@article {pmid40603926,
year = {2025},
author = {Claus, J and Top, J and Paganelli, FL and Ten Doesschate, T and Paternotte, N and Youngapelian, MJ and Schuurman, R and Willems, RJL and Leavis, H and van de Wijgert, JHHM},
title = {Nasopharyngeal microbiome composition by SARS-CoV-2 presence and severity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23185},
pmid = {40603926},
issn = {2045-2322},
abstract = {The influence of SARS-CoV-2 on the nasopharyngeal microbiome, or vice-versa, is unclear. Nasopharyngeal swabs from Dutch healthcare workers (N = 257) and hospital outpatients with respiratory symptoms (N = 143), leftover after SARS-CoV-2 testing in 2020-2021, were 16S rRNA amplicon sequenced and tested for respiratory viruses by multiplex PCR panel. The healthcare workers were younger and much healthier than the patients, and experienced less severe viral infections. In the healthcare workers, log10 estimated concentrations (ECs) of Corynebacterium were slightly increased in samples with SARS-CoV-2 versus no virus detected, regardless of symptomatology (adjusted regression coefficient 0.52, p = 0.042) but no other bacterial ECs differed. Corynebacterium and Dolosigranulum ECs were higher in very mild/asymptomatic SARS-CoV-2 episodes compared to very mild/asymptomatic episodes with no viruses detected, but lower in mild compared to very mild/asymptomatic SARS-CoV-2 episodes (-1.07, p = 0.015, and -1.37, p = 0.011, respectively). In the patients, similar but non-significant trends by SARS-CoV-2 severity (fatal, severe, moderate versus mild) were seen for Dolosigranulum, but not for Corynebacterium. In this population, the largest nasopharyngeal microbiome composition differences were seen by the presence and severity of comorbidities. These findings suggest that the Dolosigranulum EC decreases with increasing SARS-CoV-2 severity, but the clinical relevance of this finding is unclear.},
}

@article {pmid40603925,
year = {2025},
author = {Budoff, MJ and de Oliveira Otto, MC and Li, XS and Lee, Y and Wang, M and Lai, HTM and Lemaitre, RN and Pratt, A and Tang, WHW and Psaty, BM and Siscovick, DS and Hazen, SL and Mozaffarian, D},
title = {Trimethylamine-N-oxide (TMAO) and risk of incident cardiovascular events in the multi ethnic study of Atherosclerosis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23362},
pmid = {40603925},
issn = {2045-2322},
support = {R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; R01HL135920/NH/NIH HHS/United States ; },
abstract = {Trimethylamine-N-oxide (TMAO) is a gut microbiome-derived metabolite of choline, L-carnitine and lecithin, abundant in animal source foods. In experimental models, higher blood TMAO levels enhance atherosclerotic cardiovascular disease (ASCVD). However in humans, most prior studies have evaluated high risk or secondary prevention populations, and no studies have investigated relationships in a diverse, multi-ethnic population. We evaluated 6,767 US adults free of ASCVD at baseline in the community-based Multi-Ethnic Study of Atherosclerosis (MESA), including 38% identifying as White; 28%, as Black; 22%, as Hispanic; and 12%, as Chinese adults. Plasma TMAO was measured serially at baseline and 5-years, and its time-varying association with incident ASCVD determined using Cox proportional hazards. Multivariate analyses adjusted for time-varying demographics, lifestyle factors, medical history, lipid measures, antibiotic use and dietary habits. During median 11.3 years follow-up, 852 ASCVD events occurred. After multivariate adjustment, TMAO associated with higher risk of ASCVD in a dose-dependent fashion, with hazard ratios across quintiles of 1.02, 1.17, 1.23, and 1.33 (95% CI 1.02, 1.74), respectively, compared to the lowest quintile (P-trend = 0.01). Risk appeared possibly larger among Hispanic and Chinese adults; and among individuals with lower baseline renal function; although these interactions did not achieve statistical significance. Plasma concentrations of TMAO associated with higher risk of incident ASCVD in this multi-ethnic US cohort, supporting a need to test dietary and pharmacologic interventions targeting the diet-microbiome axis for potential cardiovascular risk prevention in diverse populations.},
}

@article {pmid40603801,
year = {2025},
author = {Li, H},
title = {Iron and the Intestinal Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1480},
number = {},
pages = {345-360},
pmid = {40603801},
issn = {0065-2598},
abstract = {Iron in the gut is like a double-edged sword. On one side, it is essential for numerous physiological processes, including oxygen transport and energy production, and is crucial for addressing conditions like anemia. However, on the other side, excess or unabsorbed iron can disrupt gut homeostasis, fuel harmful pathogens, contribute to dysbiosis, and promote gut inflammation. The challenge lies in finding a balance that ensures adequate iron absorption while minimizing its adverse effects on the gut microbiota. Host and microbiota in the gut have evolved sophisticated strategies to maintain iron homeostasis within the bacterial community and balance iron needs between host and gut microbiota. Disruption of this balance by excess iron could lead to serious consequences by promoting intestinal inflammation and disease progression. Current research points to promising therapeutical approaches that enhance iron absorption while suppressing iron-induced adverse effects, such as oxidative stress and dysbiosis, in the gut. These strategies offer the potential to reduce intestinal inflammation and improve gut health, paving the way for more effective therapies to mitigate disease complications.},
}

@article {pmid40603796,
year = {2025},
author = {Moreno-Navarrete, JM and Rodrigues, IG and Fernández-Real, JM},
title = {The Impact of Iron Homeostasis in Insulin-Sensitive Tissues and Gut Microbiome on Obesity-Driven Metabolic Disorders.},
journal = {Advances in experimental medicine and biology},
volume = {1480},
number = {},
pages = {253-269},
pmid = {40603796},
issn = {0065-2598},
abstract = {Iron is a crucial element for vital biological processes in both prokaryotic and eukaryotic cells, requiring precise regulation to maintain homeostasis. In humans and animal models, dysregulation of iron homeostasis is often linked to obesity-associated metabolic disturbances, which are characterized by elevated serum ferritin levels and excessive iron accumulation in insulin-dependent tissues like the liver, adipose tissue, and skeletal muscle. Prolonged iron overload in tissues induces oxidative stress, which impairs insulin sensitivity and promotes systemic insulin resistance and hyperglycemia. This creates a vicious cycle in which decreased serum hepcidin levels enhance intestinal iron absorption, further exacerbating iron accumulation. While the impact of iron on gut microbiota is well established, the role of gut microbiota in regulating body iron homeostasis is less studied. Recent studies have uncovered new mechanisms by which gut microbiota influence intestinal iron absorption and the regulation of body iron stores. In this chapter, we summarize recent findings on iron homeostasis in insulin-sensitive metabolic tissues and explore how gut microbiota can modulate body iron regulation in the context of obesity.},
}

@article {pmid40603760,
year = {2025},
author = {Tina, K and Jiatong, N and Deborah, H and Tobias, S and Doriane, A and Dirk, H},
title = {Therapeutic mechanisms of exclusive enteral nutrition in Crohn's disease.},
journal = {Seminars in immunopathology},
volume = {47},
number = {1},
pages = {28},
pmid = {40603760},
issn = {1863-2300},
abstract = {Crohn's disease (CD) is a chronic, relapsing multifactorial inflammatory condition of the gastrointestinal tract, which is diagnosed under the age of 17 in 25% of patients, categorized as pediatric CD (pCD). Exclusive enteral nutrition (EEN) is a first-line therapy for inducing remission in pCD, yet its precise mechanisms remain poorly understood. This review summarizes the complex interplay of EEN-induced protective changes in the gut microbiota, epithelial barrier function and mucosal immune responses. EEN reshapes the gut microbiome by excluding potential pathobionts from the gut mucus layer and increasing protective bacterial and dietary metabolites. Emerging evidence highlights the role of EEN in modulating mitochondrial function, tryptophan metabolism and other metabolites in the intestinal epithelium and immune cells, which may contribute to its therapeutic efficacy. However, high variability in microbiome responses across clinical cohorts and discrepancies between clinical trials and animal models warrant further research to identify functional consequences and therapeutic mechanisms of EEN.},
}

@article {pmid40603595,
year = {2025},
author = {Komatsu, H and Sugimoto, T and Ogata, Y and Miura, T and Aida, M and Nishiyama, H and Kawai, M and Yano, Y and Mori, M and Shishido, Y},
title = {Characteristics of the gut microbiota in patients with advanced non-small cell lung cancer who responded to immune checkpoint inhibitors.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23398},
pmid = {40603595},
issn = {2045-2322},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology/mortality ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Lung Neoplasms/drug therapy/microbiology/pathology/mortality ; Female ; Male ; Aged ; Middle Aged ; Treatment Outcome ; Aged, 80 and over ; },
abstract = {Despite the introduction of immune checkpoint inhibitors (ICIs) in the treatment of lung cancer, the number of deaths from lung cancer remains high, and further improvements in response rates are necessary. Recently, the gut microbiota has been reported to be involved in the therapeutic effects of ICIs; however, only a few studies have examined patients with lung cancer in this context. In the current study, we aimed to explore the association between the gut microbiota before therapy and the efficacy of ICIs in patients with advanced non-small cell lung cancer (NSCLC). The a-diversity of the intestinal microbiota in patients who responded to ICI treatment (responders) was significantly higher than that in those who did not respond to ICIs (non-responders). Additionally, the abundance of Bifidobacteriaceae was significantly higher in the responders than in the non-responders. Furthermore, patients with a high abundance of Bifidobacteriaceae had significantly longer overall survival than those with a low abundance. Counts of Levilactobacillus brevis were significantly higher in responders than in non-responders. Our findings suggest that a higher diversity of the gut microbiota and an abundance of Bifidobacterium and/or L. brevis are distinctive features of the microbiota in patients with NSCLC who respond to ICI treatment.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology/mortality
*Gastrointestinal Microbiome/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Lung Neoplasms/drug therapy/microbiology/pathology/mortality
Female
Male
Aged
Middle Aged
Treatment Outcome
Aged, 80 and over

@article {pmid40603450,
year = {2025},
author = {Yurgel, SN and Ajeethan, N and Ali, S},
title = {Rootstock microbiome as a target for manipulation to combat apple replant disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23498},
pmid = {40603450},
issn = {2045-2322},
mesh = {*Malus/microbiology/growth & development ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; *Plant Roots/microbiology ; Soil Microbiology ; Fungi/genetics/classification ; Bacteria/genetics/classification ; },
abstract = {Apple replant disease (ARD) describes a phenomenon of reduction of crop productivity in the early years of orchard establishment on sites previously planted with apple. Currently, manipulation of the soil microbiome through (bio)fumigation is the primary approach to alleviate ARD. An alternative approach to combat ARD, could involve adjusting the rootstock microbiome to better cope with biotic stress present in orchard soil. In this study we evaluated differences in microbiome structure and composition between nursery grown rootstock and mature apple trees, cultivated in Nova Scotian orchards. We found that mature apple tree roots associated microbiome dramatically differed in its diversity, structure and composition compared to that associated with saplings. Our research identified several fungal and bacterial taxa as potential candidates for further study in the context of nursery inoculation and their possible role in mitigating ARD in re-planted apple orchards. The results of this study provide a foundation for development of a synthetic community which could be used in nurseries during rootstock propagation to improve saplings adaptation to ARD soils. This approach may offer an ecologically safe and cost-effective alternative to current soil amendments to alleviate ARD consequences.},
}

*Malus/microbiology/growth & development
*Plant Diseases/microbiology/prevention & control
*Microbiota
*Plant Roots/microbiology
Soil Microbiology
Fungi/genetics/classification
Bacteria/genetics/classification

@article {pmid40603415,
year = {2025},
author = {Thompson, RM and Del Carmen Montero-Calasanz, M and George, D and Fox, EM},
title = {From pollution to reforestation: the hidden microbiome of Alnus glutinosa nodules over 30 years.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23373},
pmid = {40603415},
issn = {2045-2322},
support = {NE/S007512/1//Natural Environment Research Council/ ; RYC2019-028468-I//Spanish Ministry of Economy, Industry and Competitiveness (MINECO)/ ; },
mesh = {*Alnus/microbiology ; *Microbiota ; *Root Nodules, Plant/microbiology ; Metals, Heavy/toxicity ; Soil Microbiology ; Soil Pollutants ; Biodegradation, Environmental ; },
abstract = {Actinorhizal plants, such as Alnus glutinosa, play a critical role in ecosystem restoration, particularly in metal-contaminated soils, yet their nodule microbiome remains largely unexplored beyond Frankiaceae endosymbionts. This study presents the first comprehensive analysis of A. glutinosa root nodules under heavy metal stress, focusing on a 30-year-old chronosequence planted upon opencast coal mine spoil. Microbial diversity analysis revealed that A. glutinosa nodules harbour a distinct and conserved microbiome, dominated by Frankiaceae but also enriched with plant growth-promoting bacteria such as Bradyrhizobium, Mycobacterium, and Actinoplanes. Additionally, despite similar beta diversity between the nodules and soil, significant compositional differences were observed, reinforcing the selective nature of the nodules. However, functional profiling indicated that metabolic pathways were largely shared between nodule and soil microbiomes. Overall, this study provides new insights into the resilience and specialisation of the A. glutinosa nodule microbiome and its potential role in bioremediation within heavy metal-contaminated environments.},
}

*Alnus/microbiology
*Microbiota
*Root Nodules, Plant/microbiology
Metals, Heavy/toxicity
Soil Microbiology
Soil Pollutants
Biodegradation, Environmental

@article {pmid40603287,
year = {2025},
author = {Samarra, A and Alcañiz, AJ and Martínez-Costa, C and Marina, A and Comas, I and Segata, N and Quijada, NM and Collado, MC},
title = {Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6099},
pmid = {40603287},
issn = {2041-1723},
support = {MAMI-639226 project//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; PROMETEO2020/12//Generalitat Valenciana (Regional Government of Valencia)/ ; CIPROM2023/030//Generalitat Valenciana (Regional Government of Valencia)/ ; },
mesh = {Humans ; *Breast Feeding ; *Bifidobacterium/physiology/genetics ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Cesarean Section ; Metagenome ; Adult ; Male ; Milk, Human/microbiology ; Feces/microbiology ; },
abstract = {The assembly of the gut resistome in early life is key to infant health. Specific perinatal factors such as cesarean section (C-section), antibiotic exposure and lack of breastfeeding practices are detrimental to proper microbial development and increase the antimicrobial resistance genes (ARGs). Using 265 gut longitudinal metagenomes from 66 mother-infant pairs, we investigated how perinatal factors influence the acquisition and dynamics of ARGs during the first year of life. Our findings reveal that Bifidobacterium plays a crucial role in modulating the infant resistome, with its high relative abundance being associated with a lower ARG load. Exclusive breastfeeding during the first month of life accelerates the reduction of ARGs and ensures a lower resistome burden at six months. Moreover, early breastfeeding cessation correlates with a higher ARG load, underscoring its long-term influence on microbial resilience. Importantly, we identify exclusive breastfeeding as a key strategy to mitigate the impact of C-section delivery on the infant gut resistome, counteracting the early-life antibiotic exposure associated with this procedure and the resulting resistance acquisition. By promoting a microbiome enriched in Bifidobacterium, breastfeeding may help suppress ARG-carrying taxa, reducing the risk of resistance dissemination. Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome. Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.},
}

Humans
*Breast Feeding
*Bifidobacterium/physiology/genetics
*Gastrointestinal Microbiome/genetics/drug effects
Infant
Female
Infant, Newborn
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Cesarean Section
Metagenome
Adult
Male
Milk, Human/microbiology
Feces/microbiology

@article {pmid40603217,
year = {2025},
author = {Bouwmeester, H and Dong, L and Wippel, K and Hofland, T and Smilde, A},
title = {The chemical interaction between plants and the rhizosphere microbiome.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.06.001},
pmid = {40603217},
issn = {1878-4372},
abstract = {Research into the interaction between plants and the soil microbiota has expanded rapidly and is unravelling a plethora of interactions between plants and their root microbiota. The rhizosphere exhibits remarkable chemical diversity, driven by an evolutionary arms race. Through these chemicals, plants shape the rhizosphere microbiome using different mechanisms: organic carbon provision, antimicrobial compound production, and exudation of microbiota recruitment signals. Modern high-input agriculture may have diminished the role of natural chemical interactions and modern crops may have lost some of the relevant traits. As our understanding of root-rhizosphere interactions grows, harnessing natural mechanisms for agricultural sustainability becomes increasingly viable, potentially helping agriculture to counteract growing challenges from environmental stresses, climate change, and rising input costs.},
}

@article {pmid40603165,
year = {2025},
author = {Post, Z and Rosario Lora, D and Blogowski, W},
title = {Unraveling the sweet connection between pancreatic cancer and hyperglycemia.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2025.06.003},
pmid = {40603165},
issn = {1879-3061},
abstract = {Pancreatic adenocarcinoma (PaC) is one of the deadliest cancers, primarily due to late-stage diagnosis and limited treatment options. A bidirectional relationship exists between PaC and diabetes mellitus (DM), where glucose abnormalities both cause and result from PaC. In this review, we examine the complex pathophysiology of PaC-induced hyperglycemia, focusing on impaired insulin sensitivity, β cell dysfunction, chronic inflammation, and alterations in the gut microbiome and circadian rhythm. We discuss how PaC induces insulin resistance through disrupted signaling and proinflammatory factors, as well as β cell dysfunction through oxidative stress and adrenomedullin-mediated insulin secretion inhibition. In addition, emerging research highlights the role of the gut microbiome in PaC and hyperglycemia. Comprehensive understanding of these mechanisms is critical for early detection and improved treatment strategies for PaC.},
}

@article {pmid40603006,
year = {2025},
author = {Wiersinga, WJ and van der Poll, T},
title = {Biological drivers of the host response in sepsis.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thorax-2024-222012},
pmid = {40603006},
issn = {1468-3296},
abstract = {Sepsis is a life-threatening syndrome driven by a dysregulated host response to infection. Immune dysregulation arises from responses that initially were activated to protect against pathogens and preserve tissue integrity. Disturbed resistance mechanisms can result in excessive inflammation alongside immunosuppression, each of which is considered important biological drivers of the immunopathology of sepsis. Key inflammatory drivers are excessive proinflammatory cytokine activity, complement and coagulation system activation and endothelial dysfunction. Conversely, sepsis-induced immunosuppression is marked by lymphocyte exhaustion, reduced monocyte human leucocyte antigen-DR expression, and the emergence of myeloid-derived suppressor cells. Within this complex immunological environment, the gut microbiome influences host immunity through the release of short-chain fatty acids and bacterial metabolites. Thus far, immunomodulatory trials in patients with sepsis paid little attention to the identification of dominant biological drivers, which might enrich the population for those who are more likely to respond to a certain intervention. Recently, retrospective analyses of such trials, as well as small prospective trials, have provided proof of concept that subgroups of sepsis patients can be identified with specific immunological profiles, either based on a single biomarker or on high-dimensional data, that respond differently to immunomodulation. This review explores the biological drivers of sepsis immunopathology, highlighting the challenges in translating preclinical insights into effective therapies and the potential of personalised medicine approaches to improve sepsis outcomes.},
}

@article {pmid40602915,
year = {2025},
author = {Liu, Z and Wang, X and Zheng, G and Li, J and Qin, J and Wang, L and Ouyang, X and Wang, J and Gu, W},
title = {Effects of petroleum contamination on soil metal(loid)s and microbial communities.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {662-673},
doi = {10.1016/j.jes.2024.12.008},
pmid = {40602915},
issn = {1001-0742},
mesh = {*Soil Pollutants/analysis/toxicity ; *Soil Microbiology ; Soil/chemistry ; *Petroleum Pollution/analysis ; *Microbiota/drug effects ; *Petroleum/analysis ; *Environmental Monitoring ; *Metals/analysis ; },
abstract = {Evaluating petroleum contamination risk and implementing remedial measures in agricultural soil rely on indicators such as soil metal(loid)s and microbiome alterations. However, the response of these indicators to petroleum contamination remains under-investigated. The present study investigated the soil physicochemical features, metal(loid)s, microbial communities and networks, and phospholipid fatty acids (PLFAs) community structures in soil samples collected from long- (LC) and short-term (SC) petroleum-contaminated oil fields. The results showed that petroleum contamination increased the levels of soil total petroleum hydrocarbon, carbon, nitrogen, sulfur, phosphorus, calcium, copper, manganese, lead, and zinc, and decreased soil pH, microbial biomass, bacterial and fungal diversity. Petroleum led to a rise in the abundances of soil Proteobacteria, Ascomycota, Oleibacter, and Fusarium. Network analyses showed that the number of network links (Control vs. SC, LC = 1181 vs. 700, 1021), nodes (Control vs. SC, LC = 90 vs. 71, 83) and average degree (Control vs. SC, LC = 26.244 vs. 19.718, 24.602) recovered as the duration of contamination increased. Petroleum contamination also reduced the concentration of soil PLFAs, especially bacterial. These results demonstrate that brief exposure to high levels of petroleum contamination alters the physicochemical characteristics of the soil as well as the composition of soil metal(loid)s and microorganisms, leading to a less diverse soil microbial network that is more susceptible to damage. Future research should focus on the culturable microbiome of soil under petroleum contamination to provide a theoretical basis for further remediation.},
}

*Soil Pollutants/analysis/toxicity
*Soil Microbiology
Soil/chemistry
*Petroleum Pollution/analysis
*Microbiota/drug effects
*Petroleum/analysis
*Environmental Monitoring
*Metals/analysis

@article {pmid40602893,
year = {2025},
author = {Guo, H and Zhao, X and Yang, K and Cui, L},
title = {Optimizing mealworm rearing conditions and gut microbiome function for enhanced plastics biodegradation.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {417-429},
doi = {10.1016/j.jes.2024.12.004},
pmid = {40602893},
issn = {1001-0742},
mesh = {Animals ; *Biodegradation, Environmental ; *Tenebrio/physiology/growth & development ; *Plastics/metabolism ; *Gastrointestinal Microbiome/physiology ; Larva ; },
abstract = {Insects have become an efficient and eco-friendly bioreactor for plastics and even micro/nano-plastics biodegradation. However, the optimal conditions for rearing insects to maximize plastic biodegradation and the underlying mechanisms remain unclear, hindering its practical applications. We investigated the effects of multiple rearing factors on plastics degradation efficiency of Tenebrio molitor larvae, including larval instar, water addition frequency, plastic specific surface area and plastic types. The functional gut microbes and enzymes associated with the improved efficiency were further explored. Our findings revealed that adult larvae achieved the highest plastics degradation efficiency when receiving regular water additions without causing drowning of insects on hydrophobic plastics. Additionally, they effectively ingested foam plastics of polystyrene, polyethylene and polyurethane without prior comminution and densification. The biodegradation processes involving oxidation, cleavage and depolymerization of plastics were all demonstrated. Furthermore, foam plastic type-dependent functional microbes and enzymes that contributed to the efficient plastic degradation were identified. This work provides valuable insights into the practical applications of insects for sustainable plastics biodegradation.},
}

Animals
*Biodegradation, Environmental
*Tenebrio/physiology/growth & development
*Plastics/metabolism
*Gastrointestinal Microbiome/physiology
Larva

@article {pmid40602696,
year = {2025},
author = {Mohammed, V and Arasu, MV and Muthuramamoorthy, M and Karthick Raja Namasivayam, S and Arockiaraj, J},
title = {Neurotoxicity of food colorants: Gut dysbiosis and reduced short-chain fatty acids disrupt the enteric nervous system and lead to neurological disability.},
journal = {Toxicology letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.toxlet.2025.06.022},
pmid = {40602696},
issn = {1879-3169},
abstract = {For centuries, the practice of adding color to food has become deeply ingrained in culinary traditions, evolving into an indispensable aspect of food production today. Major food manufacturing companies extensively use colorants to enhance the visual appeal of their products. However, recent years have seen an increasing number of studies by researchers who have uncovered various health risks associated with food color additives. These studies have predominantly linked food colorants to severe health conditions such as cancer and allergies. Beyond these issues, further investigations have revealed that excessive use of food colorants can also lead to neurological disorders. Specifically, food colorants such as Tartrazine, Allura Red, Indigotine, Erythrosine, and Titanium Dioxide have been identified as significant contributors to bodily harm. Research indicates that these colorants do not directly affect the brain but impact the gut microbiome. They destroy beneficial gut bacteria, creating a pathway for neurological issues. While the direct mechanisms through which these colorants damage the gut and subsequently affect brain health are not yet fully understood, this paper aims to elucidate these pathways. Through comprehensive analysis, we demonstrate how these food colorants compromise gut health and lead to neurological impairments. By highlighting these interactions, this paper seeks to raise awareness and stimulate further research within the scientific community. Such research could pave the way for significant discoveries, providing deeper insights into the long-term effects of food colorants and leading to more informed regulatory decisions and safer food production practices in the future.},
}

@article {pmid40602642,
year = {2025},
author = {Pieńkowska, A and Fleischmann, J and Drabesch, S and Merbach, I and Wang, G and Rocha, U and Reitz, T and Marie Muehe, E},
title = {Long-term Organic Fertilization Shields Soil Prokaryotes from Metal Stress While Mineral Fertilization Exacerbates It.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126747},
doi = {10.1016/j.envpol.2025.126747},
pmid = {40602642},
issn = {1873-6424},
abstract = {Metal contamination in agricultural soils threatens prokaryote dynamics essential for soil health and crop productivity. Yet, whether fertilization in the long-run affects their resilience to metals remains unclear. This study examined the biogeochemical impacts of realistically low-dose applications of cadmium, zinc, and lead in soils subjected to 119 years of non-fertilization, mineral-fertilization (NPK), organic-fertilization (manure), or combined mineral-organic fertilization. Amended metals remained in the mobile fraction with the order: mineral }

@article {pmid40602634,
year = {2025},
author = {Ma, L and Pan, Y and Liu, H and Liu, G and Liu, W},
title = {Drying-Rewetting Legacy Mitigates Freezing-Thawing Effects on Soil Microbial Communities and Greenhouse Gas Emissions in Plateau Riparian Wetlands.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126753},
doi = {10.1016/j.envpol.2025.126753},
pmid = {40602634},
issn = {1873-6424},
abstract = {Climate change intensifies compound disturbances in soil ecosystems, yet how legacy effects from prior events shape microbial responses to subsequent stresses remains poorly understood. Here, we investigated the legacy effects of drying-rewetting (DW) and freeze-thaw (FT) on greenhouse gas (GHG) emissions and microbial community dynamics across riparian wetlands of the Tibetan Plateau with distinct land-use histories (urban, grazing, and natural). The results showed that urban soils consistently amplified CO2 emissions compared to grazing and natural lands, whereas natural soils exhibited a pronounced decline in fungal ITS gene abundance, contrasting with the resilience observed in urban and grazing counterparts. Notably, sequential DW-FT perturbations triggered cross-stress mitigation, reducing CO2 emissions and enriching Actinobacteria-a bacterial phylum negatively correlated with cumulative CO2 release. Concurrently, DW legacies drove the taxonomic restructuring of fungal communities, favoring the dominance of Ascomycota in natural soils subjected to subsequent FT cycles. Prior DW exposure uniquely amplified the relative abundance of bacterial amplicon sequence variants (ASVs) under FT fluctuations, while standalone FT legacies lacked comparable regulatory capacity. Furthermore, in bacterial co-occurrence networks exposed to two DW cycles, an incomplete cluster emerged, indicating short-term adaptation via compartmentalization. Fungal clusters under FT cycles exhibited simplified co-response patterns but activated mutualism. Our study demonstrates that DW/FT legacy effects on GHG emissions and microbial communities are land-use dependent; DW legacies mitigate FT-induced microbiome disruptions in plateau riparian soils, with fungi showing heightened sensitivity to FT and bacteria displaying adaptability to DW, highlighting taxon-specific responses to compound disturbances.},
}

@article {pmid40602565,
year = {2025},
author = {Rajeswari, G and Kumar, V and Jacob, S},
title = {Advanced lignocellulose bioprocessing for Aloe vera leaf rind through novel termite gut microbiome consortia for acetone butanol ethanol (ABE) production: Metagenomics insights and process economic analysis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145691},
doi = {10.1016/j.ijbiomac.2025.145691},
pmid = {40602565},
issn = {1879-0003},
abstract = {Consolidated bioprocessing (CBP) of lignocellulosic biomass (LCB) using microbes simplifies the process, eliminates enzyme cost and reduces the overall processing expenses. In this regard, termite gut, a potent reservoir of microbial symbionts produces various lignocellulolytic enzymes which acts synergistically to degrade LCB. However, the effectiveness of adapting the microbes with LCB for improved lignocellulolytic enzyme secretion and substrate degradation has been overlooked. Hence, in this study adaptive laboratory (ALE) of termite gut isolates was performed with various substrates such as saw dust (SD) and Aloe vera leaf rind (AVLR) under different conditions. Among the consortia, enriched termite consortium (ETC-3) showed the highest degradation of lignin (51.86 ± 2.03 %, w/w), hemicellulose (29.27 ± 1.29 %, w/w) and cellulose (41.97 ± 2.99 %, w/w) with maximum specific enzyme activities. High throughput sequencing revealed the significant enrichment of Proteobacteria (88.95 %) and Ascomycota (99.94 %) groups in ETC-3. Further, the efficiency of ETC-3 in consolidated pretreatment and bioprocessing (CPBP) and CBP of AVLR towards acetone, butanol and ethanol (ABE) production was studied. Compared to the CPBP, CBP resulted in 1.6-fold higher glucose yield which subsequently enhanced the butanol yield (7.97 ± 0.40 g/L). Finally, cost benefit analysis ensured the economic feasibility of process strategies for AVLR valorization.},
}

@article {pmid40602277,
year = {2025},
author = {Wu, H and Li, YL and Wang, Y and Wang, YG and Hong, JH and Pang, MM and Liu, PM and Yang, JJ},
title = {Anemoside B4 alleviates ulcerative colitis by attenuating intestinal oxidative stress and NLRP3 inflammasome via activating aryl hydrocarbon receptor through remodeling the gut microbiome and metabolites.},
journal = {Redox biology},
volume = {85},
number = {},
pages = {103746},
doi = {10.1016/j.redox.2025.103746},
pmid = {40602277},
issn = {2213-2317},
abstract = {Ulcerative colitis (UC) is a chronic, non-specific inflammatory disease of the intestines with a significant increase in global incidence in recent years. Oxidative stress and inflammation are two hallmarks of UC pathogenesis. Anemoside B4 (AB4), a pentacyclic triterpenoid saponin, exhibits significant antioxidant and anti-inflammatory properties and shows potential for preventing UC. Here, an animal model induced by dextran sodium sulfate (DSS) was used to investigate the effect of AB4 on UC. The results demonstrated that AB4 significantly reduces intestinal oxidative stress and inflammation in UC mice, while also protecting intestinal barrier function. Furthermore, AB4 helps restore intestinal microbial balance primarily by modulating the abundance of Lactobacillus, which enhances the metabolism of short-chain fatty acids and upregulates the production of butyric acid (BA). Pseudogerm-free mice and fecal microbiota transplantation (FMT) demonstrated that AB4 significantly mitigated UC in a gut microbe-dependent manner. Both AB4 and BA markedly activate the aromatic hydrocarbon receptor (AhR). The intestinal organoid results suggest BA may activate the AhR to inhibit ROS production and activation of NLRP3 inflammasome, thereby protecting intestinal integrity. Administration of AhR antagonists abolished the protective effects, thus confirming the involvement of AhR in the underlying mechanism. Overall, these results indicate that AB4 is an effective agent against UC mainly by activating the AhR through gut microbial short-chain fatty acid metabolites to inhibit intestinal oxidative stress and inflammation.},
}

@article {pmid40602191,
year = {2025},
author = {de Sant'Anna, FM and Chakrawarti, A and Haley, BJ and Barlow, J},
title = {The resistome of pasteurized and raw milk cheeses from the state of Vermont.},
journal = {International journal of food microbiology},
volume = {441},
number = {},
pages = {111333},
doi = {10.1016/j.ijfoodmicro.2025.111333},
pmid = {40602191},
issn = {1879-3460},
abstract = {This study investigates the resistome dynamics in cheese production, focusing on both raw milk and pasteurized varieties comparing a standard and lytic method of DNA extraction. Metagenomic analysis revealed the presence of single nucleotide polymorphism (SNP) confirmed antimicrobial resistance genes (ARGs) in core and rind samples of cheeses at different stages of ripening. No statistical significance was found between the extraction methods for antimicrobial resistance gene (ARG) classes. In pasteurized cheese, the resistome was influenced by the initial microbial composition and ripening period, with limited ARGs detected due to pasteurization. Nonetheless, detection of class B β-lactamase and Fosfomycin B resistance genes was observed in the pasteurized cheese core, possibly harbored by Bacillus cereus. Raw milk cheese exhibited a distinct resistome profile, with fluctuations in macrolide and oxazolidinone resistance genes associated with changes in microbial populations during ripening. Notably, the likely presence of multi-drug resistance genes in Lactococcus lactis highlights the importance of understanding resistance mechanisms in starter cultures. The study emphasizes the need for antimicrobial stewardship and hygiene practices in dairy production to mitigate the spread of resistance genes. Despite sequencing biases, this research contributes valuable insights into the cheese resistome, advocating for future studies to employ enhanced sequencing methods for comprehensive analysis and to develop practical strategies for resistance management in dairy products.},
}

@article {pmid40601963,
year = {2025},
author = {Munyaneza, V and Zhang, W and Haider, S and Ren, L and Ali, A and Kant, S and Ding, G},
title = {Mitigating Metal Toxicity in Plants Using Nanoparticles: Mechanisms and Implications for Sustainable Agriculture.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c04693},
pmid = {40601963},
issn = {1520-5118},
abstract = {Conventional agriculture's reliance on chemical inputs poses risks to human health and the environment. Nanotechnology offers a promising alternative through engineered nanoparticles (NPs) that have a high surface area, solubility, and reactivity. This review highlights how NPs mitigate metal toxicity and soil acidification by enhancing nutrient delivery and reducing phytotoxicity. We discuss NP-soil-plant interactions, including uptake, translocation, and physiological responses, at the cellular and molecular levels. Ecotoxicological concerns, such as NP accumulation, microbial disruption, and long-term effects, are addressed. Innovative strategies like stimuli-responsive release systems and NP-microbiome co-delivery platforms are explored to improve efficacy and safety. NPs significantly enhance plant resilience by increasing antioxidant enzyme activities by up to 60%, improving nutrient uptake efficiency, and boosting plant growth by 15-55% under aluminum stress conditions across various species, including Brassica napus. This perspective identifies key knowledge gaps and offers future perspectives, positioning nanotechnology as a sustainable tool to enhance crop productivity under metal stress while maintaining ecological balance.},
}

@article {pmid40601677,
year = {2025},
author = {Mills, K and Tan, J and Guneratne, T and Keir, L and Goldstein, M and Ventola, C and Makama, M and Ammerdorffer, A and Gülmezoglu, AM and Vogel, JP and McDougall, ARA},
title = {Maternal gut microbiome interventions to improve maternal and perinatal health outcomes: Target product profile expert consensus and pipeline analysis.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0321543},
doi = {10.1371/journal.pone.0321543},
pmid = {40601677},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Probiotics/therapeutic use ; Pregnancy ; Consensus ; *Maternal Health ; },
abstract = {OBJECTIVE: To develop a novel Target Product Profile (TPP) outlining the minimum and optimal requirements of probiotics targeting the maternal gut microbiome, create a research and development (R&D) pipeline of maternal microbiome interventions, and identify the highest potential probiotic candidates matching TPP criteria.

DESIGN: A mixed-methods study including in-depth interviews, an international survey, and online public consultation, with systematic R&D pipeline development.

SETTING: International research context in maternal gut microbiome interventions.

POPULATION: Ten stakeholder groups were included in the study for feedback on the TPP development.

METHODS: Stakeholder feedback from 23 interviews and 32 survey responses was analyzed to revise the TPP. A systematic search of databases (Adis Insight, ClinicalTrials.gov, WHO ICTRP, Ovid MEDLINE, and relevant grant databases) identified drugs, supplements, and biologics targeting the maternal gut microbiome. Probiotic candidates were matched against key TPP criteria to identify promising options for future research.

MAIN OUTCOME MEASURES: Stakeholder consensus (≥75% agreement) on TPP variables and identification of high-potential probiotic candidates.

RESULTS: The TPP met consensus for most of the 20 variables: 16 for minimum and 14 for optimal targets. Interviews raised issues concerning indication, target population, diagnostic requirements, and efficacy outcomes. Of 38 candidates identified in the maternal microbiome pipeline (2000-2023), eight were probiotics, with one high-potential candidate (Vivomixx) and two medium-potential candidates (Lactobacillus spp. and Bifidobacterium spp.) identified.

CONCLUSIONS: This study produced the first TPP and pipeline analysis for maternal gut microbiome interventions, identifying probiotics with higher potential. Few candidates reached late-phase research, highlighting the need for efficacy trials.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Female
*Probiotics/therapeutic use
Pregnancy
Consensus
*Maternal Health

@article {pmid40601568,
year = {2025},
author = {Manavalan, S and Pradeep, D and Dharmalingam, D and Semalaiyappan, J and Sivarasan, T and Venkatesan, S and Thirumal, S and Kuttiatt, VS},
title = {Comparative analysis of skin microbiome of patients with filarial lymphedema and healthy individuals.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325380},
doi = {10.1371/journal.pone.0325380},
pmid = {40601568},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Male ; *Skin/microbiology ; *Elephantiasis, Filarial/microbiology ; Adult ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Lymphedema/microbiology ; Pilot Projects ; Skin Microbiome ; },
abstract = {BACKGROUND: Lymphatic filariasis, a vector borne parasitic disease is a public health problem in the tropical region. Recurrent skin and soft tissue infections termed adenolymphangitis (ADL) is a major complication of filarial lymphedema. Understanding the changes in skin microbiome associated with this disease may provide novel insights on ADL attacks and lymphedema progression. This study investigates the changes in skin microbial flora in patients affected with filarial lymphedema.

METHODS: We employed 16S rRNA gene amplicon-based metagenomic technique to profile the skin microbiome of patients with filarial lymphedema in comparison with healthy volunteers.

RESULTS: There were notable differences in the bacterial flora between patients and healthy controls. Actinobacteria were under-represented in the patient group. Staphylococcus dominated both the groups, 63% in patients and 44% in controls. Samples from a few patients showed the presence of certain rare bacteria like Eremococcus and Facklamia.

CONCLUSION: This pilot study applying advanced molecular tools provides insight on the changes in skin microflora associated with filarial lymphedema for the first time. Further studies are necessary for a better understanding of the role of the altered skin microbiome in frequent episodes of adenolymphangitis in patients with filarial lymphedema.},
}

Humans
*Microbiota/genetics
Male
*Skin/microbiology
*Elephantiasis, Filarial/microbiology
Adult
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Case-Control Studies
*Lymphedema/microbiology
Pilot Projects
Skin Microbiome

@article {pmid40601380,
year = {2025},
author = {Bağcı, U and Ulusan Bağcı, Ö},
title = {The bibliometric analysis of documents concerning the relationship between the microbiota and urological malignancies.},
journal = {Journal of medical microbiology},
volume = {74},
number = {7},
pages = {},
doi = {10.1099/jmm.0.002041},
pmid = {40601380},
issn = {1473-5644},
mesh = {Humans ; *Bibliometrics ; *Microbiota ; *Urologic Neoplasms/microbiology ; Male ; Prostatic Neoplasms/microbiology ; Urinary Bladder Neoplasms/microbiology ; Kidney Neoplasms/microbiology ; },
abstract = {Introduction. The microbiota, which has a major impact on both health and illness, has recently become one of the most popular research topics.Hypothesis/Gap statement. To the best of our knowledge, no research has undertaken a bibliometric analysis of publications examining the connection between microbiome and urological cancer to date. In this respect, it is thought that our study will contribute to the literature.Aim. The purpose of this study is to raise awareness of the topic by performing a bibliometric analysis of the publications examining the connection between the microbiota and the most common urological cancers, including bladder, prostate, and kidney cancers.Methodology. All publications about prostate, renal and bladder cancers and microbiota indexed in Web of Science between 2000 and 2024 were included in the study.Results. A total of 310 publications were obtained. Before 2018, there were only three or fewer publications annually; however, following 2018, the number of publications increased rapidly, reaching a peak of 77 in 2024. The USA led with 98 (31.61%) documents, followed by China (60, 19.35%) and Italy (31, 10%). With 19 publications, Hirotsugu Uemura is the most contributing author, followed by Norio Nonomura with 17. Prostate cancer accounted for 45.48% of the publications, bladder cancer for 36.77% and kidney malignancies for 17.64%.Conclusion. Despite the fact that microbiota has been known for 80 years, research on the connection between microbiota and cancer accelerated after the completion of the Human Microbiome Project. The number of studies examining the connection between urological cancer and microbiota peaked in 2024 and is probably going to rise. More research is required on this topic, since the correlation between microbiota and especially prostate and bladder malignancies raises the possibility that variations in microbiota may be utilized in diagnosis, treatment and prognosis.},
}

Humans
*Bibliometrics
*Microbiota
*Urologic Neoplasms/microbiology
Male
Prostatic Neoplasms/microbiology
Urinary Bladder Neoplasms/microbiology
Kidney Neoplasms/microbiology

@article {pmid40601369,
year = {2025},
author = {Prusa, J and Gorelik, MG and Blake, KS and Dantas, G},
title = {State of omics-based microbial diagnostics of CRC.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2526132},
doi = {10.1080/19490976.2025.2526132},
pmid = {40601369},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolomics/methods ; Early Detection of Cancer/methods ; Gastrointestinal Tract/microbiology ; },
abstract = {Colorectal cancer (CRC) remains a major burden of cancer-related morbidity and mortality globally, especially when detected at later stages. Early detection through improved and more accessible diagnostics is critical for reducing the severity of CRC. As our understanding of CRC and the microbial inhabitants of the gastrointestinal tract continues to improve, it has become increasingly recognized that the bacterial component of the gut microbiome may provide diagnostic utility for detecting CRC. This is because CRC is often accompanied by shifts in bacterial taxa, and the metabolites produced or utilized by the CRC-associated gut bacterial community. Advances in sequencing and metabolite profiling technologies paired with our growing understanding of CRC-associated microbial taxa, present an opportunity for new gut microbiome-based diagnostics. In this narrative review, we discuss bacterial taxa and gut metabolites that have been investigated as predictive features for CRC diagnosis. We aim to highlight the tremendous progress that has been made in identifying gut microbiome-based features and why they should be further explored as potential CRC diagnostics. We also identify challenges that future work must address, including the impact of patient lifestyle, variation in methodology, and nonstandard data management practices. Resolving these areas of study design and implementation is key to understanding the complex bacterial communities and their by-products associated with CRC, and the development of microbial diagnostics that can detect them.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Metabolomics/methods
Early Detection of Cancer/methods
Gastrointestinal Tract/microbiology

@article {pmid40601331,
year = {2025},
author = {Li, Y and Dai, J and Wang, M and Yan, C and Xiu, M and Qu, M},
title = {Alterations in Gut Microbiota and Plasma Metabolites in Patients with Generalized Anxiety Disorder: A Multi-Omics Study.},
journal = {The International journal of neuroscience},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/00207454.2025.2529238},
pmid = {40601331},
issn = {1563-5279},
abstract = {OBJECTIVE: Microecological and metabolic disorders of the gut may be involved in the pathogenesis of generalized anxiety disorder (GAD), but clinical multi-omics evidence of this is lacking. Our study aimed to investigate characteristic alterations in the gut microbiota and plasma metabolome of patients with GAD and evaluate their clinical diagnostic value.

PATIENTS AND METHODS: Ninety subjects (60 patients with GAD and 30 healthy volunteers) were included. We employed 16S rRNA gene sequencing to characterize the gut microbiota and targeted liquid chromatography-mass spectrometry to analyze plasma metabolomic profiles.

RESULTS: GAD was associated with increased abundances of Actinobacteria, Bacteroidetes, and Escherichia-Shigella and decreased abundances of Firmicutes, Roseburia, Bifidobacterium, and Prevotellaceae_Prevotella. Metabolomic analysis revealed 19 differential metabolites (upregulated in GAD: e.g., glutamic acid, cortisol, arachidonic acid, α-linolenic acid; downregulated in GAD: e.g., γ-aminobutyric acid, serotonin, tyrosine, phenylalanine, tryptophan). Enriched metabolic pathways included phenylalanine, tyrosine, and tryptophan biosynthesis; alanine, aspartate, and glutamate metabolism; and the biosynthesis of unsaturated fatty acids. Notably, microbiome-metabolome combined analysis revealed a significant correlation between intestinal flora disorders and changes in the plasma metabolic profile. The diagnostic model constructed based on the combined omics data exhibited excellent discriminatory efficacy, with areas under curve of 0.710, 0.986, and 0.997 for the microbiome, metabolome, and combined model, respectively. ​.

CONCLUSION: This study revealed the characteristic gut microbiome-plasma metabolome covariation pattern of GAD and identified biomarker combinations with potential diagnostic value. The identified biomarker group provides new insights into the gut-brain axis mechanism of GAD, providing important theoretical support for clarifying the pathogenesis of GAD and developing precise diagnosis and treatment strategies.},
}

@article {pmid40601234,
year = {2025},
author = {Correia, DMITD and Kapoor, N and Chávez-Manzanera, E and Gowdak, LHW and Kharusi, AA and Casanueva, FF and Halpern, B and Frost, G and Aldahash, R},
title = {Emerging evidence and potential avenues to achieve durable outcomes in patients with obesity: the confluence of nutrition, and Microbiome on body composition.},
journal = {Reviews in endocrine & metabolic disorders},
volume = {},
number = {},
pages = {},
pmid = {40601234},
issn = {1573-2606},
abstract = {Obesity is a global health concern that impacts health, quality of life, and longevity in affected individuals. Comorbid cardiovascular disease, type 2 diabetes, cancer, and other conditions often accompany obesity, and researchers are actively investigating therapeutic strategies to treat obesity and mitigate the health risks associated with excess adiposity. Restrictive nutritional intake and body weight reduction through lifestyle behavioral interventions, bariatric procedures, and highly effective anti-obesity medications are all recommended treatments for obesity. Meanwhile, the caloric restriction that comes with very low-calorie diets can result in changes in body composition, most notably a progressive loss of muscle mass and/or functionality, a process that can be accelerated by aging, underlying metabolic disease, or inadequate protein intake seen with many dietary patterns. While muscle loss was previously understood as a condition only affecting older individuals, this outcome is common in patients with obesity. The term sarcopenic obesity has been used to refer to this condition, and it is now recognized as an important potential complication in all patients with obesity. Dietary challenges that influence overall body composition also have drawn attention to the gut microbiome, a topic of growing interest as there is an increasingly recognized interplay between diet, the metabolic actions of microorganisms in the gut that impact macronutrient and micronutrient production and absorption, and human health. This article will review the current understanding of obesity as a chronic disease, the impact of diet and nutritional therapy on body composition, and the potential relevance of the gut microbiome in this setting.},
}

@article {pmid40601071,
year = {2025},
author = {Su, J and Zhang, WB and Chen, YJ and Sun, B and Zhai, YP and Yuan, JM},
title = {Microbiome diversity in Haemaphysalis flava (life stage-host dependent) and Haemaphysalis longicornis ticks with zoonotic implications in Nantong, China.},
journal = {Acta parasitologica},
volume = {70},
number = {4},
pages = {142},
pmid = {40601071},
issn = {1896-1851},
support = {MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MSZ2024113//Research Project of Nantong City Science and Technology - Public Wellbeing Plan./ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; MS2023092//Research Project Foundation of the Nantong Health Commission/ ; },
mesh = {Animals ; China ; *Ixodidae/microbiology/growth & development ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Zoonoses/microbiology/transmission ; *Bacteria/classification/genetics/isolation & purification ; Rickettsia/isolation & purification/genetics ; Humans ; Life Cycle Stages ; Nymph/microbiology ; Female ; Phylogeny ; Biodiversity ; Haemaphysalis longicornis ; },
abstract = {PURPOSE: This study characterized the microbial communities of Haemaphysalis flava (H. flava) and Haemaphysalis longicornis (H. longicornis), in Nantong, China, and assessed the zoonotic implications.

METHODS: We collected both on-host and off-host ticks and performed 16S rRNA amplicon sequencing. Subsequent bioinformatic analyses included taxonomic composition assessment, community diversity evaluation, differential abundance analysis, interspecies abundance correlation and functional inference.

RESULTS: Rickettsia dominated in H. flava (77.31%), while H. longicornis exhibited higher abundances of Stenotrophomonas (10.78%), Coxiella (10.04%), and Psychrobacter (9.70%). Comparative analyses of life stages and host associations were only performed for H. flava due to limited sample sizes of H. longicornis across developmental stages. Rickettsia was enriched in on-host H. flava (90.41-90.51%) compared to off-host specimens (46.12%). α-diversity analysis showed higher microbial richness in off-host nymphs than in on-host adults. β-diversity revealed strong species-specific clustering. Network analysis demonstrated more complex microbial interactions in adult ticks. Pathogen screening detected Rickettsia japonica (R. japonica, host-specific to H. flava), Ehrlichia ewingii (E. ewingii), and Anaplasma bovis (A. bovis). Functional prediction highlighted elevated B vitamin biosynthesis pathways in nymphs, aligning with Coxiella-like endosymbionts (CLEs)'s putative nutritional role.

CONCLUSION: This study emphasizes the importance of enhanced tick surveillance and regular pathogen screening in domestic animals, particularly for spotted fever group (SFG) Rickettsia. CLEs may exhibit stage-specific abundance patterns aligned with the host's developmental nutritional requirements. These findings highlight the need for integrated One Health surveillance to mitigate tick-borne disease threats.},
}

Animals
China
*Ixodidae/microbiology/growth & development
*Microbiota
RNA, Ribosomal, 16S/genetics
Zoonoses/microbiology/transmission
*Bacteria/classification/genetics/isolation & purification
Rickettsia/isolation & purification/genetics
Humans
Life Cycle Stages
Nymph/microbiology
Female
Phylogeny
Biodiversity
Haemaphysalis longicornis

@article {pmid40601060,
year = {2025},
author = {Wang, Y and Bai, S and Yang, T and Guo, J and Zhu, X and Dong, Y},
title = {Impact of exercise-induced alterations on gut microbiota diversity and composition: comparing effects of different training modalities.},
journal = {Cell regeneration (London, England)},
volume = {14},
number = {1},
pages = {28},
pmid = {40601060},
issn = {2045-9769},
support = {82300496//National Natural Science Foundation of China/ ; CFH 2024-1-4061//Capital's Funds for Health Improvement and Research (Key Research Program)/ ; XMLX202135//Beijing Hospitals Authority Clinical medicine Development of special funding/ ; },
abstract = {Exercise has been shown to influence gut microbiota composition, but the specific effects of different exercise modalities on microbial diversity remain unclear. Understanding these differences is essential for optimizing exercise programs to enhance both physical fitness and gut health. This study compared the gut microbiota profiles of participants undergoing moderate-intensity continuous training (MICT), high-intensity interval training (HIIT), and high-intensity functional training (HIFT) using 16S rRNA gene sequencing. Thirty-one previously untrained healthy university students were randomly assigned into MICT (n = 7), HIIT (n = 12) and HIFT (n = 12). The results revealed that distinct gut microbiome profiles in participants under different exercise modes. Notably, the alpha-diversity gradually increased from the MICT group to the HIFT group. In addition, there was a progressive shift towards a Faecalibacterium-dominated microbial type from HIIT to HIFT group compared to MICT group. Individuals in the HIFT group were identified to be enriched with Lactobacillus and Limosilactobacillus, along with reduced Actinomyces and Anaeromassilibacillus. Functionally, the KEGG pathway and enzyme analysis using PICRUST2 revealed that the HIFT group exhibited prominence in muscle function-related pathways and enzymes, specifically ko00280 (valine, leucine, and isoleucine degradation), as well as the enzyme EC: 3.4.11.14 (alanine aminopeptidase). In conclusion, these findings highlight how exercise modality influences gut microbial diversity, with HIFT promoting a more favorable microbial profile compared to traditional endurance training. Understanding these effects can help tailor exercise programs to improve both fitness and gut health.},
}

@article {pmid40601033,
year = {2025},
author = {Nariman, N and Entling, MH and Krehenwinkel, H and Kennedy, S},
title = {The Microbiome of an Invasive Spider: Reduced Bacterial Richness, but no Indication of Microbial-Mediated Dispersal Behaviour.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {70},
pmid = {40601033},
issn = {1432-184X},
mesh = {Animals ; *Spiders/microbiology/physiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Introduced Species ; Symbiosis ; Europe ; Animal Distribution ; },
abstract = {Mermessus trilobatus, an invasive North American linyphiid spider, has expanded its invasion range up to 1400 km in Europe, accelerating its dispersal speed in less than 40 years. The high heritability of dispersal behaviour and the spatial sorting of high and low dispersers indicate a genetic basis of dispersal behaviour. However, microbial endosymbionts can moderate dispersal behaviour in related species (Rickettsia in Erigone atra). Hence, dispersal behaviour in M. trilobatus might also be dictated by the activity of dispersal-mediating endosymbionts. Here, we investigated the microbiome of invasive M. trilobatus spiders extracted from (1) high- and low-dispersive individuals and (2) spiders originating from locations close to the edge and core of the expansion. We examine the microbiomes for the presence of potential dispersal- and reproduction-mediating bacterial strains and compare the microbial assemblages of spiders based on their dispersal behaviour and locations of origin. The composition of microbial assemblages was similar among spiders of different geographic origins and dispersal behaviour. However, microbial richness was lower in high- than in low-dispersive individuals. Surprisingly, none of the known dispersal- or reproduction-altering endosymbionts of arthropods was identified in any tested spider. This contrasts with published results from North America, where M. trilobatus is a known host of Rickettsia and Wolbachia. Thus, the invasive European population appears to have lost its associated endosymbionts. As endosymbionts can reduce spider mobility, it is possible that their absence facilitates the spread of the invasive spider population. The absence of endosymbionts among the analysed individuals substantiates the role of genetic mechanisms behind the variable dispersal behaviour of invasive M. trilobatus in Europe.},
}

Animals
*Spiders/microbiology/physiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Introduced Species
Symbiosis
Europe
Animal Distribution

@article {pmid40601009,
year = {2025},
author = {Jing, J and Yan, X and Wang, L and Zhang, Y and Qi, W and Xi, J and Hao, Z},
title = {Gut microbiota-derived indole-3-acetic acid ameliorates calcium oxalate renal stone formation via AHR/NF‑κB axis.},
journal = {Urolithiasis},
volume = {53},
number = {1},
pages = {134},
pmid = {40601009},
issn = {2194-7236},
support = {82000672//National Natural Science Foundation of China Young Scientists Fund/ ; 82370768//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Kidney Calculi/metabolism/microbiology/prevention & control/drug therapy/chemically induced/pathology ; Rats ; *Gastrointestinal Microbiome/physiology ; *Indoleacetic Acids/metabolism/pharmacology/therapeutic use ; *Calcium Oxalate/metabolism ; Humans ; NF-kappa B/metabolism ; Male ; *Receptors, Aryl Hydrocarbon/metabolism ; Disease Models, Animal ; Cell Line ; Signal Transduction/drug effects ; Kidney/pathology/drug effects ; Female ; Oxidative Stress/drug effects ; Adult ; Rats, Sprague-Dawley ; },
abstract = {The exact mechanism of calcium oxalate stone (CaOx) formation is not fully understood. Evidence suggests that disruptions in the gut microbiota and its metabolites influence kidney stone formation. We conducted microbiome-metabolome analysis to pinpoint microbial metabolites linked to kidney stones in both patient and healthy control groups. We explored the impact of these kidney stone-related microbial metabolites on CaOx-induced stones, along with their underlying mechanisms of action. We exposed NRK-52E cells to CaOx crystals that had been pretreated with indole-3-acetic acid. Rats, induced to develop CaOx stones via ethylene glycol and ammonium chloride administration, were also treated with IAA. Our investigations encompassed assessments of Ca[2+] levels, reactive oxygen species levels, markers of oxidative stress, apoptosis levels, inflammation levels, and gene expression within AHR/NF‑κB pathway, both in cellular and tissue samples.Indole-3-acetic acid showed significantly reduction in patients with renal stones. The administration of IAA has been found to alleviate the deposition and adhesion of calcium oxide stones in the kidneys. Furthermore, IAA demonstrates beneficial effects on kidney damage and inflammation. IAA efficiently reduces intracellular levels of ROS, osteopontin, and CD44 in NRK-52E cells exposed to CaOx as well as in a rat model of stone formation. Mechanistically, IAA inhibits the activation of the NF-κB signaling pathway through the elevation of AHR in kidney stones. Our research has uncovered a novel connection between gut microbiota-derived tryptophan metabolites and kidney stones. The microbial metabolite IAA/AHR/NF-κB pathway may be a promising target for kidney stone treatment.},
}

Animals
*Kidney Calculi/metabolism/microbiology/prevention & control/drug therapy/chemically induced/pathology
Rats
*Gastrointestinal Microbiome/physiology
*Indoleacetic Acids/metabolism/pharmacology/therapeutic use
*Calcium Oxalate/metabolism
Humans
NF-kappa B/metabolism
Male
*Receptors, Aryl Hydrocarbon/metabolism
Disease Models, Animal
Cell Line
Signal Transduction/drug effects
Kidney/pathology/drug effects
Female
Oxidative Stress/drug effects
Adult
Rats, Sprague-Dawley

@article {pmid40600879,
year = {2025},
author = {Johnson, NC and Marín, C},
title = {Functional team selection as a framework for local adaptation in plants and their belowground microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf137},
pmid = {40600879},
issn = {1751-7370},
abstract = {Multicellular organisms are hosts to diverse communities of smaller organisms known as microbiomes. Plants have distinctive microbiomes that can provide important functions related to nutrition, defense, and stress tolerance. Empirical studies provide convincing evidence that in some -but not all - circumstances, belowground microbiomes help plants adapt to their local environment. The purpose of this review is to develop functional team selection (FTS) as a framework to help predict the conditions necessary for root microbiomes to generate local adaptation for their plant hosts. FTS envisions plants and their microbiomes as complex adaptive systems, and plant adaptations as emergent properties of these systems. If plants have the capacity to recognize and cultivate beneficial microbes and suppress pathogens, then it is possible for plants to evolve the capacity to gain adaptations by curating their microbiome. In resource-limited and stressful environments, the emergent functions of complex microbial systems may contribute to positive feedback linked to plant vigor, and ultimately, local adaptation. The key factors in this process are: 1) selective force, 2) host constitution, 3) microbial diversity, and 4) time. There is increasing interest in harnessing beneficial microbial interactions in agriculture and many microbial growth-promoting products are commercially available, but their use is controversial because a large proportion of these products fail to consistently enhance plant growth. The FTS framework may help direct the development of durable plant-microbiome systems that enhance crop production and diminish pathogens. It may also provide valuable insights for understanding and managing other kinds of host-microbe systems.},
}

@article {pmid40600792,
year = {2025},
author = {Ayayee, PA and Sunny, B and Montooth, KL and Rauter, CM},
title = {The Larval and Adult Female Gut Microbiomes of Two Burying Beetles (Nicrophorus spp.) With Distinct Parental Care Traits.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70137},
pmid = {40600792},
issn = {1462-2920},
support = {INBRE-P20GM103427-19//National Institute for General Medical Science (NIGMS) INBRE/ ; P30 CA036727/CA/NCI NIH HHS/United States ; //University of Nebraska-Lincoln/ ; },
mesh = {Animals ; *Coleoptera/microbiology/physiology/growth & development ; Larva/microbiology ; *Gastrointestinal Microbiome ; Female ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Behavior, Animal ; },
abstract = {Burying beetles (Nicrophorus spp.) exhibit parental care behaviours well-suited for studying gut microbiome and holobiont evolution. Theory predicts that differences in transmission can contribute to gut microbiome variations. We show that microbiome diversity estimates were comparable between reproductive females of common-garden-reared colonies of Nicrophorus marginatus (facultative parental care) and Nicrophorus orbicollis (obligate parental care). In contrast, the respective associated larvae of both species differed significantly. Furthermore, larval microbiomes clustered with respective adult female microbiomes but differed from each other. Fifteen bacterial families underscored differences in community composition between beetle species, with Wohlfahrtiimonadaceae significantly more abundant in N. orbicollis than N. marginatus. Results suggest that differences in parental transmission (trophallaxis) and larval acquisition of microbes possibly impact the parental-offspring gut microbiome dynamic. Close association of parental and larval microbiomes in the facultative parental care species is attributed to environmental acquisition from prepared carcasses and limited trophallaxis in larvae. However, the distinct larval and parental microbiomes in the obligate parental care species are attributed to the selective sorting of functionally relevant microbes from parents in larvae. Further examination of this genus's parental care behaviours and gut microbiome dynamics may offer insight into the possible evolutionary and ecological implications and general outcomes.},
}

Animals
*Coleoptera/microbiology/physiology/growth & development
Larva/microbiology
*Gastrointestinal Microbiome
Female
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Behavior, Animal

@article {pmid40600713,
year = {2025},
author = {Joos, L and Ommeslag, S and Baeyen, S and Asselberg, W and Van Loo, K and Clement, L and Debode, J and Vandecasteele, B and De Tender, C},
title = {Year-long, multiple-timepoint field studies show the importance of spatiotemporal dynamics and microbial functions in agricultural soil microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0011225},
doi = {10.1128/msystems.00112-25},
pmid = {40600713},
issn = {2379-5077},
abstract = {Despite the recognition of the complexity of soil ecosystem dynamics, most soil microbiome studies sample one field, take one sample per field, or use limited samples throughout the year. This limits our understanding of the spatiotemporal role of the soil microbiome in relation to management practices. To address these limitations, we conducted a year-long investigation of the soil microbiome in two agricultural fields, sampling multiple plots at different soil depths every 5 weeks. We examined spatial and temporal variabilities in response to the application of organic amendments (one-time biochar and annual compost application) on bacterial and fungal communities, studying both the microbial composition (metabarcoding, phospholipid fatty acids [PLFA], hot-water extractable-carbon) and activity (metatranscriptomics). Indicated by metabarcoding and PLFA, fungal communities were less affected over time per field, whereas bacteria exhibited more pronounced temporal trends. In contrast, fungi displayed clear spatial effects, while bacterial spatial differences within the field were predominantly observed in the deeper soil layer. Effects on functional roles and metabolic processes of the active microbial community were mainly related to temporal trends, especially in the topsoil. Organic amendments did not affect the microbial activity and affected fewer than 2% of the bacterial and fungal amplicon sequence variants over time. This study reveals the predominance of spatiotemporal dynamics over management practices in shaping soil microbial communities within agricultural fields, emphasizing the importance of field-specific factors, sampling depth, and community type. This ushers in the need for a well-considered experimental design and sampling strategy that accounts for spatiotemporal trends.IMPORTANCEThis study addresses a critical gap in soil microbiome research by investigating spatiotemporal effects on soil bacterial and fungal composition and activity in relation to field management practices. Moving beyond single-field and limited sampling approaches, this research conducted monthly sampling events on two fields at various depths. By combining metabarcoding, phospholipid fatty acid analysis, and metatranscriptomics, the study examined bacterial and fungal community composition, biomass, and functionality. Key findings reveal distinct responses of bacterial and fungal communities to spatiotemporal variability and management practices. Functional categories were predominantly driven by temporal trends rather than compost amendments. Temporal changes were more pronounced in the topsoil. These insights into the complex interactions between soil microbial communities, management practices, and spatiotemporal dynamics contribute significantly to soil microbiome research and sampling strategies.},
}

@article {pmid40600712,
year = {2025},
author = {Comeault, AA and Orta, AH and Fidler, DB and Nunn, T and Ellison, AR and Anspach, TA and Matute, DR},
title = {Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002725},
doi = {10.1128/msystems.00027-25},
pmid = {40600712},
issn = {2379-5077},
abstract = {Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from communities associated with six species of drosophilid flies collected from "anthropogenic" environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions, including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.IMPORTANCEWhile much attention has been given to catalogue the taxonomic diversity intrinsic to host-associated microbiomes, much less is known about the functional consequences of this variation, especially in wild, non-model host species. In this study, we use long-read sequencing to generate and analyze 103 high-quality metagenome-assembled genomes from host-associated bacterial communities from six species of wild fruit fly (Drosophila). We find that the genomes of drosophilid-associated bacteria possess diverse metabolic pathways and biosynthetic gene clusters that are predicted to generate metabolites involved in nutrition and disease resistance, among other functions. Using functional gene predictions, we show that different bacterial lineages that comprise the insect microbiome differ in predicted functional capacities. Our findings highlight the functional variation intrinsic to microbial communities of wild insects and provide a step towards disentangling the ecological and evolutionary processes driving host-microbe symbioses.},
}

@article {pmid40600491,
year = {2025},
author = {Liaquat, M and Le Gall, G and Scholey, A and Pontifex, MG and Bastiaanssen, TFS and Muller, M and Minihane, AM and Vauzour, D},
title = {APOE4 genotype shapes the role of dietary fibers in cognitive health through gut microbiota changes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2526133},
doi = {10.1080/19490976.2025.2526133},
pmid = {40600491},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Apolipoprotein E4/genetics/metabolism ; Male ; *Dietary Fiber/metabolism/administration & dosage ; Female ; Aged ; *Cognitive Dysfunction/microbiology/genetics/metabolism ; Cross-Sectional Studies ; Genotype ; Feces/chemistry/microbiology ; *Cognition ; Middle Aged ; Fatty Acids, Volatile/blood/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {APOE4, a key risk factor for Alzheimer's disease, influences gut microbiota and microbial metabolites (e.g. amino acids and dietary fiber (DF) derived short-chain fatty acids (SCFAs)). However, its role in modulating microbiota-driven DF metabolism and its effect on cognitive status remains unclear. This cross-sectional study (n = 170) investigates the association between APOE4 genotype, DF consumption, and metabolism in individuals with subjective cognitive impairment (SCI) and mild cognitive impairment (MCI) compared to healthy controls (HC). Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) and [1]H NMR metabolomic techniques were used to quantify SCFAs in serum and fecal samples, respectively. Gut microbiota speciation was carried out by 16S rRNA amplicon sequencing. We found that DF intake was significantly associated with APOE4 genotype and cognitive status, with lower consumption in APOE4 carriers (p < 0.05) and those with cognitive impairment (SCI and MCI) (p = 0.03). Differences (p < 0.05) in gut microbiota (both α- and β-diversity) and SCFAs were evident between APOE4 and non-APOE4 carriers, with stronger associations with DF consumption and cognitive status evident in non-APOE4 carriers. These findings suggest that targeting DF-induced changes in gut microbiota and serum SCFAs may be an effective strategy for mitigating cognitive impairment, but primarily in non-APOE4 carriers.},
}

Humans
*Gastrointestinal Microbiome
*Apolipoprotein E4/genetics/metabolism
Male
*Dietary Fiber/metabolism/administration & dosage
Female
Aged
*Cognitive Dysfunction/microbiology/genetics/metabolism
Cross-Sectional Studies
Genotype
Feces/chemistry/microbiology
*Cognition
Middle Aged
Fatty Acids, Volatile/blood/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40600350,
year = {2025},
author = {Dike, CR and Duan, Q and Ahmed, F and Denson, LA and Haslam, D and Minar, P and Ollberding, NJ and Papachristou, GI and Setchell, KDR and Thompson, T and Vitale, DS and Zhao, X and Abu-El-Haija, M},
title = {Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70135},
pmid = {40600350},
issn = {1536-4801},
support = {K23DK118190 (MAH)/DK/NIDDK NIH HHS/United States ; R03 DK131156 (MAH)/DK/NIDDK NIH HHS/United States ; P30DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati (LAD) and The Helmsley Charitable Trust (LAD, PM)/ ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP) is associated with gut dysbiosis. We aimed to determine if dysbiosis persisted during follow-up and whether it is associated with clinical outcomes.

METHODS: Prospective enrollment of participants <21 years with first AP. Stool samples were obtained at baseline (n = 41), 3 months (n = 19), and 12 months (n = 12) and in healthy controls (HC; n = 34). Evaluation for diabetes (DM) or prediabetes (pre-DM) was performed. At 12-month follow-up gastrointestinal (GI) symptom surveys were completed and AP recurrence-acute recurrent pancreatitis (ARP) recorded. Shotgun metagenomic sequencing was performed on extracted microbial DNA.

RESULTS: Microbial alpha diversity was lower for AP versus HC at all three time points (p < 0.008). Bray-Curtis ordinations showed the AP cohort did not cluster by time point, highlighting similarity in microbial composition over time. Within 12-month follow-up: 7/44 participants developed pre-DM/DM, 7/42 developed ARP, 16 had zero or one while 15 had multiple GI symptoms. Distinct clustering of samples was observed in the baseline samples of the group that developed ARP (p = 0.023) and in follow-up samples with multiple GI symptoms, p < 0.05. Relative abundance of most species was lower in AP samples when compared to HC at all time points with enrichment in Ruminococcus gnavus and Clostridium innocuum (AQ) (False Discovery Rate p < 0.05). Several pathways involved in protein biosynthesis were depleted in the AP cohort at all time points.

CONCLUSIONS: Gut dysbiosis persisted following AP in children at 3 and 12 months follow-up compared to HC. Microbiome signatures differed in the ARP cohort and those with multiple GI symptoms.},
}

@article {pmid40600344,
year = {2025},
author = {Fontaine, SS and Trevelline, BK},
title = {An early-life perspective is needed to explain the impact of gut microbiota on wild vertebrate phenotypes.},
journal = {The Journal of experimental biology},
volume = {228},
number = {14},
pages = {},
doi = {10.1242/jeb.250130},
pmid = {40600344},
issn = {1477-9145},
support = {PRFB 2208809//National Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Phenotype ; *Animals, Wild/microbiology ; *Vertebrates/microbiology/physiology/growth & development ; },
abstract = {Vertebrates house dense and diverse communities of microorganisms in their gastrointestinal tracts. These communities shape host physiological and ecological phenotypes in diverse ways, with implications for animal fitness in nature. Exposure to microbes during the earliest stages of life is particularly important because, during critical developmental windows, the microbiome is exceptionally plastic and interactions with microbes can have long-lasting physiological impacts on the host. Despite our understanding that early-life microbial interactions are important to host function broadly, the majority of research in this area has been performed in human or model organisms that are not representative of animals in the wild. Specifically, most gut microbiome studies in wildlife are cross-sectional and compare microbial communities across life stages using different individuals, as opposed to tracking the microbial communities and phenotypes of the same individuals from early to later life. This knowledge gap may hinder wildlife microbiome research, as the current model lacks an early-life perspective that can contextualize host phenotypic and fitness differences observed between animals at later life stages. Further, considering early-life microbial dynamics may offer insights to applied research, such as determining the optimal age to manipulate microbiomes for desired conservation outcomes. In this Commentary, we consider current understanding of the importance of early-life host-microbe interactions to vertebrate physiology across the lifespan, discuss why this perspective is necessary in wildlife studies, and provide practical recommendations for experimental designs that can address these questions, including field and laboratory approaches.},
}

Animals
*Gastrointestinal Microbiome
Phenotype
*Animals, Wild/microbiology
*Vertebrates/microbiology/physiology/growth & development

@article {pmid40600213,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {Human oral microbiome and its influence on mental health and brain disorders.},
journal = {AIMS microbiology},
volume = {11},
number = {2},
pages = {242-294},
pmid = {40600213},
issn = {2471-1888},
abstract = {The human oral microbiome can affect brain functions directly through the trigeminal nerve and olfactory system and indirectly via the oral-gut-brain axis. However, the potential link between the oral microbiome and mental health remains an area that requires further investigation. Taking into consideration that gut microbiota dysbiosis plays a role in the onset and progression of several mental disorders, as well as the potential influence of the oral microbiome on mental health via direct pathways, the present narrative review explores the role of the human oral microbiome in health and disease, along with the factors that affect its composition, with a particular focus on its potential impact on mental health, including its involvement in a range of mental disorders and brain-related conditions, such as Alzheimer's disease, Parkinson's disease, autism spectrum disorder, anxiety, depression, stress, bipolar disorder, Down's syndrome, cerebral palsy, epilepsy, and schizophrenia. Chronic oral diseases can impair the oral mucosal barrier, allowing microorganisms and endotoxins to enter the bloodstream, triggering systemic inflammation, and affecting the blood-brain barrier. This pathway can lead to neuroinflammation and cognitive dysfunction and contribute to adverse mental health effects. Additionally, translocation of oral bacteria to the gut can drive persistent inflammation and thereby affect brain health. Multiple studies suggest a potential relationship between the oral microbiome and several mental disorders, but further research is needed to strengthen the evidence surrounding these associations and to fully clarify the underlying mechanisms linking the oral microbiome to these conditions. Given the promising implications, future research should focus on elucidating the biological mechanisms through which alterations in the oral microbiome influence the development and progression of determinate neurodegenerative and neuropsychiatric disorders. Additionally, identifying reliable biomarkers linked to the oral microbiome could enhance early detection, diagnosis, and monitoring of these conditions.},
}

@article {pmid40600174,
year = {2025},
author = {Ebrahimi, R and Shahrokhi Nejad, S and Fekri, M and Nejadghaderi, SA},
title = {Advancing prostate cancer treatment: the role of fecal microbiota transplantation as an adjuvant therapy.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100420},
pmid = {40600174},
issn = {2666-5174},
abstract = {Prostate cancer (PCa) is a major cause of cancer-related deaths worldwide. While current treatments such as surveillance, surgery, and radiation are effective, they have their limitations. These can include patient incompliance due to side effects or resistance to hormonal changes, highlighting the need for alternative approaches. Human microbiota, a complex and dynamic host, plays a significant role in the homeostasis and is associated with several diseases or cancers in cases of dysregulation and dysbiosis. Research on fecal microbiota profiling and its association with certain cancers has opened new possibilities for preventing and managing tumor progression. One such possibility is fecal microbial transplantation (FMT). Studies show that different composition of urinary microbiota is found in various urinary tract diseases. Gut microbiota can regulate immune response against tumors; therefore, FMT may help modulate gut microbiota in a way that potentially enhances responses to immune checkpoint inhibitors, as suggested by emerging evidence in other cancers, though this needs further validation in PCa. Nevertheless, long-term complications and the safety of FMT are still questioned. We reviewed the roles of gut microbiota in PCa and suggested FMT as a potential tool in the treatment of PCa, which needs further investigations.},
}

@article {pmid40600173,
year = {2025},
author = {Yang, H and Gao, H and Xie, X and Wang, H and Li, X and Qiao, Q and Ma, Y and Bai, Y},
title = {Microbiome variability and role of Candida albicans in site-specific dental plaques in orthodontic adolescent patients with white spot lesions.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2522421},
pmid = {40600173},
issn = {2000-2297},
abstract = {White spot lesions (WSLs) are a common complication of orthodontic treatment. However, the cariogenic discrepancy in the supragingival microbiome between demineralized and non-demineralized surfaces and the influence of Candida albicans associated with WSLs remain unexplored. This study investigated the changes in supragingival microbiome of orthodontic adolescents with WSLs, encompassing both demineralized and non-demineralized sites, and explored C. albicans colonization in these patients. Supragingival plaques were collected from 29 orthodontic adolescents with WSLs (categorized into demineralized and non-demineralized groups based on the presence/absence of demineralization at sampling sites) and 23 healthy orthodontic adolescents. Supragingival microbiome composition was evaluated using 16S rRNA sequencing, and C. albicans colonization was identified using fungal culture methods. The supragingival microbiome on non-demineralized surfaces showed intermediate cariogenic potential between demineralized and healthy states, but closer to the demineralized state. C. albicans exhibited a propensity for colonization in WSLs patients without site-specificity. C. albicans influenced bacterial composition, with Streptococcus mutans significantly enriched on the demineralized surfaces of C. albicans-positive patients. In orthodontic adolescents with WSLs, non-demineralized surfaces showed microbiome shifts, necessitating interventions to promote a healthy microbiome. C. albicans can impact microbiome composition and potentially contribute to WSLs pathogenesis.},
}

@article {pmid40600142,
year = {2025},
author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W},
title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1516393},
pmid = {40600142},
issn = {1664-302X},
abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.

METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.

RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.

CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.},
}

@article {pmid40600111,
year = {2025},
author = {Hao, W and Wang, Z and Ma, H},
title = {Identification of core gene-gut microbiome associations in diverticulitis patients through a two-sample mendelian randomization and bioinformatics-based investigation.},
journal = {Global medical genetics},
volume = {12},
number = {3},
pages = {100065},
pmid = {40600111},
issn = {2699-9404},
abstract = {BACKGROUND: Previous studies have suggested a potential link between the gut microbiota and diverticulitis. However, the causal relationships as well as underlying mechanisms remain unclear.

METHODS: The causal effects of gut microbiota on diverticulosis & diverticulitis was assessed using two-sample Mendelian randomization analysis. The sensitivity analyses were also performed. We then used integrative bioinformatics tools to identify core genes associated with diverticulitis and explore their potential mechanisms and therapeutic targets.

RESULTS: Inverse variance weighted analysis indicated that Family XIII (OR=0.281, 95 % CI: 0.093-0.853, P = 0.025) and Defluviitaleaceae UCG-011 (OR=0.382, 95 % CI: 0.162-0.898, P = 0.027) were negatively associated with the risk of diverticulosis and diverticulitis, whereas Oscillospira (OR=3.514, 95 % CI: 1.146-10.779, P = 0.028), Ruminiclostridium 6 (OR=2.629, 95 % CI: 1.093-6.322, P = 0.031), Lachnoclostridium (OR=2.458, 95 % CI: 1.014-5.962, P = 0.047), and Desulfovibrionales (OR=2.157, 95 % CI: 1.038-4.480, P = 0.039) were positively associated with disease risk. The sensitivity analyses validated these correlations. Through SNP annotation, we identified 23 host genes associated with pathogenic gut microflora in diverticulosis and diverticulitis, and retrieved 213 diverticulitis-related genes from GeneCards. Intersection analysis revealed LRRC4C as the sole shared gene. Differential expression analysis further showed that LRRC4C was significantly downregulated in diverticulitis compared to infective colitis. Finally, eight candidate drugs were identified as potential inducers of LRRC4C expression.

CONCLUSION: The research revealed potential causal relationships between gut microbiota and diverticulitis. LRRC4C was identified as a core gene associated with pathogenic microbial traits in diverticulitis, and candidate therapeutic drugs for diverticulitis based on LRRC4C were predicted, offering novel strategies for the prevention and management of the disease.},
}

@article {pmid40600056,
year = {2025},
author = {Roy, N and Yang, S and Lee, D and Choi, K},
title = {Ecological processes influencing bacterial community assembly across plant niche compartments.},
journal = {mLife},
volume = {4},
number = {3},
pages = {294-304},
pmid = {40600056},
issn = {2770-100X},
abstract = {Understanding microbial community assembly in plants is critical for advancing agricultural sustainability. This study investigated microbial diversity and community assembly mechanisms across six compartments of tomato plants: bulk soil, rhizosphere, root, stem, flower, and seed. Using 16S rRNA amplicon sequencing, we observed that microbial richness was highest in the bulk soil and rhizosphere, with significant reductions in internal plant tissues. Co-occurrence network analysis identified distinct microbial hubs in each compartment, such as Bacillus in the root and seed, highlighting critical interactions influencing microbial dynamics. Ecological process modeling revealed that deterministic processes, such as selection, dominated in below-ground compartments, whereas stochastic processes like drift were more influential in above-ground tissues, reflecting differences in niche specificity and ecological stability. Dispersal limitation emerged as a key driver in soil-associated compartments, structuring microbial diversity. These findings advance our understanding of the ecological mechanisms shaping plant microbiomes and suggest targeted microbiome management strategies to enhance crop health, productivity, and resilience. Future research integrating functional genomics, temporal dynamics, and environmental factors is necessary to uncover the broader implications of plant-associated microbiomes.},
}

@article {pmid40600054,
year = {2025},
author = {Githaka, JM},
title = {"Misuse" of RNA-seq data in microbiome studies: A cautionary tale of poly(A).},
journal = {mLife},
volume = {4},
number = {3},
pages = {227-231},
pmid = {40600054},
issn = {2770-100X},
}

@article {pmid40600049,
year = {2025},
author = {Xu, H and Zhang, R and Zhang, X and Zhang, Z and Feng, Y and Lin, L},
title = {Pulmonary microbial spectrum of Burkholderia multivorans infection identified by metagenomic sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1577363},
pmid = {40600049},
issn = {2296-858X},
abstract = {PURPOSE: Burkholderia multivorans, a Gram-negative bacterium, often infect patients with severe immunocompromised and cystic fibrosis. B. multivorans infection is challenging to treat due to its ability to disrupt the action of multiple antimicrobial agents through intrinsic and acquired resistance mechanisms. A better understanding of the pulmonary microbial spectrum of B. multivorans infection is crucial for the prevention and treatment of B. multivorans.

CASE PRESENTATION: This case series reviewed the respiratory microbiome structure and alternations during the treatment of B. multivorans infection through metagenomic next-generation sequencing (mNGS). Analysis of mNGS data of 19 pharyngeal secretion samples collected from the 3 COVID-19 patients at different time points showed that the relative abundance of B. multivorans was fluctuated and eventually increased, indicating the possible development of drug resistance. A total of 40 antibiotic-resistant genes (ARGs) were detected. Significantly, the levels of CEOA, CEOB, and OPCM were consistent with the trends in the relative abundance of B. multivorans. Besides, we described nine previously uncharacterized non-synonymous mutations in PenA of B. multivorans. These mutations lead to amino acid changes Thr32Ala, Ala43Ser, Gln105Arg, Asn202Ser, Gln219Arg, Gly241Ala, Val259Ala, Thr279Ala, and Ser298Ile that may associate with resistance to β-lactam antibiotics.

CONCLUSION: This report shed light on the importance of rapidly diagnosis and treatment of B. multivorans infection. mNGS serve as a powerful microbial detection tool that provides a comprehensive, sensitive, and rapid method for pathogen detection and drug resistance analysis.},
}

@article {pmid40599846,
year = {2025},
author = {Portela, DS and Jain, A and Flood, M and Lavelle, A and Guerra, G and Patel, M and Aziz, O and Warrier, S and Heriot, A and Mohan, H},
title = {The microbiome of pseudomyxoma peritonei: a scoping review.},
journal = {Pleura and peritoneum},
volume = {10},
number = {2},
pages = {35-50},
pmid = {40599846},
issn = {2364-768X},
abstract = {There is growing interest in the role of the microbiome in carcinogenesis, but few studies examine the microbiome of pseudomyxoma peritonei (PMP). This scoping review summarises the microorganisms identified in PMP samples and examines the evidence of their role in disease outcomes. The methodology was developed in accordance with the PRISMA-ScR framework and checklist. Nine relevant studies were included. Microbiological testing was performed on PMP samples from 85 patients. At the phylum level, Proteobacteria was detected in greatest relative abundance in tumour tissue, cellular and acellular mucin. The relative proportion of different phyla more closely resembled the gut microbiome in inflammatory bowel disease than in a healthy gut. High-grade specimens showed significantly higher bacterial density than low-grade specimens and non-neoplastic non-perforated appendix specimens. Survival data of 58 patients were published, correlating outcomes to pre-operative antibiotic administration. Observed differences were not statistically significant. There is evidence of an altered bacterial profile in PMP samples compared to a healthy gut microbiome, the significance of which is unclear. Significant methodological challenges remain in this field of study. This scoping review supports the need for further analysis of the PMP bacterial profile, using methodologies that incorporate controls and deliver taxonomic resolution at species level.},
}

@article {pmid40599650,
year = {2025},
author = {Zhang, H and Zheng, X and Huang, Y and Zou, Y and Zhang, T and Repo, MA and Yin, M and You, Y and Jie, Z and Xu, WA},
title = {Novel potential biomarkers for predicting childhood caries via metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1522970},
pmid = {40599650},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; Child ; *Biomarkers/analysis ; *Metagenomics/methods ; Saliva/microbiology ; Female ; Male ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {BACKGROUND: Dental caries is a prevalent global health issue, particularly among children, with significant oral and overall health implications. The oral microbiome is considered a critical factor in caries development, with various microbial species implicated in the disease process.

OBJECTIVES: This study aims to explore the changes and interactions of oral microbiota in childhood caries using metagenomic analysis, and identify potential biomarkers for early caries detection and treatment.

METHODS: Saliva samples were collected from 241 children aged 6 to 9 years, categorized into caries-free (CF), low-caries (CL), and caries-severe (CS) groups. Metagenomic sequencing was performed to analyze the oral microbiome, followed by a series of statistical and functional analyses to characterize microbial diversity and function.

RESULTS: The study revealed significant differences in the microbial community composition among the groups, with the CS group exhibiting higher alpha and beta diversity than that of the CF group. Numerous unclassified microorganisms, such as Campylobacter SGB19347 and Catonella SGB4501, are intimately linked to dental caries and display intricate interaction networks, suggesting the potential formation of a distinct ecological network. In functional assessment, we identified a possible link between pectin and caries, suggesting that microorganisms that produce pectinase enzymes might play a role in the advancement of severe dental caries. Additionally, we identified 16 species as the best marker for severe dental caries, achieving an impressive AUC of 0.91.

CONCLUSION: The role of microbiota in dental caries is multifaceted, involving a complex interplay of microbial species and functions. Our findings enhance the understanding of the microbial basis of dental caries and offer potential diagnostic and therapeutic targets. The predictive capacity of the identified biomarkers warrants further investigation for early caries detection and intervention.

CLINICAL SIGNIFICANCE: The identification of novel biomarkers through metagenomic analysis enables early detection and targeted intervention for childhood caries, potentially transforming children dental care and significantly improving long-term oral health outcomes.},
}

Humans
*Dental Caries/diagnosis/microbiology
Child
*Biomarkers/analysis
*Metagenomics/methods
Saliva/microbiology
Female
Male
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid40599494,
year = {2025},
author = {Boton, N and Patel, PK and Beekmann, SE and Polgreen, PM and Buckel, WR and Mahoney, MV and Mehrotra, P and Lee, MSL},
title = {Clinician Management Preferences for Clostridioides difficile Infection in Adults: A 2024 Emerging Infections Network Survey.},
journal = {Open forum infectious diseases},
volume = {12},
number = {7},
pages = {ofaf335},
pmid = {40599494},
issn = {2328-8957},
abstract = {BACKGROUND: The 2021 Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA) guidelines for Clostridioides difficile infection (CDI) introduced new recommendations for managing initial and recurrent CDI. Since then, new microbiome-based therapies for preventing recurrent CDI have become available. We surveyed infectious diseases (ID) clinicians to understand their experiences, practices, and challenges in CDI management.

METHODS: An electronic survey was distributed to members of the IDSA Emerging Infections Network in May 2024, targeting ID physicians and healthcare professionals in the United States who manage adult CDI. The survey assessed treatment preferences, clinical practices, and barriers to accessing and prescribing CDI therapies.

RESULTS: Of the 500 respondents who reported treating CDI in the past year, 83% (417/500) indicated that vancomycin was their most frequently prescribed agent for initial, nonfulminant CDI. Additionally, 72% (357/498) reported that their institutional guidelines recommended vancomycin as the first-line agent. The most common barrier to fidaxomicin use was challenges with outpatient insurance coverage (82% [408/496]). Bezlotoxumab was available to 74% (370/500) of respondents, though 33% (165/497) indicated they do not use bezlotoxumab routinely. Most clinicians (87% [437/500]) had previously recommended fecal microbiota transplantation (FMT) for recurrent CDI, though only 48% (239/500) had current access to FMT using donor stool. Fecal microbiota live-jslm was available to 36% (179/500), and fecal microbiota spores live-brpk was available to 30% (150/500).

CONCLUSIONS: Significant barriers, including high costs, insurance challenges, and limited availability of CDI therapies, impact clinical decision-making and adherence to guideline recommendations.},
}

@article {pmid40599328,
year = {2025},
author = {Du, W and Xu, W and Hu, Y and Zhao, S and Li, F and Song, D and Shen, J and Xu, Q},
title = {Editorial: Crosslinking of feed nutrients, microbiome and production in ruminants.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1610490},
pmid = {40599328},
issn = {2297-1769},
}

@article {pmid40599184,
year = {2025},
author = {Chen, ZL and Wang, C and Wang, F},
title = {Revolutionizing gastroenterology and hepatology with artificial intelligence: From precision diagnosis to equitable healthcare through interdisciplinary practice.},
journal = {World journal of gastroenterology},
volume = {31},
number = {24},
pages = {108021},
pmid = {40599184},
issn = {2219-2840},
mesh = {Humans ; *Gastroenterology/trends/methods ; *Artificial Intelligence/trends ; *Precision Medicine/methods/trends ; *Health Equity/trends ; Deep Learning ; *Liver Diseases/diagnosis/therapy ; },
abstract = {Artificial intelligence (AI) is driving a paradigm shift in gastroenterology and hepatology by delivering cutting-edge tools for disease screening, diagnosis, treatment, and prognostic management. Through deep learning, radiomics, and multimodal data integration, AI has achieved diagnostic parity with expert clinicians in endoscopic image analysis (e.g., early gastric cancer detection, colorectal polyp identification) and non-invasive assessment of liver pathologies (e.g., fibrosis staging, fatty liver typing) while demonstrating utility in personalized care scenarios such as predicting hepatocellular carcinoma recurrence and optimizing inflammatory bowel disease treatment responses. Despite these advancements challenges persist including limited model generalization due to fragmented datasets, algorithmic limitations in rare conditions (e.g., pediatric liver diseases) caused by insufficient training data, and unresolved ethical issues related to bias, accountability, and patient privacy. Mitigation strategies involve constructing standardized multicenter databases, validating AI tools through prospective trials, leveraging federated learning to address data scarcity, and developing interpretable systems (e.g., attention heatmap visualization) to enhance clinical trust. Integrating generative AI, digital twin technologies, and establishing unified ethical/regulatory frameworks will accelerate AI adoption in primary care and foster equitable healthcare access while interdisciplinary collaboration and evidence-based implementation remain critical for realizing AI's potential to redefine precision care for digestive disorders, improve global health outcomes, and reshape healthcare equity.},
}

Humans
*Gastroenterology/trends/methods
*Artificial Intelligence/trends
*Precision Medicine/methods/trends
*Health Equity/trends
Deep Learning
*Liver Diseases/diagnosis/therapy

@article {pmid40598993,
year = {2025},
author = {Kamounah, S and Sarathi, A and Elisabeth Sørensen, C and Arumugam, M and Pedersen, AML},
title = {Microbial signatures in oral sites of patients with primary Sjögren's syndrome: Association with salivary gland hypofunction.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {6},
pages = {e2501030},
doi = {10.71150/jm.2501030},
pmid = {40598993},
issn = {1976-3794},
mesh = {Humans ; *Sjogren's Syndrome/microbiology/physiopathology ; Middle Aged ; Female ; Saliva/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Adult ; *Mouth/microbiology ; *Salivary Glands/physiopathology/microbiology ; Mouth Mucosa/microbiology ; Oral Health ; Case-Control Studies ; DNA, Bacterial/genetics ; Tongue/microbiology ; },
abstract = {This study aimed to determine if the microbiota in four different oral sites and the oral health status differ between patients with primary Sjögren's syndrome (pSS), non-pSS sicca symptoms, and healthy controls. All participants underwent an interview and clinical oral examination. Stimulated whole saliva (SWS), supragingival plaque (SGP), buccal mucosa tissue (BLM), and tongue scrape (TGS) samples from 23 pSS patients, 36 patients with sicca symptoms, not fulfilling the classification criteria for pSS (non-pSS sicca), and 21 age-matched healthy controls (HC) were analyzed using V3-V4 16S rRNA gene amplicon sequencing, and determination of amplicon sequence variants (ASVs). PSS and non-pSS sicca patients did not differ with respect to oral health status, saliva flow rates, abundance of predominant genera, relative abundance on genus level or bacterial diversity in any of the oral sites. Both patient groups differed significantly from the healthy control group in the abundance of 61 ASVs across all sites. The alpha-diversity was lower in SGP from non-pSS sicca patients (p = 0.019), and in TGS from pSS patients (p = 0.04). The proportion of variation in the beta-diversity across all four sites could be explained by the diagnosis (pSS, non-pSS sicca, and HC). However, subgrouping of patients according to their stimulated salivary flow rates (SWS > 0.7 ml/min versus SWS ≤ 0.7 ml/min), revealed significantly different abundance of three ASVs in SWS, 11 in SGP, and six in TGS. Our findings suggest that hyposalivation rather than pSS itself modifies the microbial composition in oral site-specific patterns leading to oral diseases.},
}

Humans
*Sjogren's Syndrome/microbiology/physiopathology
Middle Aged
Female
Saliva/microbiology
Male
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Aged
Adult
*Mouth/microbiology
*Salivary Glands/physiopathology/microbiology
Mouth Mucosa/microbiology
Oral Health
Case-Control Studies
DNA, Bacterial/genetics
Tongue/microbiology

@article {pmid40598608,
year = {2025},
author = {Liu, F and McNally, J and Flemming, D and Ingham, AB and Hunt, PW and Li, RW},
title = {Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {133},
pmid = {40598608},
issn = {1297-9716},
support = {58-8042-3-022-F//Agricultural Research Service/ ; 242102311161//Henan Provincial Science and Technology Research Project/ ; },
mesh = {Animals ; *Sheep Diseases/parasitology/microbiology/immunology ; Sheep ; *Trichostrongylosis/veterinary/parasitology/immunology ; *Trichostrongylus/physiology ; *Escherichia coli/physiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a significant reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P < 0.0001; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.},
}

Animals
*Sheep Diseases/parasitology/microbiology/immunology
Sheep
*Trichostrongylosis/veterinary/parasitology/immunology
*Trichostrongylus/physiology
*Escherichia coli/physiology
*Gastrointestinal Microbiome
Disease Susceptibility/veterinary/parasitology/microbiology
RNA, Ribosomal, 16S/genetics/analysis

@article {pmid40598554,
year = {2025},
author = {Omran, MM and Emam, M and Gamaleldin, M and Abushady, AM and Elattar, MA and El-Hadidi, M},
title = {Comparative analysis of statistical and deep learning-based multi-omics integration for breast cancer subtype classification.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {709},
pmid = {40598554},
issn = {1479-5876},
support = {100010434//La Caixa/ ; },
mesh = {Humans ; *Deep Learning ; *Breast Neoplasms/genetics/classification/microbiology/pathology ; Female ; *Genomics ; Transcriptome/genetics ; Gene Expression Profiling ; Multiomics ; },
abstract = {BACKGROUND: Breast cancer (BC) is a critical cause of cancer-related death globally. The heterogeneity of BC subtypes poses challenges in understanding molecular mechanisms, early diagnosis, and disease management. Recent studies suggest that integrating multi-omics layers can significantly enhance BC subtype identification. However, evaluating different multi-omics integration methods for BC subtyping remains ambiguous.

METHODS: In this study, we conducted a multi-omics integration analysis on 960 BC patient samples, incorporating three omics layers: Host transcriptomics, epigenomics, and shotgun microbiome. We compared two integration approaches the statistical-based approach (MOFA+) and a deep learning-based approach (MOGCN) for this integration. We evaluated both methods using complementary evaluation criteria. First, we assessed the ability of selected features to discriminate between BC subtypes using both linear and nonlinear classification models. Second, we analyzed the biological relevance of the selected features to key BC pathways, focusing on transcriptomics-driven insights.

RESULTS: Our results showed that MOFA+ outperformed MOGCN in feature selection, achieving the highest F1 score (0.75) in the nonlinear classification model, with MOFA+ also identifying 121 relevant pathways compared to 100 from MOGCN. Notably, one of the key pathways Fc gamma R-mediated phagocytosis and the SNARE pathway was implicated, offering insights into immune responses and tumor progression.

CONCLUSION: These findings suggest that MOFA+ is a more effective unsupervised tool for feature selection in BC subtyping. Our study underscores the potential of multi-omics integration to improve BC subtype prediction and provides critical insights for advancing personalized medicine in BC.},
}

Humans
*Deep Learning
*Breast Neoplasms/genetics/classification/microbiology/pathology
Female
*Genomics
Transcriptome/genetics
Gene Expression Profiling
Multiomics

@article {pmid40598518,
year = {2025},
author = {Song, C and Zhang, Z and Zhu, S and Tong, H},
title = {Association between the dietary index for gut microbiota and constipation in American adults.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {98},
pmid = {40598518},
issn = {1475-2891},
mesh = {Humans ; *Constipation/epidemiology/microbiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Diet/methods ; Adult ; United States/epidemiology ; Nutrition Surveys ; Prevalence ; Aged ; Cross-Sectional Studies ; },
abstract = {Constipation, a common gastrointestinal disorder, significantly impacts quality of life.Its association with gut microbiota has garnered attention.Dietary factors play a crucial role in the development and management of constipation.The recently introduced dietary index for gut microbiota (DI-GM), a measure of gut microbiota diversity, offers insights into this connection.The association between dietary gut microbiota index and constipation is a critical public health issue.This study investigated the association between DI-GM and constipation prevalence in the American population using data from 11,819 individuals from the National Health and Nutrition Examination Survey (NHANES) between 2005 and 2010.Constipation was defined using Bristol stool form scale types 1 and 2.Dietary recall information was used to determine the DI-GM score, indicating the dietary influence on the gut microbiome. Multivariate weighted logistic regression, adjusted for confounders, was performed to analyze the association between DI-GM scores and constipation prevalence.Further analyses included a subgroup analysis and restricted cubic splines to explore this association [restricted cubic spline(RCS)].An increased DI-GM index, indicating a healthier gut microbiome, was related to a decreased risk of constipation.A similar association was observed with a more favorable score for beneficial gut microbiota.Non-linear associations between DI-GM scores and constipation were identified through RCS analysis.Subgroup and interaction analyses confirmed the consistency of these findings across strata, suggesting no significant heterogeneity.These findings suggest that dietary adjustments may be an important method for preventing constipation.},
}

Humans
*Constipation/epidemiology/microbiology
*Gastrointestinal Microbiome/physiology
Male
Female
Middle Aged
*Diet/methods
Adult
United States/epidemiology
Nutrition Surveys
Prevalence
Aged
Cross-Sectional Studies

@article {pmid40598279,
year = {2025},
author = {Al-Ansari, AS and Duggan, V and Mulcahy, G and Yin, X and Brennan, L and Cotter, PD and Patel, SH and O'Donovan, CM and Crispie, F and Walshe, N},
title = {Faecal microbiota and serum metabolome association with equine metabolic syndrome in connemara ponies.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {411},
pmid = {40598279},
issn = {1746-6148},
mesh = {Horses ; Animals ; *Feces/microbiology ; *Horse Diseases/microbiology/blood/metabolism ; *Metabolome ; *Metabolic Syndrome/veterinary/microbiology/blood/metabolism ; Case-Control Studies ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Faecal microbiome and serum metabolome have been studied in human medicine to provide a better understanding of metabolic derangements including diabetes; however, equivalent studies in equine medicine are limited. This was a case-control study conducted to identify differences in faecal microbiota composition and concurrent serum metabolite patterns between metabolically normal Connemara ponies and those with Equine Metabolic Syndrome (EMS). Thirty privately owned Connemara ponies (15 EMS and 15 controls) were included in the study. EMS was diagnosed by oral sugar test (OST). Blood samples were collected before and after an oral sugar challenge. One concurrent faecal sample was collected from each pony. Sequencing of the V3-V4 region of 16S rRNA gene was used to identify the microbial communities in faecal samples and assess the differences in microbial profiles between groups. Serum metabolites were analyzed using liquid chromatography-high-resolution mass spectrometry (LC-MS). Finally, multi-omics analysis was conducted by integration of microbiota-metabolome datasets to determine potential associations between metabolites and microbiota in EMS.

RESULTS: The faecal microbiota community composition was significantly different between EMS and control groups (p = 0.04 and r[2] = 4.3%). EMS ponies showed reduced species richness and evenness compared to normal ponies, however it did not reach significant difference. The EMS ponies showed an enrichment of serum metabolites belonging to triglycerides (TGs), along with a reduction of other metabolite classes. Integrative multi-omics analysis revealed two modules in the metabolome and microbiota datasets that were significantly different between the EMS and control groups (p < 0.05).

CONCLUSIONS: This study suggests that concurrent faecal microbiota and serum metabolome features significantly differ between Connemara ponies with and without EMS. These results provide insights that may assist in the search for diagnostic markers associated with microbiota changes and novel preventative management methods to manipulate microbiota in horses with EMS.},
}

Horses
Animals
*Feces/microbiology
*Horse Diseases/microbiology/blood/metabolism
*Metabolome
*Metabolic Syndrome/veterinary/microbiology/blood/metabolism
Case-Control Studies
Male
Female
RNA, Ribosomal, 16S/genetics
*Microbiota
Gastrointestinal Microbiome

@article {pmid40598208,
year = {2025},
author = {Zhang, T and Zheng, Y and Chen, T and Gu, Y and Gong, Y and Wang, D and Li, Z and Du, Y and Zhang, L and Gao, J},
title = {Biomaterials mediated 3R (remove-remodel-repair) strategy: holistic management of Helicobacter pylori infection.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {475},
pmid = {40598208},
issn = {1477-3155},
support = {2025QN13//First Batch of Open Topics of the Shanghai Key Laboratory of Nautical Medicine and Pharmaceutical and Medical Device Transformation/ ; 82072051//National Natural Science Foundation of China/ ; JCKFKT-MS-006//National Key Laboratory Open Project for Basic Medical Science Innovation/ ; },
mesh = {*Helicobacter Infections/therapy/drug therapy/microbiology ; Humans ; *Helicobacter pylori/drug effects ; *Biocompatible Materials/chemistry/pharmacology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Animals ; Probiotics/therapeutic use ; Drug Delivery Systems ; Integrative Medicine ; Nanoparticles/chemistry ; },
abstract = {Helicobacter pylori (HP) is a major etiological agent of gastric cancer, with a global prevalence of around 50%. Current treatments, primarily based on antibiotics, face challenges such as increasing drug resistance and disruption of the gut microbiota. This review proposes a holistic integrative medicine (HIM) approach, guided by the 3R concept (Remove, Remodel, and Repair), to address these limitations. The 3R concept offers a novel paradigm for the integrated prevention and treatment of HP infections: Remove targets the direct eradication of HP by overcoming antibiotic resistance, Remodel focuses on reshaping the immune microenvironment to clear pathogens, and Repair emphasizes the restoration of the gastric mucosa and protection of the gut microbiota. We discuss the potential of biomaterials, including nanoparticles for targeted drug delivery and ROS generation, hydrogels for sustained release and mucosal repair, microspheres for enhanced drug loading and controlled release, and probiotics for microbiota restoration. Additionally, multimodal therapies such as phototherapy, sonodynamic therapy, and magnetic hyperthermia provide non-invasive, targeted treatments. These innovations align with HIM principles, integrating pathogen eradication with mucosal healing and microbiome protection. Future research should focus on optimizing these materials and validating their clinical applicability to improve patient outcomes and combat antibiotic resistance.},
}

*Helicobacter Infections/therapy/drug therapy/microbiology
Humans
*Helicobacter pylori/drug effects
*Biocompatible Materials/chemistry/pharmacology
Anti-Bacterial Agents/pharmacology/therapeutic use
Gastrointestinal Microbiome/drug effects
Animals
Probiotics/therapeutic use
Drug Delivery Systems
Integrative Medicine
Nanoparticles/chemistry

@article {pmid40597688,
year = {2025},
author = {Xu, Y and Xie, R and Weng, Y and Fang, Y and Chen, H and Tao, S and Zhang, H and Ye, Y and Deng, X and Han, A and Jiang, Q and Liang, W},
title = {Unveiling the diagnostic and pro-inflammatory role of crohn's disease: insights from 16 S-guided discovery and species-specific validation.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {468},
pmid = {40597688},
issn = {1471-230X},
support = {2022Y05//the Medical Science and Technology Project of China/ ; XGY2308//the Hospital-level Project of the First Affiliated Hospital of Ningbo University/ ; 2022z2202022//the Project Key R&D program of 2022 year of the Ningbo Science and Technology Bureau/ ; 2023j020//the Key Project of Ningbo Municipal Science and Technology Bureau/ ; SLB-6-20230912-351//the Population Welfare Foundation Medical Innovation Project of China/ ; },
mesh = {*Crohn Disease/microbiology/diagnosis ; Animals ; Humans ; *Gastrointestinal Microbiome ; Mice ; Male ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Adult ; *Clostridiales/genetics ; RNA, Ribosomal, 16S ; Disease Models, Animal ; Dextran Sulfate ; Case-Control Studies ; Middle Aged ; Species Specificity ; Interleukin-6 ; *Ruminococcus ; Colitis/microbiology/chemically induced ; },
abstract = {BACKGROUND: The rising incidence of Crohn's disease (CD) in Asia underscores the need to explore its underlying mechanisms. The interaction between gut microbiota and the host is strongly linked to CD onset and progression, yet the precise mechanisms remain unclear. Previous studies have demonstrated that Ruminococcus gnavus (R. gnavus) is closely associated with the development and progression of CD. Therefore, this study focuses on the inflammatory role of R. gnavus in CD pathogenesis.

METHODS: We performed comprehensive 16 S rRNA sequencing on fecal samples from active CD patients, inactive CD patients, and healthy controls. Alongside this, we conducted clinical data and correlation analyses. To identify key microbial genera, we developed and validated a random forest classification model. Additionally, we utilized a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6 mice to explore the inflammatory role of R. gnavus (ATCC 29149).

RESULTS: Our analysis revealed significant shifts in gut microbiome composition across different stages of CD compared to healthy controls. Notably, there was a marked decrease in Agathobacter and an increase in R. gnavus in patients with active CD. The random forest classification model, which was based on six specific genera (Agathobacter, Vicinamibacteraceae, Arthrobacter, Eubacterium coprostanoligenes group, Ruminococcus gnavus group, and Prevotella 9), achieved an AUC of 0.912, effectively distinguishing CD patients from healthy controls. In the DSS-induced colitis model, R. gnavus exacerbated inflammation, significantly increasing levels of IL-6 and TNF-α, and significantly decreasing levels of Claudin-1 and MUC2, further underscoring its critical role in CD pathogenesis.

CONCLUSION: The identified genera demonstrate potential as diagnostic biomarkers for CD, with R. gnavus playing a key role in the disease's pathogenesis by inducing inflammation in colitis models.},
}

*Crohn Disease/microbiology/diagnosis
Animals
Humans
*Gastrointestinal Microbiome
Mice
Male
Female
Feces/microbiology
Mice, Inbred C57BL
Adult
*Clostridiales/genetics
RNA, Ribosomal, 16S
Disease Models, Animal
Dextran Sulfate
Case-Control Studies
Middle Aged
Species Specificity
Interleukin-6
*Ruminococcus
Colitis/microbiology/chemically induced

@article {pmid40597678,
year = {2025},
author = {Park, TH and Kim, MJ and Lee, Y and Lee, JS and Lee, J and Park, HY and Shin, JH and Yang, JD},
title = {Comparative microbiome analysis of contracted breast capsules: a cross-sectional study.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {379},
pmid = {40597678},
issn = {1471-2180},
mesh = {Humans ; Female ; Cross-Sectional Studies ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Middle Aged ; *Breast/microbiology/pathology ; Bacterial Load ; Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; Biofilms ; },
abstract = {BACKGROUND: Despite the implication of bacterial biofilms in the etiology of capsular contracture, there is limited research on the microbial structure of the contracted capsule. Moreover, the potential role of the skin microbiome in capsular contracture remains undefined. Therefore, we conducted this study to characterize the microbiome of the breast capsular contracture by comparing it with the microbiome of biopsy without capsular contracture. We also investigated the associations between the microbial structures of the skin surrounding the breast and those of the breast capsule.

RESULTS: We collected 25 capsules, including 14 samples without capsular contracture and 11 samples with capsular contracture. Beta diversity analysis demonstrated that the microbial structures in the breast capsules were distinctly different from those in the skin. The capsular microbiota was more influenced by individual variation than by the progression of the capsular contracture. Breast capsules with capsular contracture showed a higher relative abundance of Staphylococcus, correlating positively with total bacterial load.

CONCLUSIONS: Capsular contracture is associated with an escalation in total bacterial load and an increase in the abundance of opportunistic pathogens, such as Staphylococcus. This comparative analysis of contracted breast capsules emphasizes the management of pathogens, considering bacterial load, in the occurrence of capsular contracture.},
}

Humans
Female
Cross-Sectional Studies
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Adult
Middle Aged
*Breast/microbiology/pathology
Bacterial Load
Skin/microbiology
RNA, Ribosomal, 16S/genetics
Biofilms

@article {pmid40597612,
year = {2025},
author = {Cai, X and Lin, Y and Wu, B and Luo, Y and Li, K},
title = {Sputum microbiota profiles of patients with rifampicin-resistant tuberculosis during the intensive-phase treatment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {373},
pmid = {40597612},
issn = {1471-2180},
support = {2024A03J0585//Guangzhou Science and Technology Bureau Municipal-University (Institute) Joint Funding Project/ ; A2019342//Guangdong Provincial Health Commission Funding Project/ ; 20221A011046//Guangzhou Municipal Health Commission Funding Project/ ; },
abstract = {BACKGROUND: The respiratory microbiome plays a crucial role in respiratory health and influences the onset and progression of tuberculosis (TB). However, changes in the respiratory microbiota of patients with rifampicin-resistant TB (RR-TB) during the intensive-phase treatment have not been assessed. This study aimed to investigate the impact of a six-month intensive-phase treatment of second-line anti-TB drugs on the respiratory microbiota of RR-TB patients.

METHODS: Sputum samples were collected from 14 RR-TB patients and 14 healthy controls. Microbiota composition was analyzed using 16S rRNA gene sequencing, and functional predictions were performed to assess metabolic pathway changes.

RESULTS: RR-TB patients exhibited significantly lower alpha diversity compared to healthy controls, but no significant changes were observed after six months of treatment. Beta diversity analysis revealed distinct clustering patterns between RR-TB patients and healthy controls, with no significant differences between pre- and post-treatment groups. Functional analysis showed reduced microbial functions related to pyruvate fermentation and amino acid metabolism in RR-TB patients.

CONCLUSIONS: These findings highlight the specific effects of second-line anti-TB drugs on the respiratory microbiota and suggest potential roles of respiratory ecological imbalance in RR-TB pathogenesis. Future studies could explore microbiome-based diagnostic and therapeutic strategies for RR-TB.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04091-4.},
}

@article {pmid40597595,
year = {2025},
author = {McGovern, KC and Silverman, JD},
title = {Replacing normalizations with interval assumptions enhances differential expression and differential abundance analyses.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {164},
pmid = {40597595},
issn = {1471-2105},
support = {R01GM148972-01/GM/NIGMS NIH HHS/United States ; R01GM148972-01/GM/NIGMS NIH HHS/United States ; },
mesh = {*Gene Expression Profiling/methods ; Humans ; *Computational Biology/methods ; Microbiota/genetics ; Algorithms ; },
abstract = {BACKGROUND: Methods for differential expression and differential abundance analysis often rely on normalization to address sample-to-sample variation in sequencing depth. However, normalizations imply strict, unrealistic assumptions about the unmeasured scale of biological systems (e.g., microbial load or total cellular transcription). Even slight errors in these assumptions introduce bias, leading to elevated false positive and negative rates.

RESULTS: We introduce interval assumptions as a generalization of normalizations. Unlike normalizations, our interval methods allow researchers to account for potential errors in assumptions about the system scale. Interval assumptions are also customizable and allow researchers to express more biologically plausible assumptions about scale. Interval assumptions even generalize Quantitative Microbiome Profiling (QMP), allowing researchers to account for errors in flow cytometry-based measurements of total cellular concentration. We develop a novel hypothesis testing framework that allows us to integrate interval assumptions into existing tools. We develop a modified version of the popular ALDEx2 method using interval assumptions rather than normalizations. Through real and simulated data analyses, we find that interval assumptions can dramatically decrease false positive rates (i.e., from 45% to 5%) while retaining or increasing statistical power. We also study interval assumptions under misspecification and show they still improve on normalizations.

CONCLUSIONS: Interval assumptions enhance the rigor and reproducibility of differential expression and differential abundance analyses. Our results add to a growing body of literature arguing that normalizations should be replaced with alternative methods that allow researchers to account for scale uncertainty. However, compared to recent alternatives like scale models and sensitivity analyses, interval assumptions are easier to use, are more robust to misspecification, and have stronger and more interpretable inferential guarantees.},
}

*Gene Expression Profiling/methods
Humans
*Computational Biology/methods
Microbiota/genetics
Algorithms

@article {pmid40597564,
year = {2025},
author = {Saban Güler, M and Arslan, S and Ağagündüz, D and Cerqua, I and Pagano, E and Berni Canani, R and Capasso, R},
title = {Corrigendum to "Butyrate: A potential mediator of obesity and microbiome via different mechanisms of actions" [Food Res. Int. 199 (2025) 115420].},
journal = {Food research international (Ottawa, Ont.)},
volume = {217},
number = {},
pages = {116871},
doi = {10.1016/j.foodres.2025.116871},
pmid = {40597564},
issn = {1873-7145},
}

@article {pmid40597465,
year = {2025},
author = {Yao, T and Libera, L and Lindemann, SR},
title = {Synbiotic delivery of arabinoxylan and a human-derived arabinoxylan-fermenting consortium influence mouse gut microbiome composition, metabolism, and resilience in sex-dependent ways.},
journal = {Food research international (Ottawa, Ont.)},
volume = {217},
number = {},
pages = {116709},
doi = {10.1016/j.foodres.2025.116709},
pmid = {40597465},
issn = {1873-7145},
mesh = {*Xylans/administration & dosage/metabolism/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Fermentation ; Mice ; Male ; Female ; Humans ; *Synbiotics/administration & dosage ; Dietary Fiber/administration & dosage ; Mice, Inbred C57BL ; Sorghum/chemistry ; },
abstract = {Dietary fibers are generally considered to have strong impacts on governing ecological dynamics in gut microbial communities and metabolites. However, the extent to which the ecological modification capabilities of complex polysaccharides are enhanced by the presence of fermenting microbial specialists remains underexplored. Our prior study demonstrated that sorghum arabinoxylan (AX), a complex fiber with diverse glycosidic linkages, could offer unique ecological niches to sustain a stable consortium of organisms in vitro. In this study, the synergistic effect of AX and its specialist consortium was investigated using murine model and emphasized on their collective effects on gut microbiome modulation, specifically in improving the resilience after the exposure to antibiotics. We hypothesized that 1) continuous fiber intake aids in the engraftment of the specialist microbes to remodel the target host gut, and 2) the combined effect of fiber administration and the delivery of fiber-specific organisms has a pronounced ecological modulatory effect, especially in restoring a functional microbiome disrupted by antibiotic treatment. We found that while the cross-host consortium engraftment achieved modest success; the presence of specialist consortium-either independently or in combination with AX-facilitated swift shifts in fecal microbiota composition. In addition, the administration of AX and the fermenting consortium in antibiotic-treated groups resulted in a more rapid recovery of murine native microbiome over the fiber treatment alone, indicating that gut function recovery may be facilitated by transitory microbiota that perform ecosystem engineering roles. Overall, strategically pairing ecological niches (complex polysaccharides) with their corresponding specialist microbes offers a practical approach to effectively modify the gut ecosystem, thereby overcoming adverse conditions, enhancing stability and resilience.},
}

*Xylans/administration & dosage/metabolism/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects/physiology
Fermentation
Mice
Male
Female
Humans
*Synbiotics/administration & dosage
Dietary Fiber/administration & dosage
Mice, Inbred C57BL
Sorghum/chemistry

@article {pmid40597447,
year = {2025},
author = {Thomas, MC and Waugh, G and Damjanovic, K and Vanwonterghem, I and Webster, NS and Negri, AP and Luter, HM},
title = {Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {81},
pmid = {40597447},
issn = {2524-6372},
support = {DP200100790//Australian Research Council/ ; },
abstract = {BACKGROUND: Ecological risk assessments rarely consider the impacts of environmental stress on microbial communities. Incorporating microbial community responses into these evaluations requires establishing sensitivity thresholds based on the absolute abundance of viable taxa. While essential for describing microbial community dynamics, sequencing-based analyses are typically limited to relative proportions and fail to reveal the magnitude or directionality of abundance shifts. This study presents a workflow that combines propidium monoazide (PMA) treatment and microbial load estimates with 16S rRNA gene amplicon sequencing and quantitative microbiome profiling (QMP) to assess the absolute abundance of viable taxa in seawater microbiomes.

RESULTS: Using natural seawater, microbial load estimates from droplet digital PCR (ddPCR) and flow cytometry (FC) correlated strongly for total and intact cell counts, confirming the suitability of both methods for normalising 16S rRNA gene amplicon sequencing data. We demonstrated that PMA at concentrations of 2.5–15 µM effectively inhibited PCR amplification of DNA from membrane-compromised cells, reducing 16S RNA gene copies by 24–44% relative to untreated samples. Samples with known proportions of intact cells were generated by mixing heat-killed and natural seawater, enabling absolute abundance assessments by normalising 16S rRNA gene amplicon sequencing data to intact cell loads estimated via ddPCR and FC. This approach facilitated detailed comparisons of the effects of QMP versus relative microbiome profiling (RMP) on alpha and beta diversity metrics and on relative and absolute amplicon sequence variant (ASV) abundance profiles. Unlike RMP, QMP captured significant shifts in the microbial community composition across samples with decreasing proportions of intact cells. While RMP failed to detect abundance changes at ASV-level, QMP revealed consistent abundance declines.

CONCLUSION: This workflow enhanced the accuracy in representing microbial community dynamics by addressing key limitations of RMP such as the inclusion of damaged cells or extracellular DNA and the misleading proportions of identified taxa. It is particularly suited for quantifying the magnitude and direction of changes in taxa abundance following stress exposure, making it directly applicable to microbial stress-response modelling.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00741-2.},
}

@article {pmid40597432,
year = {2025},
author = {Ehau-Taumaunu, H and Bell, TH and Sadeghi, J and Hockett, KL},
title = {Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {77},
pmid = {40597432},
issn = {2524-6372},
support = {492F//PA Vegetable Growers Association/ ; 1016871//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities.

RESULTS: Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity.

CONCLUSIONS: Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.},
}

@article {pmid40597414,
year = {2025},
author = {Kadyan, S and Park, G and Singh, TP and Patoine, C and Singar, S and Heise, T and Domeier, C and Ray, C and Kumar, M and Behare, PV and Chakrabarty, P and Efron, P and Sheffler, J and Nagpal, R},
title = {Microbiome-based therapeutics towards healthier aging and longevity.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {75},
pmid = {40597414},
issn = {1756-994X},
mesh = {Humans ; *Longevity ; *Gastrointestinal Microbiome ; *Healthy Aging ; *Aging ; *Microbiota ; Animals ; },
abstract = {The gut microbiome is our lifetime companion, regulating our health from birth throughout the lifespan. The gut microbiome composition changes continually with age, influencing both physiological and immunological development. Emerging evidence highlights the close association, and thus implication, of the microbiome with healthy disease-free aging and longevity. Accordingly, targeting the gut microbiome is emerging as a promising avenue to prevent, alleviate, and ameliorate aging-related disorders. Herein, we provide a prospective and inclusive framework of the close connection of the gut microbiome with human aging, while contemplating how this association is intertwined with age-related diseases. We delve into recently emerging and potential microbiome-based therapeutics that are projected to aid in alleviating myriad aging-related diseases, thereby enhancing the health and well-being of the aging population. Finally, we present a foundation and perspective underlining the prospects of microbiome-based therapeutics developed and tailored precisely for the elderly, with the overarching goal of promoting health and longevity.},
}

Humans
*Longevity
*Gastrointestinal Microbiome
*Healthy Aging
*Aging
*Microbiota
Animals

@article {pmid40597409,
year = {2025},
author = {Neidhöfer, C and Neuenhoff, M and Sib, E and Rehm, A and Dias, LR and Neumann, B and Steinmann, J and Döhla, M and Kherabi, Y and Budimir, A and Hajjar, C and Khatib, R and Axtmann, K and Schwab, K and Brossart, P and Engelhart, S and Mutters, NT and Bierbaum, G and Janssen, S and Parčina, M},
title = {Multicenter exploration of microbial communities in hospital toilets reveals: antibiotic exposure in a nosocomial settings selects for coEnterococcus over commensal taxa.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {78},
pmid = {40597409},
issn = {2047-2994},
mesh = {Humans ; Cross-Sectional Studies ; *Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology ; *Toilet Facilities ; *Microbiota/drug effects ; *Bacteria/drug effects/classification/genetics/isolation & purification ; Hospitals ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Multiple, Bacterial ; },
abstract = {BACKGROUND: Excessive antibiotic utilization in hospital settings catalyzes the emergence and dissemination of multidrug resistant (MDR) bacteria, with sanitary facilities serving as critical vectors for their propagation. This study investigated the impact of patient antibiotic exposure on microbial diversity in hospital sanitary facilities, as well as the emergence of uniform communities and prospering taxa under antibiotic pressure.

METHODS: For this purpose a cross-sectional study was conducted between September 2022 and April 2023 from eight hospitals in seven cities across five countries, representing a diverse mix of tertiary care, military, oncological, psychiatric, and general teaching hospitals to analyze bacterial population differences in hospital toilets on wards with high versus minimal antibiotic administration using 16s rRNA amplicon sequencing.

RESULTS: PCoA analysis with Bray-Curtis and unweighted UniFrac metrics revealed microbial clustering influenced by antibiotic exposure and geography. Among all taxa analyzed, Enterococcus showed the strongest and most consistent association with high-exposure environments, making it one of the most striking findings in our dataset.

CONCLUSION: Routine overuse of antimicrobial agents aimed at false patient safety promotes a high-risk environment in the sanitary facilities of respective wards. Hence, the issue of hospital acquired infections with MDR pathogens transcends mere pathogen spread, entailing significant changes to both environmental and microbial landscapes over time. The situation signals an emerging ecological problem within healthcare environments, and highlights the urgency for an integrated approach to antimicrobial stewardship. The low detection of key nosocomial Gram-negative genera likely reflects the focus on toilets rather than sinks or showers.},
}

Humans
Cross-Sectional Studies
*Anti-Bacterial Agents/pharmacology
*Cross Infection/microbiology
*Toilet Facilities
*Microbiota/drug effects
*Bacteria/drug effects/classification/genetics/isolation & purification
Hospitals
RNA, Ribosomal, 16S/genetics
Drug Resistance, Multiple, Bacterial

@article {pmid40597405,
year = {2025},
author = {Yao, R and Hulshof, TG and van Hees, HMJ and Cools, A and Merckx, M and Maes, D and Janssens, GPJ},
title = {Grass hay mixed-in creep feed or separately-fed differentially affects digestive development in pre- and post-weaning piglets.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {92},
pmid = {40597405},
issn = {1674-9782},
abstract = {BACKGROUND: Based on observations in feral pigs, the role of dietary fibre and structure may be underestimated in suckling piglet nutrition. This study investigated the effect of grass hay offered to suckling piglets either separately or included in their creep feed, combined with nursery diets with or without grass pellet inclusion on growth performance and gastrointestinal development.

METHODS: Thirty-six litters (14-15 piglets per litter) were divided into three equal groups of 12 litters per treatment during the suckling phase: control group (CON) received regular creep feed; GH group received chopped grass hay as-is in separate feeders alongside regular creep feed; PGH group received regular creep feed but barley and wheat were replaced by 28% grass pellets. After weaning (d 23), each litter was split into two dietary treatments in a split-plot design (pre-wean treatment as main plot). Two of the pre-wean diets were also offered until d 14 post-weaning, i.e., CON (CON nursery diet, CON-C, GH-C, PGH-C) and PGH (GH nursery diet, CON-GH, GH-GH, PGH-GH). Thereafter, transitioning to a diet containing 13% wheat/barley or grass pellets, respectively, until d 39 post-weaning. Gastrointestinal morphology, gene expression of intestinal nutrient transporters and barrier proteins, metabolite profile and microbiota were assessed on the day before weaning, d 10 and d 38 post-weaning. A total of 24 piglets were sacrificed at each dissection point.

RESULTS: At weaning, GH group had consumed 7 g/piglet grass hay, and PGH group had consumed 46 g/piglet creep feed. One day before weaning, GH piglets showed heavier emptied small intestine (P = 0.044) and colon (P = 0.065), higher SCFA production in proximal segments and lower SCFA production in colon (P < 0.05). Higher abundance of Prevotellaceae NK3b31 group was observed in caecal and colonic content of PGH compared to GH group (P < 0.05), and PGH group showed a lower energy conversion ratio (net energy intake/gain, P = 0.035). Following weaning, GH nursery group had a reduced average daily gain (226 vs. 183 g, P < 0.001) during d 0-14, while this group showed compensatory growth afterwards (P = 0.056). Main plot effects on increased expressions of CLDN3 and FFAR2 were observed in GH and PGH by d 38 post-weaning (P < 0.05). An interaction effect showed greater luminal abundance of the Prevotellaceae NK3b31 group in GH-GH and PGH-GH groups compared to CON-GH on d 38. The GH nursery diet showed a better energy conversion ratio (P = 0.006) with no influence on body weight and their SCFA production shifted towards proximal segments.

CONCLUSION: In conclusion, feeding a structured and fibre-rich diet to suckling piglets enhance their digestive tract development and adapt their microbiome to fibre digestion in later life. Maintaining a fibre-rich diet from suckling to nursery is recommended, though this come with a transient reduction in weight gain caused by lower feed intake that, however, can be recovered afterwards accompanied with an optimized energy conversion ratio.},
}

@article {pmid40597335,
year = {2025},
author = {Drake, MJ and Pierdon, M and DeMers, G and Daniel, SG and Bittinger, K and Redding, LE},
title = {The effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {71},
pmid = {40597335},
issn = {2524-4671},
abstract = {Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets. However, little is known about zinc's effect on the microbiome of the gestating sow and her neonatal piglets. Even less is known about its effects on the sow and piglet resistome, which is important because dietary zinc can co-select for antimicrobial resistance. The goal of this randomized controlled dietary feeding trial was to assess the effect of high levels of dietary zinc in the last week of gestation on the microbiomes and resistomes of the gestating sow and her neonatal piglets. Seventy-three gestating sows were randomized to receive a diet with standard zinc levels (125 ppm) or high zinc levels (2500 ppm) approximately one week prior to their anticipated farrowing date. Fecal samples were collected from sows at enrollment and at farrowing and from piglets within 3 days of parturition. Fecal samples underwent 16sS rRNA gene sequencing, and a subset of samples underwent shotgun metagenomic sequencing. Statistically significant differences in richness, diversity and taxonomic composition were observed over time, and sows in the treatment group had significantly higher alpha diversity at farrowing (p = 0.04) and significantly altered levels of 3 taxa (Turicibacter, unclassified Clostridiaceae, and unclassified Christensenellaceae). Several antimicrobial resistance genes were significantly more abundant in the zinc group at farrowing compared to the control group, including tetracycline resistance genes [tet(O); tet(W); tet(32); tet(O/W)]; aminoglycoside resistance genes (APH(3')-IIIa), macrolide-lincosamide-streptogramin (MLS) resistance genes (lsaB; macB); and others (kdpE, Pseudomonas aeruginosa CpxR). No significant differences were observed in the piglet microbiomes or resistomes across sow treatment groups. Overall, high levels of dietary zinc had modest effects on the sow microbiome during the feeding trial. Increases in antimicrobial resistance genes in zinc supplemented sows suggest that supranutritional levels of dietary zinc should be avoided in gestating sows.},
}

@article {pmid40597298,
year = {2025},
author = {Bao, XW and Wang, QH and Li, T and Li, Y and Bian, ZY and Liu, SJ and He, LY and Niu, SQ and Guo, JL},
title = {Ophiocordyceps sinensis-induced changes in Thitarodes xiaojinensis: from intestinal barrier destruction, microbiome dysbiosis to immune responses at the molecular level.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {183},
pmid = {40597298},
issn = {1741-7007},
support = {2023M730381//China Postdoctoral Science Foundatio/ ; 2024NSFSC0052, 2024NSFSC1832//The Natural Sciences Foundation of Sichuan Province/ ; 2024NSFSC0052, 2024NSFSC1832//The Natural Sciences Foundation of Sichuan Province/ ; 82373998, 81872959, 81373920//National Natural Sciences Foundation of China/ ; },
mesh = {Animals ; *Hypocreales/physiology ; Hemolymph/microbiology/immunology ; *Host-Pathogen Interactions/immunology ; *Dysbiosis/microbiology/immunology ; *Moths/microbiology/immunology ; *Gastrointestinal Microbiome ; Intestines/microbiology ; },
abstract = {BACKGROUND: The entomopathogenic fungus (EPF) Ophiocordyceps sinensis has a long-term coexistence with its host insect, Thitarodes xiaojinensis, making it a unique model for host-pathogen interactions. Hemolymph, a critical component in insects, plays an essential role in maintaining both nutritional and immune homeostasis. However, the mechanism of the host's immune response remains unclear when O. sinensis proliferates in the hemolymph.

RESULTS: O. sinensis caused damage to the insect's intestinal barrier, facilitating the translocation of gut bacteria into the hemocoel. Subsequently, the presence of O. sinensis and opportunistic pathogenic bacteria from the gut disrupted the homeostasis of the hemolymph microbiota, resulting in an increase in bacterial diversity. This disruption triggered a series of physiological responses in the host, including elevated levels of endocrine hormones specifically 20-hydroxyecdysone (20E) and juvenile hormone 3 (JH3). Additionally, there was an enhancement of antioxidant capacity, as indicated by increased total antioxidant capacity and glutathione S-transferase activity, along with the production of antimicrobial peptides (AMPs) as part of the immune defense. Notably, the rise in 20E levels during O. sinensis infection might have significantly contributed to the increased production of AMPs.

CONCLUSIONS: O. sinensis infection significantly alters T. xiaojinensis physiology. Humoral immunity in infected hosts is primarily in response to hemolymph microbial homeostasis due to intestinal translocation. Among them, 20E upregulates AMP-related genes, suggesting a key immune strategy for managing microbial imbalances while tolerating fungal pathogens.},
}

Animals
*Hypocreales/physiology
Hemolymph/microbiology/immunology
*Host-Pathogen Interactions/immunology
*Dysbiosis/microbiology/immunology
*Moths/microbiology/immunology
*Gastrointestinal Microbiome
Intestines/microbiology

@article {pmid40597096,
year = {2025},
author = {Hong, S and Lim, MY and Chung, WH and Shin, JH and Nam, YD},
title = {Deciphering gut microbiome patterns from host preferences and microbial interactions in healthy Korean individuals.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {185},
pmid = {40597096},
issn = {1741-7007},
support = {E0170600-08//Korea Food Research Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Republic of Korea ; Adult ; Male ; *Microbial Interactions ; Female ; Middle Aged ; Young Adult ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: The gut microbiome is crucial for human health maintenance and disease development, yet limited understanding of its structure and maintenance hinders effective microbiome-based health improvement strategies. We investigated gut microbiome compositional patterns in healthy Koreans (n = 890), identifying six clusters (I-VI) with unique compositions and host preferences.

RESULTS: Each cluster had a distinct topological structure within the microbial interaction network, underscoring its diverse roles in maintaining microbial communities. Cluster II, predominated by Bacteroides and Faecalibacterium, was consistently found across individuals and centrally located within the microbial interaction network. Cluster III, mainly composed of Oscillospira and Coprococcus, and IV, dominated by Enterobacteriaceae and Bacteroides fragilis, demonstrated mutually exclusive relationships, reflecting affinities for host clusters with varied dietary patterns and microbial diversity. Clusters V and VI linked different microbial clusters, and cluster I had separate subcommunities.

CONCLUSIONS: This study reveals intricate structures and interactions within microbial communities, offering insights into the gut microbiome ecology and guiding health enhancement strategies.},
}

Humans
*Gastrointestinal Microbiome
Republic of Korea
Adult
Male
*Microbial Interactions
Female
Middle Aged
Young Adult
Bacteria/classification/genetics

@article {pmid40596914,
year = {2025},
author = {Lin, Y and Wang, FT and Xia, K and Gao, RY and Jiao, YR and Fang, M and Chen, CQ},
title = {Impact of terminal ileal microbiota dysbiosis and tryptophan metabolism alterations on mental disorders in patients with Crohn's disease.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {473},
doi = {10.1186/s12876-025-04007-6},
pmid = {40596914},
issn = {1471-230X},
support = {82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; 82470555//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/psychology/metabolism/complications ; *Tryptophan/metabolism ; Female ; Male ; *Dysbiosis/microbiology/metabolism/complications ; *Gastrointestinal Microbiome ; Adult ; *Ileum/microbiology/metabolism ; Middle Aged ; *Mental Disorders/microbiology/metabolism/etiology ; Intestinal Mucosa/microbiology/metabolism ; Case-Control Studies ; Brain-Gut Axis ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic non-specific inflammatory bowel disease with an increasing incidence worldwide. Patients with CD are facing elevated risk for mental disorders (MD) than healthy people, and chronic psychological stress is considered to trigger deterioration and relapse of CD. The microbiome-gut-brain axis (MGBA) is recognized as a crucial factor in unraveling this connection. Whereas, so far, few studies have revealed the relationship of the microbiota communities and tryptophan catabolites of the terminal ileum mucosa on gut-brain communication.

MATERIALS AND METHODS: A total of 52 patients with CD, along with 11 patients with colorectal cancers recruited as controls, were enrolled in this study. The participants completed Patient Health Questionnaire-9 and Generalized Anxiety Disorder-7 Questionnaire. The terminal ileal mucosa was collected during surgery. We profiled the microbiota composition of 37 patients and quantified the tryptophan catabolites of 28 patients utilizing 16 S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry, respectively. In addition, bioinformatics methods were used to elucidate the interrelationships between psychological states, microbial communities, and tryptophan catabolites.

RESULTS: CD patients with MD showed a significant reduction in microbial diversity within the ileal mucosa. Regarding microbial composition, Prevotella was relatively enriched in CD patients with MD, along with lower relative abundances of Akkermansia and Faecalibacterium. Furthermore, significant disparities in the levels of Picolinic acid (PA), Kynurenic acid (KYNA), Nicotinic acid (N-Acid), and Indole-3-carbaldehyde (ICAld) were detected within the ileal mucosa of CD patients comorbid with MD. A pronounced correlation was observed between PA levels and anxiety scale scores. The heightened abundance of Prevotella may be closely associated with altered levels of PA, N-Acid, and KYNA.

CONCLUSION: Alterations in the microbial composition of the terminal ileum may interact with changes in tryptophan metabolism and are associated with MD in patients with CD undergoing surgery.},
}

Humans
*Crohn Disease/microbiology/psychology/metabolism/complications
*Tryptophan/metabolism
Female
Male
*Dysbiosis/microbiology/metabolism/complications
*Gastrointestinal Microbiome
Adult
*Ileum/microbiology/metabolism
Middle Aged
*Mental Disorders/microbiology/metabolism/etiology
Intestinal Mucosa/microbiology/metabolism
Case-Control Studies
Brain-Gut Axis

@article {pmid40596862,
year = {2025},
author = {Gemeda, MT and Meka, AF and Mamo, AN and Bekele, GK and Ali, J and Abas, MK},
title = {Diversity of antibiotic resistance genes and mobile genetic elements of Sof Umer Cave microbiomes, Ethiopia.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {41},
pmid = {40596862},
issn = {2730-6844},
mesh = {*Microbiota/genetics ; *Interspersed Repetitive Sequences ; Ethiopia ; *Caves/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Genetic Variation ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; },
abstract = {Antibiotic resistance is a major global health concern that caused by the overuse and misuse of antibiotics. Mobile genetic elements have a roles in the transmission of antibiotic resistance genes. The distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave have yet to be explored. To map the distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave using high-throughput shotgun sequencing. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit. Purified environmental DNA was sequenced using a NovaSeq PE150. Analysis of the pathogen host interaction database revealed the predominance of pathogenic organisms such as Xanthomonas oryzae, Acinetobacter baumannii, Erwinia amylovora, and Mycobacterium tuberculosis. Similarly, analysis of the virulence factor database confirmed the presence of Type IV pili (VF1240), lipopolysaccharides, capsules, heme biosynthesis (VF0758), and alginate. More than 800 antibiotic resistance genes were identified, with 50% related to glycopeptide resistance, followed by antibiotic resistance genes associated with multidrug efflux pumps (30%), aminoglycoside resistance genes (10%), and unknown genes. A variety of mobile genetic elements were also identified, highlighting their importance in the genetic diversity and adaptation of the microbiome of Sof Umer Cave. These findings underscore the importance of the Sof Umer Cave habitat as a reservoir for antibiotic resistance, emphasizing the need for ongoing monitoring to enhance the understanding and control of antibiotic resistance genes.},
}

*Microbiota/genetics
*Interspersed Repetitive Sequences
Ethiopia
*Caves/microbiology
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
Genetic Variation
Anti-Bacterial Agents/pharmacology
*Genes, Bacterial

@article {pmid40596781,
year = {2025},
author = {Zhao, T and Vink, SN and Jia, X and Erban, A and Schaarschmidt, S and Kopka, J and Zuther, E and Treder, K and Michałowska, D and Guyoneaud, R and Elzenga, JTM and Attard, E and Salles, JF},
title = {Unveiling Potato Cultivars With Microbiome Interactive Traits for Sustainable Agricultural Production.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70019},
pmid = {40596781},
issn = {1365-3040},
support = {//This study was funded by ERA-NET Cofund SusCrop project potatoMETAbiome, which is supported by the European Union's Horizon 2020 research and innovation program (grant agreement No 771134; French National Agency, grant number -ANR-18-SUSC-0001) and part of the Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE-JPI)./ ; },
abstract = {Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive trait (MIT), such as root biomass, exudate patterns and the rhizosphere microbiome, can enhance agricultural sustainability by interacting effectively with soil microbiomes, which in turn, promotes plant growth and resistance to stress, thereby reducing reliance on synthetic crop protectants. Through a stepwise selection process (in silico and in vitro) that started with approximately 1000 potato genotypes, we chose 51 potato cultivars based on known phenotypical properties and distinct root exudate patterns. We conducted a greenhouse experiment to evaluate their capacity to interact with the soil microbiome and to assess their MIT scores. Our findings revealed that cultivars significantly influence plant growth, metabolite profiles, and rhizosphere fungal community composition. Moreover, we observed a positive correlation between microbial community diversity and root biomass. Additionally, leaf metabolites were correlated with rhizosphere bacterial composition, supporting the plant holobiont framework. Utilising z-scores, we aggregated all data related to plant growth, metabolomes, and microbiomes, creating a classification of 51 cultivars based on a gradient of MIT scores. By examining the distribution of low, intermediate, and high MIT, we identified a group of 11 potato cultivars suitable for further studies to assess their resilience and productivity under low-input production systems. This study provides an in-depth correlation between microbiome and several plant traits across 51 cultivars, offering tools to facilitate and expedite the incorporation of microbiome traits into breeding goals to support sustainable agriculture.},
}

@article {pmid40596614,
year = {2025},
author = {Lin, Z and Luo, H and Pan, S and Li, Y and Zhou, X and Zhao, J and Xu, X and Li, X and Wang, Y and Lv, G and Lin, Z and Lin, H and Qi, W},
title = {Effects of Paeoniae Radix Rubra on lowering lipid via bioinformatics and gut microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21117},
pmid = {40596614},
issn = {2045-2322},
support = {20230204006YY//Jilin Province Science and Technology Development Program/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Paeonia/chemistry ; Animals ; Computational Biology/methods ; *Hyperlipidemias/drug therapy/metabolism ; Male ; Mice ; Molecular Docking Simulation ; Diet, High-Fat/adverse effects ; *Lipid Metabolism/drug effects ; *Hypolipidemic Agents/pharmacology/chemistry ; *Drugs, Chinese Herbal/pharmacology/chemistry ; Lipids/blood ; *Plant Extracts/pharmacology/chemistry ; },
abstract = {Hyperlipidemia, a metabolic disorder characterized by abnormal lipid levels, is closely linked to an increased risk of cardiovascular disease. In this study, we investigated the hypolipidemic properties of Paeoniae Radix Rubra and its regulatory effects on gut microbiota composition in a high-fat diet model. Using UHPLC-QE-MS/MS, we identified its chemical constituents and applied bioinformatics, network pharmacology, and molecular docking to virtually screen for bioactive compounds and molecular targets. Gelomulide N and (E)-5-[(1 S,4aR,8aR)-2-formyl-5,5,8a-trimethyl-1,4,4a,6,7,8-hexahydronaphthalen-1-yl]-3-(acetoxymethyl)pent-2-enoic acid were identified as potential active compounds. Paeoniae Radix Rubra exhibited notable hypolipidemic, hepatoprotective, and gut microbiota-restoring effects, potentially influencing the mevalonate pathway by interacting with proteins such as P53, HMGCR, and SREBP2, which may contribute to reduced cholesterol synthesis. These findings indicate that the Paeoniae Radix Rubra could serve as a potential therapeutic strategy for hyperlipidemia, possibly mediated through modulation of lipid metabolism pathways and gut microbiota remodeling.},
}

*Gastrointestinal Microbiome/drug effects
*Paeonia/chemistry
Animals
Computational Biology/methods
*Hyperlipidemias/drug therapy/metabolism
Male
Mice
Molecular Docking Simulation
Diet, High-Fat/adverse effects
*Lipid Metabolism/drug effects
*Hypolipidemic Agents/pharmacology/chemistry
*Drugs, Chinese Herbal/pharmacology/chemistry
Lipids/blood
*Plant Extracts/pharmacology/chemistry

@article {pmid40596567,
year = {2025},
author = {Bianchi, P and Jacques, C and Theunis, J and Jamin, EL and Orlandi, C and Cauhape, L and Alvarez-Georges, S and Alves, A and Simcic-Mori, A and Lauze, C and Gravier, E and Carballido, F and Ribet, V and Bessou-Touya, S and Duplan, H},
title = {Clinical profiling of skin microbiome and metabolome during re-epithelialization.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22282},
pmid = {40596567},
issn = {2045-2322},
mesh = {Humans ; *Microbiota ; *Skin/microbiology/metabolism ; *Metabolome ; Male ; Female ; Adult ; *Re-Epithelialization ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Wound Healing ; Metabolomics/methods ; Bacteria/genetics/classification ; Skin Microbiome ; },
abstract = {We investigated changes in skin microbiome and metabolome linked to wound healing and how these are affected by a formula known to improve re-epithelialization. In a clinical study with 21 subjects, forearm lesions were induced by epidermal laser ablation. The areas were left untreated or treated with the formula. Re-epithelialization was monitored for 18 days. Skin swabs were analyzed for microbiome diversity using 16 S rRNA gene sequence analysis. Selected species analyzed using digital droplet polymerase chain reaction. Metabolomic profiles were analyzed by ultra-high performance liquid chromatography-high-resolution mass spectrometry. Microbiota alpha-diversity (richness and evenness) was markedly reduced by laser ablation and returned to pre-ablation levels on Day 5. Formula application accelerated the re-epithelialization time (RT), which was more efficient for slow healing (RTs of 15-19 days) than quick healing (10-12 day RTs) subjects. The repairing effect was associated with greater microbiota diversity and species-specific growth of commensal bacteria. Levels of several metabolites on untreated skin at the RT and the extent of the impact of the formula were different in slow and quick healers. The formula significantly modified the skin metabolome, whereby metabolites involved in promoting wound healing were increased and metabolites consumed by the commensal bacteria were decreased.},
}

Humans
*Microbiota
*Skin/microbiology/metabolism
*Metabolome
Male
Female
Adult
*Re-Epithelialization
Middle Aged
RNA, Ribosomal, 16S/genetics
Wound Healing
Metabolomics/methods
Bacteria/genetics/classification
Skin Microbiome

@article {pmid40596535,
year = {2025},
author = {Zennami, K and Nukaya, T and Ishikawa, K and Tomozawa, S and Kawai, A and Nakamura, W and Muto, Y and Saruta, M and Motonaga, T and Takenaka, M and Takahara, K and Kusaka, M and Sumitomo, M and Shiroki, R},
title = {Exposure to ileal feces with frailty-associated dysbiosis elevates gastrointestinal complication risk after intracorporeal urinary diversion.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22333},
pmid = {40596535},
issn = {2045-2322},
mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; Female ; *Urinary Diversion/adverse effects ; Aged ; *Feces/microbiology ; Middle Aged ; *Postoperative Complications/etiology/microbiology ; *Ileum/microbiology ; *Frailty/complications/microbiology ; *Gastrointestinal Diseases/etiology/microbiology ; Gastrointestinal Microbiome ; Urinary Bladder Neoplasms/surgery ; Risk Factors ; Aged, 80 and over ; Antibiotic Prophylaxis ; },
abstract = {The composition of the distal ileum microbiota and the impact of fecal exposure during intracorporeal urinary diversion (ICUD) on gastrointestinal (GI) complications remain unclear. This study included 146 patients with bladder cancer who underwent ICUD without bowel preparation and received only a single day of antibiotic prophylaxis. Fecal samples were collected directly from the distal ileum during surgery, and ascitic fluid was obtained postoperatively from abdominal drains. Among the patients, 129 (88.3%) had minimal microbial growth in ileal feces, while 17 (11.7%) showed significant colonization. The most commonly identified organisms were Streptococcus, Enterococcus, Enterobacter, Klebsiella, and Candida. The incidence of GI complications was significantly higher in patients with positive ileal fecal cultures compared to those with no detectable growth (39.4% vs. 7.7%, P < 0.001), and even more pronounced in patients with positive ascitic cultures (72.5% vs. 11.3%, P < 0.001). Multivariate analysis identified positive ascitic cultures as an independent predictor of GI complications. Additionally, frailty was significantly associated with the presence of microbial growth in ascitic fluid. These findings suggest that, although the distal ileal microbiota is largely suppressed under short-term antibiotic prophylaxis, the presence of intra-abdominal bacteria or fungi is strongly linked to postoperative GI complications, including ileus. Frailty may contribute to microbial dysbiosis and the persistence of intra-abdominal pathogens, particularly Enterococcus and Enterobacter species.},
}

Humans
*Dysbiosis/microbiology/complications
Male
Female
*Urinary Diversion/adverse effects
Aged
*Feces/microbiology
Middle Aged
*Postoperative Complications/etiology/microbiology
*Ileum/microbiology
*Frailty/complications/microbiology
*Gastrointestinal Diseases/etiology/microbiology
Gastrointestinal Microbiome
Urinary Bladder Neoplasms/surgery
Risk Factors
Aged, 80 and over
Antibiotic Prophylaxis

@article {pmid40596493,
year = {2025},
author = {He, Y and Li, L and Li, Y and Wang, X and Qian, L and Yang, J and Jiang, M},
title = {Mendelian randomization study reveals causal association between skin microbiome and skin cancers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21590},
pmid = {40596493},
issn = {2045-2322},
mesh = {Humans ; *Skin Neoplasms/microbiology/genetics ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Skin/microbiology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Carcinoma, Squamous Cell/microbiology/genetics ; Melanoma/microbiology/genetics ; Carcinoma, Basal Cell/microbiology/genetics ; Keratosis, Actinic/microbiology/genetics ; Skin Microbiome ; },
abstract = {Increasing evidence indicates a link between the skin microbiome and different types of skin cancer, but it is still uncertain if this connection is causal. This study aimed to investigate the causal relationship between genetically predicted skin microbiome and skin cancer, including basal cell carcinoma (BCC), cutaneous squamous cell carcinoma (CSCC), cutaneous melanoma (CM), and actinic keratosis (AK). A two-sample Mendelian randomization (MR) analysis was conducted using summary datasets of public genome-wide association study (GWAS) statistics. Multiple methods, including inverse variance weighted (IVW), MR-Egger, weighted median, weighted mode, and robust adjusted profile score (RAPS), were applied. Sensitivity analyses were performed to assess the robustness of the results, and a reverse MR analysis was conducted to evaluate potential reverse causality. A total of 1224 SNPs were selected as instrumental variables (IVs) for 78 genus-level skin microbes. Six genus-level skin microbes exhibited suggestive associations with skin cancer. Sensitivity and horizontal pleiotropy analyses confirmed the robustness of these relationships. Reverse MR analysis showed no evidence of reverse causality between the identified skin microbiota taxa and skin cancers. This study identifies potential causal relationships between skin microbiota and four skin cancers. Additional studies are needed to confirm these results and elucidate the underlying mechanisms.},
}

Humans
*Skin Neoplasms/microbiology/genetics
*Mendelian Randomization Analysis
*Microbiota/genetics
*Skin/microbiology
Genome-Wide Association Study
Polymorphism, Single Nucleotide
Carcinoma, Squamous Cell/microbiology/genetics
Melanoma/microbiology/genetics
Carcinoma, Basal Cell/microbiology/genetics
Keratosis, Actinic/microbiology/genetics
Skin Microbiome

@article {pmid40596352,
year = {2025},
author = {Barriga-Medina, N and Decker, T and Ramirez-Villacis, DX and León-Reyes, AE and Dong, V and Worley, C and Ruales, C and Pieterse, C and Leon-Reyes, A},
title = {Exploring fungal pathogens to control the plant invasive Rubus niveus on Galapagos Island San Cristobal.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20358},
pmid = {40596352},
issn = {2045-2322},
support = {POA 010//Galapagos Science Center/ ; 001//SPINOZA GRANT/ ; 007//Caja Chica Grant/ ; },
mesh = {*Rubus/microbiology ; *Introduced Species ; *Plant Diseases/microbiology/prevention & control ; *Fungi/pathogenicity/genetics/isolation & purification/classification ; Ecuador ; Plant Leaves/microbiology ; Fruit/microbiology ; },
abstract = {The Galapagos ecosystem faces threats from invasive species displacing native and endemic species. Rubus niveus (Hill raspberry) is particularly problematic invasive plant, covering approximately 30,000 hectares across the archipelago and rapidly outcompeting native vegetation. Current control methods, such as manual removal and herbicide application, have proven ineffective. This research aimed to identify endemic fungi pathogenic to R. niveus for potential population suppression. To achieve this goal, we sampled leaves, fruits, and stems of R. niveus in the agricultural areas of San Cristobal, Galapagos. Microbiome composition analysis of healthy and diseased R. niveus leaves revealed differences in fungal communities, representing a greater abundance of pathogenic genera in diseased tissue. These genera included Alternaria, Septoria, Fusarium, Colletotrichum, and Phanerochaete, representing well-known pathogens. Among 595 fungi isolated from Hill raspberry samples with lesions, 226 were tested for pathogenicity on healthy Hill raspberry leaves, resulting in five possible candidates consistently causing lesions. Further characterization through morphology and DNA analysis confirmed these candidates as Lasiodiplodia theobromae, Colletotrichum gloesporioides, Fusarium concentricum, Phanerochaete chrysosporium, and Penicillium rolfsii. Future research will explore the suitability of these fungal pathogens as biocontrol agents of invasive Hill rapberry.},
}

*Rubus/microbiology
*Introduced Species
*Plant Diseases/microbiology/prevention & control
*Fungi/pathogenicity/genetics/isolation & purification/classification
Ecuador
Plant Leaves/microbiology
Fruit/microbiology

@article {pmid40596264,
year = {2025},
author = {Li, X and Zuo, S and Li, M and Li, Q and Su, L},
title = {Novel gut bacteria species Paenibacillus ilasis with phosphorus degrading and soluble starch hydrolysis abilities isolated from fresh feces of rhinoceros.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21750},
pmid = {40596264},
issn = {2045-2322},
support = {2024ZD0407903//Biological Breeding- National Science and Technology Major Project/ ; Grant No. 2424003//China Agricultural University Young Talent Program in Life Science/ ; 2021YFF0702900//National Key Research and Development Program of China/ ; 2021-I2M-1-039//CAMS initiative for Innovative Medicine of China/ ; },
mesh = {*Paenibacillus/isolation & purification/genetics/metabolism/classification ; Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Perissodactyla/microbiology ; Phylogeny ; Hydrolysis ; RNA, Ribosomal, 16S/genetics ; *Starch/metabolism ; *Phosphorus/metabolism ; },
abstract = {The genus Paenibacillus, known for its diverse sources, is a valuable reservoir of antimicrobial compounds, enzymes and other valuable chemicals, with applications in medicine, agriculture, and bioremediation. Despite this, Paenibacillus strains, particularly those isolated from unique environments, remain underexplored, limiting our understanding of their potential, capabilities and taxonomic classifications. The gut microbiome of large herbivores, such as rhinoceroses, harbors underexplored microbial diversity with unique metabolic capabilities. In this study, a Gram-stain-negative, facultatively aerobic, motile, spore-forming, rod-shaped bacterial strain, NGMCC 1.200843[T] (= CGMCC 1.64763[T] = JCM 37214[T]), was isolated from fresh rhinoceros feces and characterized its taxonomic status and metabolic potential. Phylogenetic, phenotypic, and chemotaxonomic analyses confirmed the isolate as a novel species within the genus Paenibacillus, closely related to Paenibacillus lautus DSM 3035[T] (98.62% 16S rRNA gene similarity). The average nucleotide identity (ANI) and the digital DNA-DNA hybridization values were below the threshold for species delineation. The major cellular fatty acids were anteiso-C15:0, C16:0 and iso-C16:0 (> 10%) and the polar lipid profile contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified phospholipids (PL1-2) and one phosphatidyl choline (PC). The total DNA G + C content was 49.69 mol%. The isolate exhibited significant phosphate solubilization and starch hydrolysis activities in plate assays, suggesting a role in nutrient cycling within the rhinoceros gut. We propose the name Paenibacillus ilasis sp. nov. for this strain. These findings enhance our understanding of gut microbial diversity in herbivores and lay the foundation for future applications in agriculture or industry.},
}

*Paenibacillus/isolation & purification/genetics/metabolism/classification
Animals
*Gastrointestinal Microbiome
*Feces/microbiology
*Perissodactyla/microbiology
Phylogeny
Hydrolysis
RNA, Ribosomal, 16S/genetics
*Starch/metabolism
*Phosphorus/metabolism

@article {pmid40596241,
year = {2025},
author = {Tan, J and Xiong, Z and Yu, S and Lu, W and Yu, L},
title = {Mendelian randomization study revealed a gut microbiota-immune system-kidney junction axis in chronic kidney disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21685},
pmid = {40596241},
issn = {2045-2322},
support = {221101187687947//Self-funded project of Qingyuan Science and Technology Plan/ ; A2022128 and A2024781//Project of Guangdong Medical Science and Technology Research Fund/ ; },
mesh = {*Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/microbiology/genetics/immunology ; Humans ; *Mendelian Randomization Analysis ; Glomerular Filtration Rate ; Genome-Wide Association Study ; *Kidney/metabolism ; Cytokines/metabolism ; *Immune System/metabolism ; },
abstract = {The alterations of the gut microbiome and cytokine profiles and an elevated risk has correlated with kidney disease progression. However, the causal relationship between gut microbiota and chronic kidney disease (CKD) or related kidney function, and whether cytokines and immune cells act as mediators, remains unclear. Using genome-wide association studies (GWAS) data for CKD, estimated glomerular filtration rate (eGFR) and UACR (urinary albumin to creatinine) from the CKDGen consortium, microbiome data from the MiBioGen consortium and the Dutch Microbiome Project (DMP), 41 cytokine and 731 immune cell traits were identified from large-scale GWAS summary data. We performed two-sample Mendelian randomization (MR) analysis to analyses the causal relationships between gut microbiome, circulating cytokines, immune cells and CKD, eGFR and UACR. In addition, we investigated whether cytokines and immune cells are the mediating factor in the pathway from gut microbiome to CKD, eGFR and UACR. We demonstrated the causal relationships between 8 gut microbiotas in MiBioGen and 8 gut microbiota and 6 metabolism pathways in DMP with CKD, 7 gut microbiotas in MiBioGen and 7 gut microbiota and 3 metabolism pathways with eGFR and 4 gut microbiotas in MiBioGen and 10 gut microbiota and 3 metabolism pathways in DMP with UACR. Additionally, we identified 25 cytokine and immune cell characteristics associated with CKD, 18 with eGFR and 22 with UACR. Importantly, we identified no cytokine, but several immune cell properties that mediate the effects of microbiome on CKD, eGFR and UACR through mediation MR analysis. For instance, Alistipes indistinctus and Alistipes putredinis affects CKD via CD28 + CD45RA + CD8 + T cell. The mediation effects highlighted the intricate relationship between gut microbiome exposure, immune cell activity, and their combined influence on CKD. This data supports a causal effect of the gut microbiome on CKD, eGFR and UACR and underscores the value of MR in clarifying causal relationships identified in microbiome-wide association studies. Circulating immune cells may act as mediators in the pathway linking gut microbiota to CKD progression.},
}

*Gastrointestinal Microbiome
*Renal Insufficiency, Chronic/microbiology/genetics/immunology
Humans
*Mendelian Randomization Analysis
Glomerular Filtration Rate
Genome-Wide Association Study
*Kidney/metabolism
Cytokines/metabolism
*Immune System/metabolism

@article {pmid40595952,
year = {2025},
author = {Koltai, E and Mozaffaritabar, S and Zhou, L and Kolonics, A and Koike, A and Tanisawa, K and Park, J and Torma, F and Radak, Z},
title = {PGC-1 alpha overexpression in the skeletal muscle results in a metabolically active microbiome which is independent of redox signaling.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20527},
pmid = {40595952},
issn = {2045-2322},
mesh = {Animals ; *Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; *Muscle, Skeletal/metabolism/microbiology ; Mice ; Signal Transduction ; Oxidation-Reduction ; Physical Conditioning, Animal ; Male ; *Gastrointestinal Microbiome ; Colon/metabolism/microbiology ; *Microbiota ; Mitochondria/metabolism ; Mice, Transgenic ; },
abstract = {In this study, we investigated the potential relationship between the mitochondrial network and the microbiome using wild-type and skeletal muscle-specific PGC-1α (Pparg coactivator 1 alpha) overexpressing mice, both with and without exercise training. Basal PGC-1α levels were significantly higher in the skeletal muscle (J Physiol Biochem 80:329-335, 2024. https://doi.org/10.1007/s13105-024-01006-1) and, notably, in the colon, which is anatomically proximal to the microbiome. However, no significant changes were observed in cell signaling or mitochondria-related proteins within the colon. On the other hand, mitochondrial H2O2 production in the colon decreased in the PGC-1α overexpressing group. The relative abundance of several bacterial taxa differed between wild-type and PGC-1α overexpressing groups at baseline condition, indicating a shift in the microbiome milieu probably to cope with the increased metabolism, enhanced short-chain fatty acid utilization, and improved endurance capacity. Ten weeks of exercise training differentially modulated the host microbiome in PGC-1α overexpressing and wild-type mice, facilitating adaptations to a broad range of exercise-induced challenges. The results of this study provide new insights into the possible cross-talk between mitochondria and the microbiome.},
}

Animals
*Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics
*Muscle, Skeletal/metabolism/microbiology
Mice
Signal Transduction
Oxidation-Reduction
Physical Conditioning, Animal
Male
*Gastrointestinal Microbiome
Colon/metabolism/microbiology
*Microbiota
Mitochondria/metabolism
Mice, Transgenic

@article {pmid40595711,
year = {2025},
author = {Amabebe, E and Tatiparthy, M and Kammala, AK and Richardson, LS and Taylor, BD and Sharma, S and Menon, R},
title = {Vaginal pharmacomicrobiomics modulates risk of persistent and recurrent bacterial vaginosis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {115},
pmid = {40595711},
issn = {2055-5008},
mesh = {Female ; Humans ; *Vaginosis, Bacterial/microbiology/drug therapy ; *Vagina/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Microbiota/drug effects ; Recurrence ; Bacteria/drug effects/classification ; Biofilms/drug effects ; },
abstract = {Bacterial vaginosis (BV) is the most commonly diagnosed vaginal infection in women of reproductive age, with most patients unaware that they have BV due to its asymptomatic nature. BV is a dysbiotic condition defined by a deviation from the healthy Lactobacillus dominance to a polymicrobial anaerobic bacterial community that increases the risk of sexually transmitted infections and adverse reproductive outcomes, including spontaneous preterm birth. The increasing number of infectious agents in BV, biofilm persistence and antibiotic resistance in the vaginal canal hinder effective treatments with antibiotics leading to consistent recurrence of BV in many women (30-70%). Like in the gut, these vaginal drug-microbiome interactions termed pharmacomicrobiomics could alter drug disposition, mechanism of action, and toxicity that reduce the efficacy of antibiotics and increase the risk of persistent and recurrent BV and its sequelae. For instance, both vaginal epithelial and bacterial cells co-exist and possess enzymes that metabolize antibiotics, and transporter proteins that expel drugs and toxins, rendering them ineffective. Despite significant progress on pharmacomicrobiomics in the gut, little is known about this phenomenon in the vaginal microenvironment, which harbors a consequential microbiota and a major source of infection and antibiotic resistance. Therefore, to improve therapeutic outcomes and reduce the rate of persistent/recurrent BV and infection-associated preterm birth, we present an overview of the evidence pertaining to the effect of vaginal microbiome-drug interactions and efficacy of antibiotics against recurrent BV. We also highlight plausible mechanistic underpinnings of these interactions and implications for treatment modalities to combat infection-associated preterm birth.},
}

Female
Humans
*Vaginosis, Bacterial/microbiology/drug therapy
*Vagina/microbiology
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Microbiota/drug effects
Recurrence
Bacteria/drug effects/classification
Biofilms/drug effects

@article {pmid40595695,
year = {2025},
author = {Rosell-Cardona, C and Cryan, JF and Clarke, G and Kittel-Schneider, S},
title = {Host-microbiome relationship in depression: can human induced pluripotent stem cells play a role in unravelling mechanisms?.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {117},
pmid = {40595695},
issn = {2055-5008},
support = {101034270//INSPIRE COFUND Marie Skłodowska-Curie grant/ ; },
mesh = {Humans ; *Induced Pluripotent Stem Cells/physiology ; *Gastrointestinal Microbiome/physiology ; *Depression/microbiology/therapy ; *Host Microbial Interactions ; },
abstract = {Depression is highly prevalent, with many patients not responding to existing treatments. The gut microbiota plays a key role in its pathophysiology, offering new therapeutic avenues. Human-based research is essential to uncover mechanisms and validate new targets. Given CNS inaccessibility, human induced pluripotent stem cells (hiPSCs) offer an innovative model. This review explores the emerging field of hiPSCs and their potential in advancing microbiota-gut-brain axis science and depression research.},
}

Humans
*Induced Pluripotent Stem Cells/physiology
*Gastrointestinal Microbiome/physiology
*Depression/microbiology/therapy
*Host Microbial Interactions

@article {pmid40595471,
year = {2025},
author = {Durack, J and Piceno, Y and Vuong, H and Fanelli, B and Good, DA and Hasan, NA and Dadlani, M and Weiss, L and Oh, J and Kostic, AD and Dawson, TL and Caballero-Arias, H and Colwell, RR},
title = {Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5542},
pmid = {40595471},
issn = {2041-1723},
mesh = {*Skin/microbiology ; Humans ; *Microbiota/genetics ; Adult ; Malassezia/genetics/isolation & purification ; Female ; Bacteria/genetics/classification/isolation & purification ; Male ; RNA, Ribosomal, 16S/genetics ; Lipid Metabolism ; Skin Microbiome ; },
abstract = {The adult skin microbiome typically exhibits low microbial complexity, particularly on sebaceous sites, where lipophilic Cutibacterium and Malassezia spp. predominate. Current understanding of healthy skin microbiome is largely based on western, industrialized populations, with limited representation of diverse cultures and lifestyles. Here, we investigate the skin microbiome of a remote indigenous Yanomami community and reveal a complex microbial ecosystem comprising 115 previously unreported bacterial genomes. The Yanomami skin microbiome includes genera common to western populations alongside diverse environmental taxa that form multiplex interactions with the dominant eukaryote Malassezia globosa. Functional profiling indicates that this microbiome supports skin homeostasis by fortifying barrier integrity through lipid metabolism and acid production and mitigating oxidative stress. Longitudinal monitoring of western expeditioner' skin demonstrates acquisition of the Yanomami microbiome following Amazonian immersion and its subsequent loss upon return to an industrialized setting. These findings reveal that diverse, environmentally enriched microbiota may confer skin benefits that are overlooked in current models of healthy skin.},
}

*Skin/microbiology
Humans
*Microbiota/genetics
Adult
Malassezia/genetics/isolation & purification
Female
Bacteria/genetics/classification/isolation & purification
Male
RNA, Ribosomal, 16S/genetics
Lipid Metabolism
Skin Microbiome

@article {pmid40595444,
year = {2025},
author = {Minabou Ndjite, G and Jiang, AK and Ravel, CT and Grant, MR and Jiang, X and Hall, B},
title = {Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {970},
pmid = {40595444},
issn = {2399-3642},
support = {1R35GM155208-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Sweetening Agents/metabolism ; *Fructose/metabolism ; Adult ; *Clostridium/genetics/enzymology/metabolism ; },
abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.},
}

*Gastrointestinal Microbiome
Humans
*Sweetening Agents/metabolism
*Fructose/metabolism
Adult
*Clostridium/genetics/enzymology/metabolism

@article {pmid40594971,
year = {2025},
author = {Furmanczyk, EM and Tartanus, M and Malusà, E},
title = {Analysis of medium-term impact of multifunctional living mulches on soil biological fertility of an organic apple orchard.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22422},
pmid = {40594971},
issn = {2045-2322},
support = {SUSCROP/II/BioHortiTech/01/2021//Narodowe Centrum Badań i Rozwoju/ ; SUSCROP/II/BioHortiTech/01/2021//Narodowe Centrum Badań i Rozwoju/ ; SUSCROP/II/BioHortiTech/01/2021//Narodowe Centrum Badań i Rozwoju/ ; },
mesh = {*Malus/growth & development ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Bacteria/classification/genetics ; Fragaria/growth & development ; Ecosystem ; Mentha piperita/growth & development ; *Organic Agriculture/methods ; },
abstract = {Living mulches, particularly when designed with officinal plants, beside competing against weeds of a fruit crop, could provide other ecosystem services. The impact on soil chemical and biological features of Alchemilla vulgaris, Fragaria vesca and Mentha x piperita after four years of establishment as understorey living mulches in an organic apple orchard was evaluated. Soil nutrients level was not affected by the living mulches. The combined effect of season and living mulch affected bacterial activity, which reverberated on phyla and taxa abundance. Only few genera were unique to each living mulch species, but the abundance of 213 genera was differentially modified by the living mulches. The soil level of P and K, the metabolism of several C sources, and the bacterial activity and Shannon Index were highly correlated with the relative abundance of about a third of identified bacterial taxa. The analysis of bacterial abundance data gathered since the establishment of the trial was showing a different trend in shaping bacterial soil microbiome depending on the living mulch species.},
}

*Malus/growth & development
*Soil Microbiology
*Soil/chemistry
Microbiota
Bacteria/classification/genetics
Fragaria/growth & development
Ecosystem
Mentha piperita/growth & development
*Organic Agriculture/methods

@article {pmid40594788,
year = {2025},
author = {Sun, YD and Zhang, H and Gong, XL and Li, YM and Han, R and Zhou, CX and Han, JJ},
title = {Multiomics reveals metformin's dual role in gut microbiome remodeling and hepatic metabolic reprogramming for MAFLD intervention.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22699},
pmid = {40594788},
issn = {2045-2322},
support = {NSFC No. 82272101//the National Natural Science Foundation of China/ ; No.2018YFE0126500//the National Key Research and Development Program of China/ ; No. ZR2021MH060//the Natural Science Foundation of Shandong Province/ ; },
mesh = {*Metformin/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Non-alcoholic Fatty Liver Disease/metabolism/drug therapy/pathology/microbiology ; Male ; Rats ; *Liver/metabolism/drug effects/pathology ; Rats, Wistar ; Lipid Metabolism/drug effects ; Metabolomics/methods ; Hypoglycemic Agents/pharmacology ; Lipidomics ; Disease Models, Animal ; Metabolic Reprogramming ; Multiomics ; },
abstract = {Metabolic Associated Fatty Liver Disease (MAFLD), previously known as Non-Alcoholic Fatty Liver Disease, is a growing global health issue associated with obesity, type 2 diabetes, and metabolic syndrome. This study investigates the potential of metformin, a common anti-diabetic drug, to slow the progression of MAFLD using a multi-omics approach. Male Wistar rats were fed a choline-deficient diet to induce MAFLD and treated with metformin through their drinking water for 48 weeks. We conducted a comprehensive analysis including liver histology, untargeted metabolomics, lipidomics, and gut microbiome profiling to assess the effects of metformin on liver and gut metabolic patterns. Metformin administration led to significant changes in gut microbiome diversity and the abundance of specific microbial species in MAFLD rats. Histological analysis showed that metformin-treated rats had reduced lipid accumulation and fibrosis in the liver compared to untreated MAFLD rats. Metabolomic and lipidomic analyses revealed that metformin corrected abnormal lipid metabolism patterns, reduced hepatic fat deposition, and influenced key metabolic pathways associated with MAFLD progression. Our findings suggest that metformin has a protective role against MAFLD by modulating gut microbiota and liver metabolism, thereby slowing the progression of hepatic fibrosis. This study provides insights into the therapeutic potential of metformin for MAFLD by addressing metabolic pattern disorders and abnormal changes in gut microbial diversity, highlighting its impact on lipid metabolism and gut-liver axis interactions.},
}

*Metformin/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Non-alcoholic Fatty Liver Disease/metabolism/drug therapy/pathology/microbiology
Male
Rats
*Liver/metabolism/drug effects/pathology
Rats, Wistar
Lipid Metabolism/drug effects
Metabolomics/methods
Hypoglycemic Agents/pharmacology
Lipidomics
Disease Models, Animal
Metabolic Reprogramming
Multiomics

@article {pmid40594702,
year = {2025},
author = {Beeby, N and Pierre, LJ and Guy, RFJ and Justin, R and Victor, TA and Rossi, G and van den Hout, L and Rothman, JM and Amato, KR and Webster, TH and Baden, AL},
title = {Climate, diet, and nutrition drive gut microbiome variation in a fruit-specialist primate.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21110},
pmid = {40594702},
issn = {2045-2322},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet ; *Fruit ; *Climate ; Madagascar ; },
abstract = {Much of what we know about drivers of mammalian gut microbiome (GM) variation focuses on limited seasonal data, or effects of dietary fiber, particularly in leaf-eating and grazing taxa. We know little about the synergistic relationships between climate, diet, nutrition, and GM dynamics in wild mammals-particularly in fruit-eating taxa. Here, we examined GM variation across 12 months in a fruit-specialist primate, the black-and-white ruffed lemur (Varecia variegata), which is known to experience substantial environmental variation in its rainforest habitat in Madagascar. We used mixed modeling approaches to estimate the effects of climate, diet, and nutrient intakes on GM alpha diversity and differential abundances. We found substantial intra- and inter-individual GM variation. Climate and nutrient intakes impacted GM alpha diversity, and in addition to degree of frugivory and dietary diversity, each drove changes in differential abundance of unique combinations of microbial taxa. The degree of frugivory predicted few microbial abundances while nutrient intakes predicted a wide diversity, with fibers and non-structural carbohydrates showing inverse patterns to those of fat, indicating that nutrients are more important in driving the GM than simply the food types consumed. These results highlight how physiological flexibility facilitated by GM plasticity may be key to fruit-specialists' survival of fruit scarcity.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Diet
*Fruit
*Climate
Madagascar

@article {pmid40594486,
year = {2025},
author = {Yang, Z and Wang, Y and Wang, Y and Zhou, J and Wang, R and Shi, M and Bao, M and Wang, B and Yuan, R},
title = {Analysis on gut microbiota diversity of wild Asian elephants (Elephas maximus) from three regions of Yunnan Province.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20692},
pmid = {40594486},
issn = {2045-2322},
support = {Grant No. 82460392//National Natural Science Foundation of China/ ; Grant No. YNWR-QNBJ-2020-089//The Youth Talent Program of Yunnan "Ten-thousand Talents Program"/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; China ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; High-Throughput Nucleotide Sequencing ; },
abstract = {Studying the gut microbiome diversity of Asian elephants (Elephas maximus) is crucial for understanding their environmental adaptability, health status, and conservation needs. In this study, high-throughput sequencing of the 16S rRNA gene was utilized to analyze and compare the microbial community composition and diversity of 50 wild Asian elephants from three regions in Yunnan Province. The results indicated significant differences in gut microbiome richness among the regions, and the lowest diversity observed in the Lincang region. Principal coordinate analysis (PCoA) revealed that the microbial community structure of the Lincang population was markedly different from that of the other two regions. At the phylum level, Firmicutes, Proteobacteria, and Bacteroidetes were the dominant bacterial groups across all three regions. However, in the Lincang region, the abundance of Proteobacteria was the highest and significantly greater than in the other regions. Additionally, the levels of potential pathogenic bacteria, such as Acinetobacter and Stenotrophomonas, were significantly elevated in the Lincang population compared to the other two regions. Therefore, future conservation efforts need to integrate ecological restoration with microbiome monitoring to mitigate the microbial dysbiosis caused by human disturbances.},
}

Animals
*Elephants/microbiology
*Gastrointestinal Microbiome/genetics
China
RNA, Ribosomal, 16S/genetics
Biodiversity
*Bacteria/genetics/classification/isolation & purification
Phylogeny
High-Throughput Nucleotide Sequencing

@article {pmid40594438,
year = {2025},
author = {Sugiyama, T and Hasegawa, K},
title = {Synergistic actions of symbiotic bacteria modulate the insecticidal potency of entomopathogenic nematode Steinernema monticolum KHA701.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22550},
pmid = {40594438},
issn = {2045-2322},
mesh = {Animals ; *Symbiosis ; Xenorhabdus/physiology ; *Insecticides ; *Rhabditida/microbiology ; Larva/parasitology/microbiology ; Photorhabdus/physiology ; Moths/parasitology ; Microbiota ; },
abstract = {Entomopathogenic nematodes (EPNs), primarily Steinernema and Heterorhabditis, form symbiotic relationships with bacteria from the genera Xenorhabdus and Photorhabdus, respectively. These bacteria exhibit insecticidal activity and suppress competing microorganisms, allowing EPNs and their symbionts to dominate insect cadavers. While monoxenic associations are fundamental to EPN-bacteria interactions, recent studies suggest that EPNs may harbor a diverse array of symbiotic bacteria with consistent associations. However, the role of these additional symbiotic bacteria in EPN pathogenesis and the complexity of their interactions remain unclear. In this study, Steinernema monticolum KHA701 was newly isolated using the Galleria mellonella bait method. Compared to the highly pathogenic Heterorhabditis bacteriophora TT01, S. monticolum KHA701 demonstrated superior insecticidal activity against G. mellonella larvae and exhibited a broad host range, targeting 63 arthropod species across 18 orders and 41 families. Microbiota analysis of S. monticolum KHA701 infective juveniles identified 34 bacterial species, including Xenorhabdus hominickii, from the nematode body. Five bacteria-Elizabethkingia miricola, Serratia marcescens, Pseudomonas protegens, Staphylococcus sp., and X. hominickii-were confirmed to be highly pathogenic to Zophobas morio and Periplaneta fuliginosa larvae. Notably, the combination of X. hominickii with any of the other four bacteria significantly enhanced the insecticidal activity of S. monticolum KHA701 against G. mellonella. These findings suggest that S. monticolum KHA701 utilizes a diverse community of bacterial symbionts to enhance its insecticidal efficacy, providing novel insights into the ecological strategies of EPNs.},
}

Animals
*Symbiosis
Xenorhabdus/physiology
*Insecticides
*Rhabditida/microbiology
Larva/parasitology/microbiology
Photorhabdus/physiology
Moths/parasitology
Microbiota

@article {pmid40594421,
year = {2025},
author = {Pan, X and Gao, Y and Zhang, Y and Suzuki, K and He, J and Chen, X and Jiang, L and Zhang, A},
title = {Gut microbiota differences in children classified by extreme physical fitness and physical activity levels from a Chinese Cross-Sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21351},
pmid = {40594421},
issn = {2045-2322},
support = {2022YFC3600204//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFC3600204//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; *Physical Fitness/physiology ; *Exercise/physiology ; Male ; Cross-Sectional Studies ; Female ; China ; Feces/microbiology ; East Asian People ; },
abstract = {This study investigated the diversity, structure, dominant microbial populations, and their relationships with physical fitness (PF) and physical activity (PA) metrics within the gut microbiota of children by comparing the gut microbiome composition and functional differences across four groups: low PA-high PF, high PA-high PF, high PA-low PF, and low PA-low PF. A total of 6,074 children aged 6-9 years were selected from full-time ordinary primary and secondary schools. Based on the quartiles of PF and PA, we sampled 120 individuals from each of the four groups (30/group) and collected fecal samples for high-throughput sequencing to analyze the gut microbiome composition. This study revealed that children with high PF exhibited a more abundant and diverse gut microbiome within the same PA level group. Under high PA conditions, the Chao1 and Shannon indices of the high PF group were significantly higher. Different dominant microbial taxa were identified within each group, and specific microbial populations were significantly correlated with various physical and exercise-related indices. This study indicates that the composition of children's gut microbiota varies significantly based on the combined levels of PA and PF. Children with high PF show greater microbial diversity within similar PA levels, particularly under high PA conditions.},
}

Humans
*Gastrointestinal Microbiome
Child
*Physical Fitness/physiology
*Exercise/physiology
Male
Cross-Sectional Studies
Female
China
Feces/microbiology
East Asian People

@article {pmid40594354,
year = {2025},
author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO},
title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22448},
pmid = {40594354},
issn = {2045-2322},
support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; },
abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.},
}

*Solanum lycopersicum/microbiology/genetics
*Microbiota/genetics
Soil Microbiology
Rhizosphere
Ecuador
Plant Roots/microbiology
Biodiversity
*Adaptation, Physiological
Phylogeny

@article {pmid40594317,
year = {2025},
author = {Song, X and Li, JN and Wang, D and Han, ZY and Yan, XX and Yang, ZH and Xu, J and Wang, Q and Wu, D},
title = {Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20549},
pmid = {40594317},
issn = {2045-2322},
support = {32170788//National Natural Science Foundation of China/ ; 2022-PUMCH-B-023//National High Level Hospital Clinical Research Funding/ ; ZK108000//National Key Clinical Specialty Construction Project/ ; 7232123//Natural Science Foundation of Beijing/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Pancreatitis/microbiology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Acute Disease ; Bacteria/genetics/classification ; },
abstract = {Gut microbiota play a critical pathogenic role in acute pancreatitis (AP). This study aimed to investigate the composition and function of gut microbiota during the recovery phase of AP. Rectal swab samples obtained from 12 AP patients of varying severity during both the acute and recovery phases were sequenced using shotgun metagenomic sequencing. We analysed α-diversity, enterotypes, and the dominant microbiome composition, and performed differential analysis of gut microbiota composition and functional enrichment. During the recovery phase of AP, microbial diversity remained decreased, and minimal difference were observed in the structural diversity of the microbiome. There was an increasing tendency of beneficial bacteria (Bacteroidales) and a decreasing tendency of harmful bacteria (Firmicutes) in the recovery phase of mild AP (MAP). However, in the recovery phase of moderately severe AP (MSAP) and severe AP, Enterococcus abundance increased compared with that in the acute phase. Some signalling pathways showed opposite trends in the recovery phase of MAP and MSAP compared to the acute phase. These results suggested that gut microbiome composition and function are associated with AP recovery, which may inform strategies for the treatment and prognosis of AP.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Pancreatitis/microbiology
Male
Female
Middle Aged
Adult
Aged
Acute Disease
Bacteria/genetics/classification

@article {pmid40594248,
year = {2025},
author = {Kang, MG and Choi, JH and Kim, SH and Jeong, TB and Kim, JY and Kim, JW and Lee, CY},
title = {Efficacy and safety of Lactobacillus plantarum GCWB1001 for respiratory health in a double blind randomized placebo controlled trial.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22700},
pmid = {40594248},
issn = {2045-2322},
mesh = {Humans ; *Lactobacillus plantarum/physiology ; Male ; Female ; Middle Aged ; Double-Blind Method ; Adult ; Aged ; *Probiotics/therapeutic use/administration & dosage/adverse effects ; *Cough/therapy ; *COVID-19/complications/therapy ; Treatment Outcome ; Young Adult ; *Dyspnea/therapy ; SARS-CoV-2 ; Sputum ; },
abstract = {Respiratory symptoms like prolonged cough and breathlessness have increased post-COVID-19, even in those with normal chest X-rays and FEV1/FVC ratios. This study assessed the benefits of Lactobacillus plantarum GCWB1001 on such symptoms in individuals without asthma or COPD. In a double-blind, randomized, placebo-controlled trial, 126 participants aged 19-70 were included. Exclusions were for asthma, COPD, abnormal chest X-rays, or recent antibiotic use. The primary outcome was the Breathlessness, Cough, and Sputum Scale (BCSS), with secondary outcomes including Visual Analogue Scale (VAS) scores for respiratory function. The total BCSS score at 12 weeks did not differ significantly between the GCWB1001 and placebo groups. Secondary endpoints such as sputum and breathlessness showed numerical improvements, particularly in males and participants over 40, but these findings were not statistically significant after correction for multiple comparisons. No serious adverse events were reported, indicating safety. Although this study did not demonstrate a clear clinical benefit, the exploratory trends suggest that additional, larger-scale trials may be needed to determine if these observations reflect a meaningful effect.},
}

Humans
*Lactobacillus plantarum/physiology
Male
Female
Middle Aged
Double-Blind Method
Adult
Aged
*Probiotics/therapeutic use/administration & dosage/adverse effects
*Cough/therapy
*COVID-19/complications/therapy
Treatment Outcome
Young Adult
*Dyspnea/therapy
SARS-CoV-2
Sputum

@article {pmid40594086,
year = {2025},
author = {Leifels, M and Cheng, D and Cai, J and Nadhirah, N and Mohidin, AF and Santillan, E and Woo, Y and Hill, E and Wu, SW and Boon, N and Favere, J and Whittle, AJ and Wuertz, S},
title = {Biofilm detachment significantly affects biological stability of drinking water during intermittent water supply in a pilot scale water distribution system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22408},
pmid = {40594086},
issn = {2045-2322},
support = {3S85419//the FWO Flanders/ ; 3S85419//the FWO Flanders/ ; S006221N//FWO-SBO Biostable project/ ; S006221N//FWO-SBO Biostable project/ ; },
mesh = {*Biofilms/growth & development ; *Drinking Water/microbiology ; *Water Supply ; *Water Microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Flow Cytometry ; Water Quality ; Bacteria/genetics/classification ; Water Purification ; },
abstract = {Intermittent service provision (IWS) in piped drinking water distribution systems is practiced in countries with limited water resources; it leads to stagnant periods during which water drains completely from de-pressurized pipes, increasing the likelihood of biofilm detachment upon reconnection when water is supplied to the consumer and thus affecting water quality. Our study examines the impact of uninterrupted or continuous water supply (CWS) and IWS on microbial communities and biofilm detachment, using data from three 30-day experiments conducted in an above-ground drinking water testbed with 90-m long PVC pipes containing residual monochloramine. Flow cytometry (FCM) revealed a significant increase in total and intact cell concentrations when water was supplied intermittently compared to CWS, and the microbial alpha-diversity was significantly higher in CWS sections by both 16S rRNA gene metabarcoding and phenotypic fingerprinting of flow cytometry data. Nitrate levels in the water were significantly higher during initial intermittent flow due to the activity of nitrifying bacteria in biofilms exposed to stagnant water in pipes. Overall, biofilm detachment significantly affects the biological stability of drinking water delivered through IWS compared to CWS. We developed a novel biofilm detachment potential index derived from FCM data to estimate the minimum amount of water needed to be discarded before microbial cell counts and community composition return to baseline levels.},
}

*Biofilms/growth & development
*Drinking Water/microbiology
*Water Supply
*Water Microbiology
RNA, Ribosomal, 16S/genetics
Pilot Projects
Flow Cytometry
Water Quality
Bacteria/genetics/classification
Water Purification

@article {pmid40593847,
year = {2025},
author = {Russ, D and Fitzpatrick, CR and Saha, C and Law, TF and Jones, CD and Kliebenstein, DJ and Dangl, JL},
title = {An effluent pump family distributed across plant commensal bacteria conditions host- and organ-specific glucosinolate detoxification.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5699},
pmid = {40593847},
issn = {2041-1723},
support = {IOS-1917270//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; },
mesh = {*Glucosinolates/metabolism ; *Arabidopsis/microbiology/metabolism/genetics ; Symbiosis ; Microbiota/genetics ; *Bacterial Proteins/metabolism/genetics ; *Bacteria/genetics/metabolism ; Inactivation, Metabolic ; Plant Shoots/microbiology/metabolism ; },
abstract = {In nature, plants recruit a diverse microbial community, the plant microbiome, that is distinct from the surrounding soil community. To understand the forces that shape the plant microbiome we need to characterize the microbial traits that contribute to plant colonization. We used barcoded mutant libraries to identify bacterial genes that contribute to the colonization of a monocot and a eudicot host. We show that plant colonization is influenced by dozens of genes. While some of these colonization genes were shared between the two host plant species, most were highly specific, benefiting the colonization of a single host and organ. We characterized an efflux pump that specifically contributes to Arabidopsis shoot colonization. This efflux pump is prevalent across Pseudomonadota genomes yet benefits the bacterial association with only a small subset of Arabidopsis thaliana accessions. Leveraging genomic diversity within Arabidopsis thaliana, we confirmed that specific glucosinolate breakdown products are detoxified by this family of efflux pumps. The broad prevalence of this efflux pump family suggests that its members contribute to protection of commensal bacteria from collateral damage of plant glucosinolate-based defense responses to herbivores and necrotrophic pathogens.},
}

*Glucosinolates/metabolism
*Arabidopsis/microbiology/metabolism/genetics
Symbiosis
Microbiota/genetics
*Bacterial Proteins/metabolism/genetics
*Bacteria/genetics/metabolism
Inactivation, Metabolic
Plant Shoots/microbiology/metabolism

@article {pmid40593813,
year = {2025},
author = {Wende, M and Osbelt, L and Eisenhard, L and Lesker, TR and Damaris, BF and Mutukumarasamy, U and Bielecka, A and D H Almási, É and Winter, KA and Schauer, J and Pfennigwerth, N and Gatermann, S and Schaufler, K and Schlüter, D and Galardini, M and Strowig, T},
title = {Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5426},
pmid = {40593813},
issn = {2041-1723},
mesh = {*Escherichia coli/drug effects/isolation & purification/physiology/growth & development/genetics ; *Drug Resistance, Multiple, Bacterial ; *Gastrointestinal Microbiome/drug effects/physiology ; Animals ; Humans ; Mice ; Klebsiella oxytoca/physiology ; Probiotics ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/microbiology ; Female ; Antibiosis ; },
abstract = {Human gut colonization by multi-drug resistant Enterobacterales (MDR-E) poses a risk for subsequent infections. Because of the collateral damage antibiotics cause to the microbiota, microbiome-based interventions aimed at promoting decolonization have garnered interest. In this study, we evaluate the strain-specific potential of 430 commensal Escherichia coli isolates to inhibit the growth of an MDR E. coli strain. Comparative analyses using in vitro, ex vivo, and mouse models reveal that only a subset of commensal strains can facilitate gut decolonization. Bioinformatic and experimental analyses of the antagonism among representative strains demonstrate that both direct and indirect carbohydrate competition contribute to niche exclusion between E. coli strains. Finally, the combination of a protective E. coli strain with a Klebsiella oxytoca strain enhances the inhibitory potential against metabolically diverse MDR E. coli strains and additional MDR-E species, highlighting that rationally designed metabolically complementary approaches can contribute to developing next-generation probiotics with broad-spectrum activity.},
}

*Escherichia coli/drug effects/isolation & purification/physiology/growth & development/genetics
*Drug Resistance, Multiple, Bacterial
*Gastrointestinal Microbiome/drug effects/physiology
Animals
Humans
Mice
Klebsiella oxytoca/physiology
Probiotics
Anti-Bacterial Agents/pharmacology
*Escherichia coli Infections/microbiology
Female
Antibiosis

@article {pmid40593739,
year = {2025},
author = {Xing, J and Niu, T and Yu, T and Zou, B and Fan, S and Wang, C and Shi, C and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, D and Yang, G and Yang, W},
title = {Gut microbiota-derived isovaleric acid ameliorates influenza virus infection via gut-lung axis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {116},
pmid = {40593739},
issn = {2055-5008},
support = {U21A20261//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Orthomyxoviridae Infections/drug therapy/virology/microbiology ; Mice ; Influenza A Virus, H1N1 Subtype/drug effects ; *Lung/virology/drug effects/pathology/microbiology ; *Influenza A Virus, H9N2 Subtype/drug effects ; Disease Models, Animal ; Prevotella ; Pentanoic Acids ; Hemiterpenes ; },
abstract = {H9N2 influenza virus infections represent a significant respiratory health concern, yet the functional role of gut microbiota during infection progression remains poorly understood. Here, we show that H9N2 infection causes dose-dependent alterations in gut microbial communities in a mammalian infection model, particularly the depletion of Prevotella species. Prophylactic administration of Prevotella copri improved survival and clinical outcomes in infected mice by restructuring the gut microbiome, promoting beneficial bacteria, and suppressing pathogens. Metabolomic profiling revealed increased isovaleric acid levels in the intestine and serum. Isovaleric acid pretreatment reduced pulmonary inflammation, alleviated tissue damage, and preserved epithelial integrity. Isovaleric acid pretreatment alleviates lung inflammation, reduces tissue damage, and maintains epithelial integrity. Additionally, isovaleric acid mitigates infection caused by the H1N1 influenza virus. These findings highlight the immunomodulatory role of gut commensals and their metabolites in antiviral defense, offering a new approach to influenza virus treatment.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Orthomyxoviridae Infections/drug therapy/virology/microbiology
Mice
Influenza A Virus, H1N1 Subtype/drug effects
*Lung/virology/drug effects/pathology/microbiology
*Influenza A Virus, H9N2 Subtype/drug effects
Disease Models, Animal
Prevotella
Pentanoic Acids
Hemiterpenes

@article {pmid40593735,
year = {2025},
author = {Flores Ventura, E and Esteban-Torres, M and Gueimonde, M and van Sinderen, D and Koren, O and Hall, LJ and Segata, N and Valles-Colomer, M and Collado, MC},
title = {Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {121},
pmid = {40593735},
issn = {2055-5008},
support = {CEX2021-001189-S-20-1//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; PID2022-139328OA-I00//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; 898088//European Union's Horizon 2020/ ; SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; 220876/Z/20/Z//Wellcome Trust Investigator/ ; Beatriz Galindo Junior Fellowship BG22/00172//Ministerio de Universidades/ ; 639226/ERC_/European Research Council/International ; },
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; *Bifidobacteriales Infections/transmission/microbiology ; *Bifidobacterium/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Mothers ; Vagina/microbiology ; },
abstract = {Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.},
}

Female
Humans
Infant
Infant, Newborn
Pregnancy
*Bifidobacteriales Infections/transmission/microbiology
*Bifidobacterium/classification/genetics/isolation & purification
Gastrointestinal Microbiome
*Infectious Disease Transmission, Vertical
Metagenomics
Mothers
Vagina/microbiology