy SI microbiome and identifying potential biomarkers. The SI microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness, and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct SI metabolic footprint, with bile acids and amino acids being the most abundant classes of metabolites. Host and host/microbe-derived bile acids were particularly abundant in SI samples. The application of a fast culturomics approach to two SI samples enabled species-level characterization, resulting in the identification of 90 bacterial species, including five potential novel species. The present study demonstrates the efficacy of our novel sampling MD in enabling comprehensive SI microbiome analysis through an integrative multi-omics approach, allowing the identification of distinct microbiome signatures between SI and fecal samples.

As a heterogeneous disease, endometriosis is associated with diagnostic delay. Delayed diagnosis, physical discomfort, hormone therapy, and inconvenience in daily life and work all contribute to a decreased quality of life for endometriosis patients. Early clinical diagnosis is highly important for the intervention and treatment of endometriosis. Currently, reliable non-invasive diagnostic methods are lacking, and laparoscopic examination combined with pathological diagnosis is considered the "gold standard" for definitively diagnosing endometriosis. An increasing number of studies have confirmed the correlation between endometriosis and microbial ecological changes. Microbial dysbiosis is an important factor in the development and progression of endometriosis. Certain key microbial species and their metabolites can induce functional alterations in endometrial cells through various mechanisms, often preceding the emergence of clinical symptoms. Endometriosis are chronic inflammatory diseases, with an immunoinflammatory response as the pathological foundation. The microbiome may participate in the pathological mechanisms of endometriosis through multiple pathways, including mediating inflammatory responses, regulating immune responses, participating in estrogen regulation, interfering with metabolic activities, and modulating the gut-brain axis. Therefore, the microbiome holds potential as an early non-invasive diagnostic and therapeutic target for endometriosis patients. This study summarizes and analyses the correlations between microorganisms and their metabolites and the onset of endometriosis, aiming to provide novel insights into the etiology, diagnosis, and treatment of endometriosis.

The gut microbiome, a complex community of microorganisms residing in the intestinal tract, plays a dual role in colorectal cancer (CRC) development, acting both as a contributing risk factor and as a protective element. This review explores the mechanisms by which gut microbiota contribute to CRC, emphasizing inflammation, oxidative stress, immune evasion, and the production of genotoxins and microbial metabolites. Fusobacterium nucleatum, Escherichia coli (pks+), and Bacteroides fragilis promote tumorigenesis by inducing chronic inflammation, generating reactive oxygen species, and producing virulence factors that damage host DNA. These microorganisms can also evade the antitumor immune response by suppressing cytotoxic T cell activity and increasing regulatory T cell populations. Additionally, microbial-derived metabolites such as secondary bile acids and trimethylamine-N-oxide (TMAO) have been linked to carcinogenic processes. Conversely, protective microbiota, including Lactobacillus, Bifidobacterium, and Faecalibacterium prausnitzii, contribute to intestinal homeostasis by producing short-chain fatty acids (SCFAs) like butyrate, which exhibit anti-inflammatory and anti-carcinogenic properties. These beneficial microbes enhance gut barrier integrity, modulate immune responses, and inhibit tumor cell proliferation. Understanding the dynamic interplay between pathogenic and protective microbiota is essential for developing microbiome-based interventions, such as probiotics, prebiotics, and fecal microbiota transplantation, to prevent or treat CRC. Future research should focus on identifying microbial biomarkers for early CRC detection and exploring personalized microbiome-targeted therapies. A deeper understanding of host-microbiota interactions may lead to innovative strategies for CRC management and improved patient outcomes.

The field of precision nutrition aims to develop dietary approaches based on individual biological factors such as genomics or the gut microbiota. The gut microbiota, which is the highly individualized and complex community of microbes residing in the colon, is a key contributor to human physiology. Although gut microbes play multiple roles in the metabolism of nutrients, their role in modulating the absorption of dietary energy from foods that escape digestion in the small intestine has the potential to variably affect energy balance and, thus, body weight. The fate of this energy, and its subsequent impact on body weight, is well described in rodents and is emerging in humans. This narrative review is focused on recent clinical evidence of the role of the gut microbiota in human energy balance, specifically its impact on energy available to the human host. Despite recent progress, remaining gaps in knowledge present opportunities for developing and implementing strategies to understand causal microbial mechanisms related to energy balance. We propose that implementing rigorous microbiota-focused measurements in the context of innovative clinical trial designs will elucidate integrated diet-host-gut microbiota mechanisms. These mechanisms are primed to be targets for precision nutrition interventions to optimize energy balance to achieve desired weight outcomes. Given the magnitude and impact of the obesity epidemic, implementing these interventions within comprehensive weight management paradigms has the potential to be of public health significance.

The microbiome of the gut is a complex ecosystem that contains a wide variety of microbial species and functional capabilities. The microbiome has a significant impact on health and disease by affecting endocrinology, physiology, and neurology. It can change the progression of certain diseases and enhance treatment responses and tolerance. The gut microbiota plays a pivotal role in human health, influencing a wide range of physiological processes. Recent advances in computational tools and artificial intelligence (AI) have revolutionized the study of gut microbiota, enabling the identification of biomarkers that are critical for diagnosing and treating various diseases. This review hunts through the cutting-edge computational methodologies that integrate multi-omics data-such as metagenomics, metaproteomics, and metabolomics-providing a comprehensive understanding of the gut microbiome's composition and function. Additionally, machine learning (ML) approaches, including deep learning and network-based methods, are explored for their ability to uncover complex patterns within microbiome data, offering unprecedented insights into microbial interactions and their link to host health. By highlighting the synergy between traditional bioinformatics tools and advanced AI techniques, this review underscores the potential of these approaches in enhancing biomarker discovery and developing personalized therapeutic strategies. The convergence of computational advancements and microbiome research marks a significant step forward in precision medicine, paving the way for novel diagnostics and treatments tailored to individual microbiome profiles. Investigators have the ability to discover connections between the composition of microorganisms, the expression of genes, and the profiles of metabolites. Individual reactions to medicines that target gut microbes can be predicted by models driven by artificial intelligence. It is possible to obtain personalized and precision medicine by first gaining an understanding of the impact that the gut microbiota has on the development of disease. The application of machine learning allows for the customization of treatments to the specific microbial environment of an individual.

The rhizosphere, a biologically active zone where plant roots interface with soil, plays a crucial role in enhancing plant health, resilience, and stress tolerance. As a key component in achieving Sustainable Development Goal 2, the rhizosphere is increasingly recognized for its potential to promote sustainable agricultural productivity. Engineering the rhizosphere microbiome is emerging as an innovative strategy to foster plant growth, improve stress adaptation, and restore soil health while mitigating the detrimental effects of conventional farming practices. This review synthesizes recent advancements in omics technologies, sequencing tools, and synthetic microbial communities (SynComs), which have provided insights into the complex interactions between plants and microbes. We examine the role of root exudates, composed of organic acids, amino acids, sugars, and secondary metabolites, as biochemical cues that shape beneficial microbial communities in the rhizosphere. The review further explores how advanced omics techniques like metagenomics and metabolomics are employed to elucidate the mechanisms by which root exudates influence microbial communities and plant health. Tailored SynComs have shown promising potential in enhancing plant resilience against both abiotic stresses (e.g., drought and salinity) and biotic challenges (e.g., pathogens and pests). Integration of these microbiomes with optimized root exudate profiles has been shown to improve nutrient cycling, suppress diseases, and alleviate environmental stresses, thus contributing to more sustainable agricultural practices. By leveraging multi-disciplinary approaches and optimizing root exudate profiles, ecological engineering of plant-microbiome interactions presents a sustainable pathway for boosting crop productivity. This approach also aids in managing soil-borne diseases, reducing chemical input dependency, and aligning with Sustainable Development Goals aimed at global food security and ecological sustainability. The ongoing research into rhizosphere microbiome engineering offers significant promise for ensuring long-term agricultural productivity while preserving soil and plant health for future generations.

The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry, and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species, and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation, and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection, and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization, and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.