@article {pmid40568210,
year = {2025},
author = {Chen, M and Zeng, SY and Lu, SJ and Shi, M and Zhang, QQ},
title = {Early re-examination of chest CT may be unnecessary when patients with psittaci pneumonia at low and intermediate risk on Pneumonia Severity Index present with response to initial treatment.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1574706},
pmid = {40568210},
issn = {2296-858X},
abstract = {BACKGROUND: Chlamydia parrot pneumonia (CPS) is a rare community-acquired pneumonia (CAP) caused by Chlamydia parrot infection. With the development of metagenomic second-generation sequencing technology (mNGS), its diagnostic rate has improved in recent years. However, there are few clinical studies on Chlamydia parrot pneumonia, especially for patients with low and intermediate pneumonia severity index (PSI), and the necessity of early review of chest computed tomography (CT) is not clear. This study aimed to explore the clinical significance of early review of chest CT in patients with low and intermediate risk of Chlamydia parrot pneumonia with PSI after initial treatment was effective.

METHODS: Retrospective analysis of 8 patients with Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) admitted to Zhejiang Provincial Tongde Hospital from January 2020 to December 2022 (PSI score ≤ 130 points). All patients had improved clinical symptoms and inflammatory markers after receiving antibiotic treatment, and chest CT was reexamined within 5-12 days. Evaluate the correlation between imaging changes before and after treatment and clinical symptoms and inflammatory indicators (CRP, PCT, WBC, etc.).

RESULTS: After treatment, the patient's body temperature, CRP, PCT and other indicators decreased significantly (P < 0.05). However, early CT reexamination showed that imaging progressed in 5 cases (62.5%), was stable in 2 cases (25%), and only 1 case (12.5%) showed partial improvement (P > 0.05). Nevertheless, none of the patients had a deterioration in their condition later on and finally achieved imaging recovery. Clinicians did not adjust the treatment plan when imaging progressed, and only 1 case was given glucocorticoid additionally.

CONCLUSION: For patients with low- intermediate risk Chlamydia psittaci pneumonia with low PSI, if clinical symptoms and inflammatory markers improve, early reexamination of chest CT may have no additional clinical value and does not affect treatment decisions. Therefore, it is not recommended to routinely perform early CT re-examination for such patients to reduce unnecessary consumption of medical resources. Larger sample studies are needed in the future for further verification.

CLINICAL TRIAL REGISTRATION: https://www.medicalresearch.org.cn/login, identifier MR-33-25003507.},
}

@article {pmid40567259,
year = {2025},
author = {Li, Q and Jiang, J and Li, J and Zhang, W and Xin, Y and He, B and He, S and Tu, C and Guo, Y and Gong, W},
title = {Complexity of Diarrhea-Associated Viruses in Stunted Pigs Identified by Viral Metagenomics.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {1974716},
pmid = {40567259},
issn = {1865-1682},
mesh = {Animals ; Swine ; *Swine Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; Metagenomics ; Phylogeny ; China/epidemiology ; },
abstract = {Viral diarrhea poses a severe threat to the health and growth of piglets, especially when caused by co-infection with multiple diarrhea-associated viruses. In this study anal swabs were collected from pigs older than 3 months from a farm in Gansu province, China, and subjected to viral metagenomic analysis. They had been suffering from diarrhea and their growth was significantly retarded. A total of 18 viruses were identified by high-throughput sequencing (HTS) in pooled samples from 22 stunted pigs and (separately) three healthy pigs. They included 15 diarrhea-associated RNA viruses with five porcine rotaviruses (PoRVs), porcine epidemic diarrhea virus (PEDV), a torovirus, and a sapelovirus present only in the stunted pigs. Among the identified PoRVs, PoRVBs showed a much greater genetic diversity than other PoRVs with multiple variant gene sequences identified in segments VP1 (2), VP2 (3), VP3 (4), VP4 (5), VP7 (5), NSP1 (2), NSP3 (3), NSP4 (2), and NSP5 (4), with 1-3 new genotypes being defined within each segment except NSP5. Unexpectedly, PoRVF was identified for the first time in pigs, with all gene segments exhibiting low nucleotide (56.5%-79.4%) and amino acid sequence identities (46.2%-92.0%) with previously identified avian RVF reference strains. Phylogenetic analysis showed that multiple variant strains of PAstV2 (6) and PAstV4 (13) were found in stunted pigs, and other enteric viruses were highly homologous with reference strains. Overall, the findings indicate that the stunted pigs may serve as a hotbed for the propagation of diarrhea-associated viruses and that they should be isolated and treated as early as possible.},
}

Animals
Swine
*Swine Diseases/virology/epidemiology
*Diarrhea/veterinary/virology/epidemiology
Metagenomics
Phylogeny
China/epidemiology

@article {pmid40566942,
year = {2025},
author = {Kara, K and Yilmaz Öztaş, S and Baytok, E},
title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.},
journal = {Veterinary medicine and science},
volume = {11},
number = {4},
pages = {e70447},
doi = {10.1002/vms3.70447},
pmid = {40566942},
issn = {2053-1095},
support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; },
mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; },
abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.

OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.

METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24 h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.

RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p < 0.05). Thyme pulp exhibited the highest NH3-N levels (75.14 mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93 mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p < 0.05).

CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.},
}

*Fermentation
*Rumen/microbiology/metabolism/physiology
Animals
Cattle
Metagenomics
Animal Feed/analysis
*Metagenome
Gastrointestinal Microbiome
Digestion

@article {pmid40566543,
year = {2025},
author = {von Känel, G and Steinmann, LY and Mauz, B and Lukesch, R and Küenzi, P},
title = {It Is Useless to Resist: Biofilms in Metalworking Fluid Systems.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060890},
pmid = {40566543},
issn = {2075-1729},
support = {n.a.//Blaser Swisslube AG/ ; },
abstract = {Biofouling, the undesirable deposition of microorganisms on surfaces, is ubiquitous in aqueous systems. This is no different for systems running with water-miscible metalworking fluids (MWFs), which additionally contain many organic chemicals that create favorable conditions for growth and metabolism. Biofilm formation is thus inevitable, as there is no shortage of wetted surfaces in metalworking systems. MWF manufacturers tried in vain to offer resistance by using biocides and biostatic compounds as ingredients in concentrates and as tank-side additives. We report here that such elements, alone or as components of MWFs, did not prevent biofilm formation and had negligible effects on pre-established laboratory biofilms. Moreover, biofilms in metalworking systems are interwoven with residues, sediments, and metal swarfs generated during machining. Again, co-incubation of such "real" biofilms with MWFs had no significant effect on population size-but on population composition! The implications of this finding are unclear but could provide a starting point for the treatment of biofouling, as biofilm population structure might be of importance. Finally, we show that bacteria gain function in biofilms and that they were able to degrade a toxic amine in MWFs, which the same bacteria were unable to do in planktonic form.},
}

@article {pmid40565719,
year = {2025},
author = {Landi, N and Scognamiglio, M and Muscariello, L and Marasco, R and Palazzo, A and De Chiara, I and Ragucci, S and Pedone, PV and Fiorentino, A and Di Maro, A},
title = {Chemical Traits and Microbial Population Characterization of 'Asprinio' Grape Must, a Local Vine Cultivated in Campania Region (Italy).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/foods14122110},
pmid = {40565719},
issn = {2304-8158},
support = {CUP B53C22001790006//"ITACA.SB" (Project No. IR0000009) funded by the European Union's NextGenerationEU under the MUR call 3264/2021 PNRR M4/C2/L3.1.1./ ; CUP E25I22000010007//'Rigenerazione culturale e sociale dei borghi storici del Matese - Castello del Matese e Letino', (Unione europea - NextGenerationEU)/ ; },
abstract = {'Asprinio' grape is used to produce a white wine from the Campania region, known as 'Asprinio' (DOC since 1993). A plethora of approaches was adopted to characterize the organic compounds (e.g., free amino acids and other metabolites) and microbial population (bacteria and fungi) in 'Asprinio' grape must by collecting samples from three different vineyards cultivated with the 'alberata' training system. The average free amino acid content of 'Asprinio' grape must showed quantitative variations, but no significant statistical differences were found. On average, proline was the most abundant free amino acid (~282 mg/L; 47.9%), followed by arginine (~66 mg/L; 11.5%) and glutamine (~25.2 mg/L; 4.2%). On the other hand, the total polyphenol content (TPC) of 'Asprinio' grape must was different, like their antioxidant activity, which increased when the TPC content was higher. Moreover, 1D and 2D NMR spectra highlighted the presence of high sugars amount (in particular glucose) as well as trans-caftaric acid, trans-coutaric acid, trans-fertaric acid, and the cis-isomers of these cinnamate esters. Finally, the evaluation of the microbial communities in the 'Asprinio' grape must revealed the presence of several representative bacterial phyla-mainly Bacteroidota, Proteobacteria, and Actinobacteriota-as well as various fungal genera, including Cladosporium, Hanseniaspora, Aspergillus, and Saccharomyces. Notably, these microorganisms, which contribute to the fermentation process and influence the final wine flavor, have been found in different proportions in the grape musts analyzed. Our results contribute to increasing knowledge of the 'Asprinio' grape, an indigenous vine of Southern Italy.},
}

@article {pmid40565014,
year = {2025},
author = {Monareng, NJ and Ncube, KT and van Rooi, C and Modiba, MC and Mtileni, B},
title = {A Systematic Review on Microbial Profiling Techniques in Goat Milk: Implications for Probiotics and Shelf-Life.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125551},
pmid = {40565014},
issn = {1422-0067},
support = {PMDS240528221992//National Research Foundation/ ; },
mesh = {Goats ; Animals ; *Milk/microbiology ; *Probiotics ; *Microbiota ; *Food Microbiology ; Humans ; },
abstract = {Due to its high digestibility, rich nutrient profile, and potential probiotic content, goat milk is an essential nutritional resource, particularly for individuals with cow milk allergies. This review summarises the current state of microbial diversity in goat milk, emphasising the implications for quality, safety, and probiotic potential. This systematic review adhered to PRISMA guidelines, conducting a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar using keywords related to microbial profiling in goat milk. The inclusion criteria targeted English-language studies from 2000 to 2025 that utilised high-throughput or next-generation sequencing methods. Out of 126 articles screened, 84 met the eligibility criteria. The extracted data focused on microbial diversity, profiling techniques, and their respective strengths and limitations in evaluating probiotic potential and spoilage risks. The review addresses the challenges linked to microbial spoilage and the composition and functional roles of microbial communities in goat milk. With species such as Bacillus and Pseudomonas playing crucial roles in fermentation and spoilage, key findings emphasise the prevalence of microbial phyla, including Proteobacteria, Firmicutes, and Actinobacteria in goat milk. The review also explores the probiotic potential of the goat milk microbiota, highlighting the health benefits associated with strains such as Lactobacillus and Bifidobacterium. Significant discoveries underline the necessity for advanced multi-omics techniques to thoroughly define microbial ecosystems and the substantial gaps in breed-specific microbiota research. Important findings illustrate the need for enhanced multi-omics techniques, given the challenges of host RNA and protein interference, low microbial biomass, and limited goat-specific reference databases, for optimising probiotic development, spoilage prevention strategies, and integrating metagenomics, metabolomics, metaproteomics, and metatranscriptomics to improve milk quality and safety as some of the future research objectives. This study emphasises the importance of understanding goat milk microbiology to advance dairy science and enhance human health.},
}

Goats
Animals
*Milk/microbiology
*Probiotics
*Microbiota
*Food Microbiology
Humans

@article {pmid40564305,
year = {2025},
author = {Rodriguez, AE and Britez, JD and Pisón-Martínez, ML and Delgado, FO and Balbiani, F and Berardo, CC and Gramaglia, C and Cuba, F and Poklepovich, TJ and Moreno, C and Francinelli, G and Morici, G and Arias, M and Schapiro, J and Barbano, P and Tomazic, ML},
title = {Evaluating Good Husbandry Practices and Organic Fermented Additives for Coccidiosis Control in a Pilot Study Using Slow-Growing Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121752},
pmid = {40564305},
issn = {2076-2615},
support = {FONTAGRO ATN/RF 18136 RG//Inter-American Development Bank/ ; PNSA PDL01-I113 and PE-I078//INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA/ ; },
abstract = {The Argentine Campero-INTA slow-growing chicken, a widely used breed in family poultry farming, faces high coccidiosis prevalence, impairing productivity. Control often relies on management and drugs due to vaccination costs. This pilot study assessed the breed's susceptibility to local Eimeria and the impact of good animal welfare practices (AWPs) and an organic fermented additive, locally produced, combined with AWPs (OF-AWPs). Two trials evaluated productive (body weight gain and feed conversion), infection (oocyst excretion and lesion score), and histopathological parameters (villus height and crypt depth). The productivity (PI) and anticoccidial (ACI) indexes were calculated. Metagenomic analysis of the additive was also conducted. Mild to moderate coccidiosis significantly reduced PI (7.99-16.83 vs. 29.29 in unchallenged controls). In the second trial, AWPs showed good anticoccidial efficacy (ACI 173.9), while OF-AWPs demonstrated high efficacy, especially in birds of 28 days (ACI 180.6), improving productive parameters, reducing oocyst shedding, and enhancing the villus height to crypt depth ratio. Over a 75-day cycle, the OF-AWP increased the PI by 24.44% compared to untreated chickens (108.8 vs. 87.43). Lactic acid bacteria were the main component of the organic fermented additive. This research highlights the potential of an agroecological strategy to manage coccidiosis in Campero-INTA chickens.},
}

@article {pmid40564077,
year = {2025},
author = {Theis, BF and Park, JS and Kim, JSA and Zeydabadinejad, S and Vijay-Kumar, M and Yeoh, BS and Saha, P},
title = {Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061357},
pmid = {40564077},
issn = {2227-9059},
abstract = {The human gut microbiome is intricately linked to systemic and organ-specific immune responses and is highly responsive to dietary modulation. As metagenomic techniques enable in-depth study of an ever-growing number of gut microbial species, it has become increasingly feasible to decipher the specific functions of the gut microbiome and how they may be modulated by diet. Diet exerts both supportive and selective pressures on the gut microbiome by regulating a multitude of factors, including energy density, macronutrient and micronutrient content, and circadian rhythm. The microbiome, in turn, contributes to local and systemic immune responses by providing colonization resistance against pathogens, shaping immune cell activity and differentiation, and facilitating the production of bioactive metabolites. Emerging research has strengthened the connections between the gut microbiome and cardiometabolic disorders (e.g., cardiovascular disease, obesity, type-2 diabetes), autoimmune conditions (e.g., type-1 diabetes, rheumatoid arthritis, celiac disease), respiratory disease, chronic kidney and liver disease, inflammatory bowel disease, and neurological disorders (e.g., Alzheimer's, Parkinson's disease, depressive disorders). Here, we outline ways in which dietary factors impact host response in diseases through alterations of gut microbiome functionality and composition. Consideration of diet-mediated microbial effects within the context of the diseases discussed highlights the potential of microbiome-targeted treatment strategies as alternative or adjunct therapies to improve patient outcomes.},
}

@article {pmid40563973,
year = {2025},
author = {Qumsani, AT},
title = {Gut Microbiome Engineering for Diabetic Kidney Disease Prevention: A Lactobacillus rhamnosus GG Intervention Study.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060723},
pmid = {40563973},
issn = {2079-7737},
abstract = {The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal microflora offers novel therapeutic avenues for safeguarding renal function against diabetic complications. This investigation sought to determine the nephroprotective potential of Lactobacillus rhamnosus GG (LGG) administration in diabetic nephropathy models. Six experimental cohorts were evaluated: control, probiotic-supplemented control, diabetic, diabetic receiving probiotic therapy, diabetic with antibiotics, and diabetic treated with both antibiotics and probiotics. Diabetic conditions were established via intraperitoneal administration of streptozotocin (50 mg/kg) following overnight fasting, according to validated protocols for experimental diabetes induction. Probiotic therapy (3 × 10[9] CFU/kg, bi-daily) began one month before diabetes induction and continued throughout the study duration. Glycemic indices were monitored at bi-weekly intervals, inflammatory biomarkers, renal function indices, and urinary albumin excretion. The metabolic profile was evaluated through the determination of HOMA-IR and the computation of metabolic syndrome scores. Microbiome characterization employed 16S rRNA gene sequencing alongside metagenomic shotgun sequencing for comprehensive microbial community mapping. L. rhamnosus GG supplementation substantially augmented microbiome richness and evenness metrics. Principal component analysis revealed distinct clustering of microbial populations between treatment groups. The Prevotella/Bacteroides ratio, an emerging marker of metabolic dysfunction, normalized following probiotic intervention in diabetic subjects. Results: L. rhamnosus GG administration markedly attenuated diabetic progression, achieving glycated hemoglobin reduction of 32% compared to untreated controls. Pro-inflammatory cytokine levels (IL-6, TNF-α) decreased significantly, while anti-inflammatory mediators (IL-10, TGF-β) exhibited enhanced expression. The renal morphometric analysis demonstrated preservation of glomerular architecture and reduced interstitial fibrosis. Additionally, transmission electron microscopy confirmed the maintenance of podocyte foot process integrity in probiotic-treated groups. Conclusions: The administration of Lactobacillus rhamnosus GG demonstrated profound renoprotective efficacy through multifaceted mechanisms, including microbiome reconstitution, metabolic amelioration, and inflammation modulation. Therapeutic effects suggest the potential of a combined probiotic and pharmacological approach to attenuate diabetic-induced renal pathology with enhanced efficacy.},
}

@article {pmid40563865,
year = {2025},
author = {Zhao, L and Dong, XN and Cui, H and Sun, LY and Mu, R and Nie, M and Kang, JM and Bu, N and Zhang, YS and Qi, ZH and Li, ZX and Zhang, ZL and Zhang, XY and Ding, YL and Wang, R and Wang, Y and Liu, YH},
title = {Comparative Analysis of Microbial Communities in Each Developmental Stage of Dermacentor nuttalli in Two Regions in Inner Mongolia, China.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060613},
pmid = {40563865},
issn = {2079-7737},
support = {32260887//National Natural Science Foundation of China/ ; },
abstract = {Dermacentor is the most widely distributed tick genus in China. Dermacentor nuttalli, a predominant tick species in Inner Mongolia, can carry and transmit pathogenic microorganisms. Here, D. nuttalli were collected from Ordos (O-D) and Hinggan League (H-D) in the Inner Mongolia. D. nuttalli specimens at different developmental stages were subsequently reared under identical laboratory conditions. Sample processing, nucleic acid extraction, high-throughput sequencing, and microbial community analyses were conducted. Bacterial communities in O-D and H-D were annotated to 8 phyla, 145 genera and 16 phyla, 141 genera, respectively, with Proteobacteria showing the highest relative abundance. Differences in dominant bacterial genera were observed across developmental stages between the two regions. The most abundant bacterial species were Arsenophonus_uncultured_bacterium in O-D and Rickettsia japonica in H-D. Viral communities were annotated to 4 orders, 25 families, 61 genera, and 126 species in O-D and 6 orders, 28 families, 49 genera, 135 species in H-D. Notable difference in the viral genera with >1% abundance were identified at different developmental stages in the two regions. To our knowledge, this is the first study to compare microbial community compositions of D. nuttalli across developmental stages in two Inner Mongolian regions under under identical rearing conditions and to report the presence of R. japonica, Tacheng Tick Virus-2, and bovine viral diarrhea virus in D. nuttalli.},
}

@article {pmid40563782,
year = {2025},
author = {Hong, SH and Roh, HW and Nam, YJ and Kim, TW and Cho, YH and Son, SJ and Hong, CH},
title = {Age- and Sex-Specific Gut Microbiota Signatures Associated with Dementia-Related Brain Pathologies: An LEfSe-Based Metagenomic Study.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060611},
pmid = {40563782},
issn = {2076-3425},
support = {2024-ER0505-00//Korea National Institute of Health (KNIH)/ ; GRRCAjou2023-B02//Gyeonggi-do Regional Research Center program of Gyeonggi province/ ; RS-2022-KH130309//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; RS-2021-KH113821//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
abstract = {BACKGROUND/OBJECTIVES: Emerging evidence suggests that gut microbiota composition is influenced by both age and sex and may contribute to dementia-related brain pathologies. However, comprehensive microbiome-based biomarker discovery stratified by these factors remains limited.

METHODS: We performed a metagenomic analysis of the gut microbiota of participants stratified by sex (female vs. male) and age (<75 vs. ≥75 years). Alpha diversity (observed operational taxonomic unit, Chao1, Shannon, and Simpson) and linear discriminant analysis effect size analyses were conducted to identify dominant taxa associated with Alzheimer's pathology, vascular pathology, and dementia-related structural brain changes.

RESULTS: Females and non-elderly participants (aged < 75 years) exhibited higher gut microbial diversity, characterized by an increased abundance of Bifidobacterium spp. and Blautia spp., whereas males and elderly participants (aged ≥ 75 years) exhibited increased levels of Bacteroides spp. and Bacteroidia, which have been associated with inflammation and dysbiosis. Several taxa, including Bifidobacterium spp. were consistently identified as potential protective biomarkers, while Bacteroides spp. was linked to a higher risk of dementia-related brain pathologies.

CONCLUSIONS: Our findings demonstrate distinct age- and sex-specific differences in gut microbiota composition that may be closely associated with the pathophysiology of dementia-related brain pathologies. These results demonstrate that gut microbiota may serve as potential biomarkers for monitoring cerebrovascular conditions, potentially contributing to the development of personalized therapeutic strategies.},
}

@article {pmid40563710,
year = {2025},
author = {Kazen, AB and Umfleet, LG and Aboulalazm, FA and Cohen, AD and Terhune, S and Mason, L and Obarski, S and Franczak, M and Kindel, TL and Wang, Y and Kirby, JR},
title = {Gut Microbiota and Neurovascular Patterns in Amnestic Mild Cognitive Impairment.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060538},
pmid = {40563710},
issn = {2076-3425},
support = {1R21AG075501-24A1/NH/NIH HHS/United States ; },
abstract = {Background/Objectives: The interplay between the gut microbiome (GMB) and neurovascular function in neurodegeneration is unclear. The goal of this proof-of-concept, cross-sectional study is to identify relationships between the GMB, neurovascular functioning, and cognition in amnestic mild cognitive impairment (aMCI), the prototypical prodromal symptomatic stage of Alzheimer's disease (AD). Methods: Participants (n = 14 aMCI and 10 controls) provided fecal samples for GMB sequencing (16S and shotgun metagenomics), underwent MRI, and completed cognitive testing. Cerebral vascular reactivity (CVR), cerebral blood flow (CBF), and arterial transit time (ATT) were assessed. Statistical analyses evaluated the relationships between discriminatory taxa, cerebrovascular metrics, and cognition. Results: Sequencing revealed differentially abundant bacterial and viral taxa distinguishing aMCI from controls. Spearman correlations revealed that bacteria known to induce inflammation were negatively associated with CVR, CBF, and cognition, and positively associated with ATT. A reciprocal pattern emerged for the association of taxa with gut health. Conclusions: Our results provide preliminary evidence that pro-inflammatory gut bacterial and viral taxa are associated with neurovascular dysfunction and cognitive impairment in prodromal AD, highlighting their potential as candidate microbial biomarkers and targets for early intervention.},
}

@article {pmid40563261,
year = {2025},
author = {Gao, J and Zhu, H and Gao, J and Xu, G},
title = {Characteristics of Intestinal Microbiota and Host Gene Regulation in Coilia nasus Responding to Stress.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060626},
pmid = {40563261},
issn = {2076-3921},
support = {32302976//the National Natural Science Foundation of China/ ; BK20230179//the Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//the National Key Research and Development Program of China/ ; JSGS [2021]134//the Jiangsu Province seed industry revitalization "revealing-list" project/ ; },
abstract = {Transport stress in aquaculture poses significant challenges to fish health by inducing oxidative stress and intestinal damage. This study investigated the effects of transport stress on intestinal microbiota, host gene regulation, and metabolic responses in Coilia nasus. The fish were subjected to simulated transport conditions, followed by an analysis of their intestinal antioxidant capacity, inflammatory factors, transcriptome sequencing, metagenomic profiling, and metabolomic assays. The results revealed that transport stress significantly suppressed antioxidant enzyme activities (e.g., catalase, superoxide dismutase, glutathione peroxidase) and elevated oxidative damage (malondialdehyde, lipid peroxidation) alongside upregulating pro-inflammatory cytokines. The transcriptomic analysis identified differentially expressed genes enriched in the lipid metabolism and ferroptosis pathways, with the increased lipid peroxidation and iron overload activating ferroptosis. The metagenomic data showed an altered gut microbiota composition, including increased Aeromonas and reduced beneficial metabolites (e.g., propionic acid, bile acids). Correlation analyses linked the microbial shifts and metabolite changes to ferroptosis and barrier dysfunction. These findings demonstrate that transport stress disrupts intestinal redox balance, induces ferroptosis, and reshapes gut microbiota, collectively compromising intestinal integrity and health in C. nasus.},
}

@article {pmid40563104,
year = {2025},
author = {Trutschel, L and Kruger, B and Czaja, A and Brueck, M and Sackett, J and Druschel, G and Rowe, A},
title = {Sulfide Oxidation Products Support Microbial Metabolism at Interface Environments in a Marine-Like Serpentinizing Spring in Northern California.},
journal = {Geobiology},
volume = {23},
number = {4},
pages = {e70026},
pmid = {40563104},
issn = {1472-4669},
support = {80NSSC21K0482/NASA/NASA/United States ; },
mesh = {Oxidation-Reduction ; California ; *Sulfides/metabolism ; *Bacteria/metabolism/classification/genetics ; *Natural Springs/microbiology/chemistry ; Microbiota ; },
abstract = {Interface environments between extreme and neutrophilic conditions are often hotspots of metabolic activity and taxonomic diversity. In serpentinizing systems, the mixing of high pH fluids with meteoric water, and/or the exposure of these fluids to the atmosphere can create interface environments with distinct but related metabolic activities and species. Investigating these systems can provide insights into the factors that stimulate microbial growth, and/or what attributes may be limiting microbial physiologies in native serpentinized fluids. To this aim, changes in geochemistry and microbial communities were investigated for different interface environments at Ney Springs-a marine-like terrestrial serpentinization system where the main serpentinized fluids have been well characterized geochemically and microbially. We found that reduced sulfur species from Ney Springs had large impacts on the community changes observed at interface environments. Oxygen availability at outflow environments resulted in a relative increase in the taxa observed that were capable of sulfur oxidation, and in some cases light-driven sulfur oxidation. A combination of cultivation work and metagenomics suggests these groups seem to predominantly target sulfur intermediates like polysulfide, elemental sulfur, and thiosulfate as electron donors, which are present and abundant to various degrees throughout the Ney system. Fluid mixing with meteoric water results in more neutral pH systems which in turn select for different sulfur-oxidizing taxa. Specifically, we see blooms of taxa that are not typically observed in the primary Ney fluids, such as Halothiobacillus in zones where fluids mix underground with meteoric water (~pH 10) or the introduction of Thiothrix into the nearby creek as fluids enter at the surface (~pH 8). This work points to the potential importance of oxidants for stimulating microbial respiration at Ney Springs, and the observation that these serpentinized fluids act as an important source of reduced sulfur, supporting diverse taxa around the Ney Springs system.},
}

Oxidation-Reduction
California
*Sulfides/metabolism
*Bacteria/metabolism/classification/genetics
*Natural Springs/microbiology/chemistry
Microbiota

@article {pmid40562730,
year = {2025},
author = {Vetterli, D and Zennaro, M and Tacchini, V and Lobrinus, JA and Prendki, V and Lazarevic, V and Schrenzel, J},
title = {Next-Generation Sequencing Techniques to Diagnose Culture-Negative Subacute Native Aortic Endocarditis.},
journal = {Emerging infectious diseases},
volume = {31},
number = {7},
pages = {1478-1481},
doi = {10.3201/eid3107.241739},
pmid = {40562730},
issn = {1080-6059},
mesh = {Humans ; Male ; *Aortic Valve/microbiology ; *Endocarditis/diagnosis/microbiology ; *Endocarditis, Bacterial/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Streptococcus gordonii/genetics/isolation & purification ; Aged, 80 and over ; },
abstract = {Next-generation sequencing might improve diagnosis of infective endocarditis. A case in Switzerland was initially attributed to Solobacterium moorei bacteria. Metagenomic analysis of the affected heart valve detected Streptococcus gordonii, but not S. moorei, illustrating that the results of molecular detection can vary depending on sampling time and anatomic site.},
}

Humans
Male
*Aortic Valve/microbiology
*Endocarditis/diagnosis/microbiology
*Endocarditis, Bacterial/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
Streptococcus gordonii/genetics/isolation & purification
Aged, 80 and over

@article {pmid40562294,
year = {2025},
author = {Zhang, J and Zhan, H and Xu, H and Wang, R and Li, Z and Feng, F and Wu, H and Xu, Z and Wang, S and Guo, Y and Li, Y},
title = {Infectious agents in dilated cardiomyopathy: Genetic interactions, autoimmunity, mechanisms, and therapeutic approaches.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {103860},
doi = {10.1016/j.autrev.2025.103860},
pmid = {40562294},
issn = {1873-0183},
abstract = {Dilated cardiomyopathy (DCM) is a heterogeneous myocardial disorder characterized by left ventricular dilation and systolic dysfunction in the absence of ischemic, hypertensive, or valvular heart disease. Although its precise etiology remains unclear, it is widely recognized as a multifactorial disease arising from complex interactions between genetic predisposition and environmental triggers. Among these, infectious agents have been implicated in the pathogenesis of various subtypes, particularly inflammatory and idiopathic DCM. These agents can contribute to disease onset and progression through direct cardiomyocyte injury, immune-mediated chronic inflammation, and other yet-to-be-defined mechanisms. Infection-driven autoimmune activation is another potential key contributor to DCM, potentially linking infectious exposure to sustained myocardial damage. However, the precise role of various infectious agents in DCM initiation and progression, as well as their interactions with genetic predisposition and autoimmune activation, is inadequately understood. Improving understanding of infection-related etiologies could facilitate development of targeted therapeutic strategies; however, significant challenges persist in identifying causative and novel pathogens, and translating this into clinical practice. Therefore, this review explores the complex interactions between infectious agents, genetic predisposition, and autoimmune responses in DCM pathogenesis. We summarize current evidence on the role of infectious agents in DCM and emerging therapeutic strategies aimed at treating infection-related DCM. Finally, we outline future research directions to advance understanding of infection-associated DCM and improve patient outcomes. We reveal that a deeper understanding of host-microbe interactions, immune pathways, and genetic predisposition is essential for advancing DCM research. Furthermore, integrating genomics, metagenomics, and antibody and immunological profiling is crucial for developing personalized therapeutic strategies for this complex disease.},
}

@article {pmid40562247,
year = {2025},
author = {Yang, X and Wang, W and Liu, X and Xie, S and Feng, J and Lv, J},
title = {Nitrogen metabolism functional shifts of indigenous bacteria and effect on nitrogen removal in microalgae-based municipal wastewater treatment system across aeration modes.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132881},
doi = {10.1016/j.biortech.2025.132881},
pmid = {40562247},
issn = {1873-2976},
abstract = {Although the effect of aeration intensity on the performance of microalgae-based wastewater treatment systems has been widely studied, the impact of aeration mode has received less attention. This study explored how different aeration modes influence nitrogen metabolism in microalgae-based wastewater systems using metagenomic analysis. Both continuous aeration (CA) and intermittent aeration (IA) supported rapid bacterial growth and effective pollutant removal. Compared to CA, IA and no-aeration modes significantly enhanced bacterial nitrification and denitrification. Key nitrogen-metabolizing genera such as Paracoccus, Acidovorax, and Rhizobium played major roles in nitrogen cycling. Their abundances were closely associated with NH4[+]-N, NO3[-]-N, NO2[-]-N, total phosphorus, chemical oxygen demand, dissolved oxygen, bacterial number, and total biomass. Overall, environmental changes induced by different aeration modes significantly shaped indigenous bacterial communities involved in nitrogen metabolism, thereby influencing the abundances of nitrogen metabolism-related genes and, ultimately, nitrogen removal performance.},
}

@article {pmid40562089,
year = {2025},
author = {Gu, P and Xu, Y and Li, X},
title = {Chronic Low-Dose Cadmium Exposure Disrupts Gut Microbiota and Lipid Metabolism to Induce Liver Injury.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115603},
doi = {10.1016/j.fct.2025.115603},
pmid = {40562089},
issn = {1873-6351},
abstract = {Cadmium (Cd) is a widespread environmental pollutant linked to liver injury and metabolic dysfunction, yet the gut-liver axis mechanisms remain unclear. We investigated chronic low-dose Cd exposure (100 nM CdCl2, 12 weeks) in mice using integrated metagenomic and metabolomic profiling. Despite intact intestinal morphology, Cd exposure induced hepatic inflammation, steatosis, and elevated transaminases. Shotgun metagenomics revealed gut microbiota shifts, with enrichment of Prevotella and depletion of Turicibacter. Fecal metabolomics showed disrupted bile acid detoxification and lipid remodeling. Functional analysis indicated upregulation of microbial fatty acid metabolism genes, suggesting compensatory but dysregulated responses. These findings demonstrate that chronic Cd exposure perturbs gut microbiota and metabolic outputs, driving liver injury via microbiota-mediated mechanisms. Our study highlights the gut-liver axis as a key target of Cd toxicity and points to microbiota-based interventions as potential therapies.},
}

@article {pmid40561629,
year = {2025},
author = {Deng, Z and Xie, Y and Yu, H and Zhang, X and Tan, T and Kuang, W and Han, Z and Li, Y and Wang, H and Zhang, N and Zhang, C},
title = {Harnessing deep-sea cold seep microbiomes for reductive dehalogenation: from culturomics and genomics insights.},
journal = {Water research},
volume = {285},
number = {},
pages = {124072},
doi = {10.1016/j.watres.2025.124072},
pmid = {40561629},
issn = {1879-2448},
abstract = {Deep-sea cold seeps harbor a rich and diverse repertoire of reductive dehalogenase-encoding genes (rdhA), yet their potential for reductive dehalogenation remains largely unexplored. In this study, we investigated the microbial debromination of 2,4,6-tribromophenol (TBP) in cold seep sediment microcosms. By optimizing culture conditions with different nutrient sources and substrate concentrations, we established a highly efficient debrominating microbial consortium capable of completely degrading 50 μM TBP within 72 h. Metagenomic analysis revealed Bin3, a novel bacterium affiliated with Peptococcaceae, as a key dehalogenator harboring multiple rdhA genes. Microbial community analysis demonstrated that nutrient availability significantly influenced beta diversity (community composition) but had only a minor effect on alpha diversity. Through degradation kinetics, co-occurrence network analysis, normalized stochasticity ratio analysis, and metagenomic quantification, we found that supplementing lactate along with 0.05 % yeast extract significantly enhanced TBP degradation efficiency and facilitated the targeted enrichment of key dehalogenating microbes (with relative abundance increasing from <1 % to 32 %). Comparative genomic analysis indicated that Bin3 has undergone specific adaptations through expansion of gene families involved in pili formation, cell motility, nutrient acquisition, and diverse metabolic pathways, potentially enhancing its competitiveness in deep-sea cold seep environments. This study advances our understanding of deep-sea dehalogenating microbiomes and their adaptation to extreme environments, providing insights into their ecological significance and potential applications in pollutant bioremediation.},
}

@article {pmid40561623,
year = {2025},
author = {Zhang, Y and Wang, M and Wu, H and Cheng, W and Zhao, L and Yu, G and Ren, J},
title = {Hydroperiodic dynamics of microbial-mediated nitrogen cycling and its multi-element coupling effect in the Weihe River.},
journal = {Water research},
volume = {285},
number = {},
pages = {124057},
doi = {10.1016/j.watres.2025.124057},
pmid = {40561623},
issn = {1879-2448},
abstract = {The aquatic ecosystem is affected by both human activities and climate change, and the excessive input and imbalance of nitrogen (N) have become an environmental issue of global concern. In this study, based on metagenomic sequencing, network analysis, random forest and structural equation model were used to investigate the hydroperiod dynamics, driving mechanisms of N cycling and the coupling effects of N, carbon (C) and sulfur (S) cycling in the Weihe River. The results showed that the nitrogen concentration and pathways exhibited heterogeneity during the high, normal and low water periods. Nitrogen fixation and organic nitrogen mineralization were abundant during the high water period, and nitrification, anammox were dominant during the low water period. The co-occurrence network of bacteria and nitrogen cycling genes was dominated by positive correlations, and Limnohabitans, Flavobacterium, and Polynucleobacter showed diverse metabolic potentials. Redundancy analysis showed that nitrogen cycling genes were more sensitive to substrate changes in the high and low water periods, and dependent on basic physicochemical conditions during the normal water period. A structural equation model revealed that climatic conditions, water properties, and microbial communities had positive effects on nitrogen cycling genes (standard effects of 0.154, 0.347, 0.603), with microbial-gene collaboration driving core functionality. The strong positive correlation of the co-occurrence network of C, N, and S functional genes revealed the elemental synergies. The multi-element coupled cycling networks showed more complex and stronger interactions during the normal water periods, and the efficiency of cross-element metabolism was reduced during low water periods. This study holds significance in understanding the ecological effects of microbial-mediated nitrogen cycling and multi-element coupled cycling in rivers, and provides a theoretical basis for nutrient control in micro-polluted rivers.},
}

@article {pmid40560512,
year = {2025},
author = {Pramanik, K and Sen, A and Dutta, S and Mandal, GS and Paramanik, B and Das, A and Chatterjee, N and Ghorai, AK and Ali, MN},
title = {Microbial populations under fluoride stress: a metagenomic exploration from Indian soil.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {221},
pmid = {40560512},
issn = {1573-0972},
mesh = {*Soil Microbiology ; *Fluorides/analysis ; India ; Metagenomics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Soil/chemistry ; Fungi/genetics/classification/drug effects/isolation & purification ; Archaea/genetics/classification/drug effects/isolation & purification ; Metagenome ; Phylogeny ; Microbiota/drug effects ; },
abstract = {Fluoride exposure, even at a low concentration, significantly impairs crop growth and productivity by inhibiting metabolic enzymes and disrupting photosynthesis. Addressing this challenge, microbial de-fluoridation emerges as a vital strategy to improve soil health, enhance crop growth, and ensure agricultural sustainability. This study analyzed topsoil samples (0-0.2 m depth) from rice fields in three blocks of Purulia district, West Bengal-Arsha, Jhalda-I, and Joypur. Fluoride content in the samples ranged from 58.76 ± 0.76 mg/kg to 282.9 ± 4.9 mg/kg (total) and 1.57 ± 0.02 mg/kg to 2.97 ± 0.03 mg/kg (available). The metagenomic analysis of the collected soil samples revealed diverse microbial communities comprising archaea, bacteria, fungi, and viruses, with Actinobacteria (phylum), Hyphomicrobiales (order), and Nocardioidaceae (family) being the dominant prokaryotes. Arsha soil with comparatively low fluoride contamination exhibited the highest microbial diversity (11,891 taxa), followed by Joypur (11,528 taxa) and Jhalda-I (11,358 taxa), with Arsha showing nearly double the unique microbial taxa compared to the other locations. Clusters of orthologous groups of proteins functional analysis identified 60,898 genes in Arsha, 63,403 genes in Jhalda-I, and 73,334 genes in Joypur, while Kyoto encyclopedia of genes and genomes analysis revealed 9,385, 9,104, and 10,633 genes, respectively. Key genes associated with fluoride metabolism-inorganic pyrophosphatase, divalent metal cation transporter mntH, and putative fluoride ion transporter crcB-were abundant across all sites, highlighting the influence of fluoride on microbial community structure. This study provides the first comprehensive report on soil microbial communities in fluoride-rich areas, highlighting the potential of native fluoride-tolerant microbes to mitigate fluoride toxicity in agricultural soils and offer sustainable, microbe-based solutions to fluoride contamination.},
}

*Soil Microbiology
*Fluorides/analysis
India
Metagenomics
*Bacteria/genetics/classification/drug effects/isolation & purification
Soil/chemistry
Fungi/genetics/classification/drug effects/isolation & purification
Archaea/genetics/classification/drug effects/isolation & purification
Metagenome
Phylogeny
Microbiota/drug effects

@article {pmid40559797,
year = {2025},
author = {Hai, C and Gong, H and Xu, Y and Liu, X and Bai, C and Su, G and Yang, L and Li, G},
title = {Loss of Myostatin Alters Gut Microbiota and Carbohydrate Metabolism to Influence the Gut-Muscle Axis in Cattle.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
pmid = {40559797},
issn = {2306-7381},
support = {2023ZD0404803//Scientific and Technological Innovation 2030/ ; 32360837, 32341052//National Natural Science Foundation of China/ ; 2022JBGS0025//Inner Mongolia Open Competition Projects/ ; 2022LJRC0006//Inner Mongolia Science and Technology Leading Team/ ; 2021ZD0009, 2021ZD0008, 2022ZD0008, 2023KJHZ0028//Inner Mongolia Science and Technology Major Projects/ ; NJYT23138//Inner Mongolia Young Talents Projects/ ; 2023MS03004//Inner Mongolia Natural Science Foundation/ ; 2022ZY0212//Central Government Guides Development/ ; NK2022130203//National Agricultural Science and Technology Project/ ; XTCX2023-06//Collaborative Innovation among Universities in Hohhot/ ; JYBGCSYS2022//Ministry of Education Engineering Centre Project/ ; 2023A02011-1//Xinjiang Uygur Science and Technology Major Project/ ; },
abstract = {The gut-muscle axis plays a vital role in host metabolism and health. Although the MSTN gene is a well-known negative regulator of muscle growth, its role in intestinal function and metabolism remains unclear. Understanding this connection is crucial for revealing the systemic impact of MSTN gene editing and its potential to improve metabolic efficiency in livestock. In this study, we investigated the influence of MSTN deletion on gut microbiota composition and carbohydrate metabolism in the cecum and colon of cattle. Using integrated metagenomic, metabolomic, serum biochemical, and muscle transcriptomic analyses, we found significant alterations in microbial communities and key metabolic pathways. Hallella and Escherichia in the colon, as well as Alishewanella in the cecum, were closely linked to carbohydrate metabolism. Differential microbes and metabolites influenced key metabolic pathways, including glycolysis/gluconeogenesis and lipopolysaccharide biosynthesis. Functional gene analysis identified Bacteroides as the most critical bacterium affecting glycolysis/gluconeogenesis. Additionally, genes related to carbohydrate esterases were upregulated. These changes correlated with reduced serum glucose and insulin levels while increasing muscle gene expression related to glucose-to-lactose conversion. Overall, MSTN gene editing alters gut microbiota composition and carbohydrate metabolism in the cecum and colon, thereby influencing host glucose metabolism and energy homeostasis.},
}

@article {pmid40559651,
year = {2025},
author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M},
title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.},
journal = {Marine drugs},
volume = {23},
number = {6},
pages = {},
pmid = {40559651},
issn = {1660-3397},
support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation & purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; },
abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Polysaccharides/pharmacology/isolation & purification
*Undaria/chemistry
*Anti-Inflammatory Agents/pharmacology
Caco-2 Cells
Coculture Techniques
*Butyrates/metabolism
THP-1 Cells
Colon/microbiology/drug effects
Feces/microbiology
Cytokines/metabolism
Adult
Fatty Acids, Volatile/metabolism
Edible Seaweeds

@article {pmid40559609,
year = {2025},
author = {Mziray, SR and Githinji, G and de Laurent, ZR and Mbelele, PM and Mohammed, KS and Wadugu, BD and Grundy, BS and Heysell, SK and Mpagama, SG and Chilongola, JO},
title = {Deploying Metagenomics to Characterize Microbial Pathogens During Outbreak of Acute Febrile Illness Among Children in Tanzania.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559609},
issn = {2076-0817},
support = {TMA2016SF-1463-REMODELTZ//European & Developing Countries Clinical Trials Partnership/ ; },
mesh = {Humans ; Tanzania/epidemiology ; Child ; *Metagenomics/methods ; Male ; Female ; *Disease Outbreaks ; *Fever/microbiology/epidemiology ; Cross-Sectional Studies ; *Bacteria/genetics/classification/isolation & purification ; Child, Preschool ; Adolescent ; High-Throughput Nucleotide Sequencing ; Acute Disease ; },
abstract = {Outbreaks of infectious diseases contribute significantly to morbidity and mortality in resource-limited settings, yet the capacity to identify their etiology remains limited. We aimed to characterize microbes and antimicrobial resistance (AMR) genes in Tanzanian children affected by an acute febrile illness (AFI) outbreak using metagenomic next-generation sequencing (mNGS). A cross-sectional study was conducted on archived blood samples from children who presented with AFI between 2018 and 2019. Total nucleic acids were extracted from 200 µL of blood, and complementary DNA (cDNA), along with enriched pathogenic DNA, was sequenced using the Illumina MiSeq platform. mNGS data were analyzed using CZ-ID Illumina mNGS bioinformatics pipeline v7.0. Results were obtained from 25 participants (mean age: 11.6 years; SD ± 5), of whom 36% had a moderate to high-grade fever. The following five potential microbial causes of AFI were identified: Escherichia coli (n = 19), Paraclostridium bifermentans (n = 2), Pegivirus C (n = 2), Shigella flexneri (n = 1) and Pseudomonas fluorescens (n = 1), with E. coli being the most prevalent. Twelve AMR genes were detected, including mdtC, acrF, mdtF, and emrB. E. coli harbored most of the AMR genes previously associated with resistance to commonly used antibiotics. mNGS offers a promising complementary approach to conventional diagnostics for identifying pathogens and AMR profiles in vulnerable populations.},
}

Humans
Tanzania/epidemiology
Child
*Metagenomics/methods
Male
Female
*Disease Outbreaks
*Fever/microbiology/epidemiology
Cross-Sectional Studies
*Bacteria/genetics/classification/isolation & purification
Child, Preschool
Adolescent
High-Throughput Nucleotide Sequencing
Acute Disease

@article {pmid40559526,
year = {2025},
author = {Kim, M and Fida, M and Abu Saleh, OM and Ranganath, N},
title = {From Culture-Negative to DNA-Positive: The Molecular Revolution in Infective Endocarditis Diagnosis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559526},
issn = {2076-0817},
mesh = {Humans ; *Endocarditis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; DNA, Bacterial/genetics ; Metagenomics/methods ; },
abstract = {Infective endocarditis (IE) remains a diagnostic challenge, particularly in cases where microbiological diagnosis is not established. Advances in molecular diagnostics have expanded the ability to identify causative pathogens beyond traditional culture-based methods. This review explores the role of molecular assays, including pathogen-specific PCR, multiplex PCR, broad-range PCR, and shotgun metagenomic sequencing, in diagnosing IE. These molecular techniques enhance pathogen detection, especially in patients with prior antibiotic exposure, and improve diagnostic accuracy in culture-negative IE. Broad-range PCR assays and metagenomic sequencing offer the untargeted detection of a wide spectrum of organisms. Despite their advantages, limitations such as availability, interpretation challenges, and a lack of antimicrobial susceptibility testing remain. A multimodal approach integrating molecular diagnostics with conventional methods is essential to optimize patient management. Further research is needed to refine diagnostic algorithms and improve cost-effectiveness in clinical practice.},
}

Humans
*Endocarditis/diagnosis/microbiology
*Molecular Diagnostic Techniques/methods
DNA, Bacterial/genetics
Metagenomics/methods

@article {pmid40559436,
year = {2025},
author = {Domilescu, I and Miutescu, B and Horhat, FG and Popescu, A and Nica, C and Ghiuchici, AM and Gadour, E and Sîrbu, I and Hutanu, D},
title = {Gut-Microbiome Signatures Predicting Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer: A Systematic Review.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
pmid = {40559436},
issn = {2218-1989},
abstract = {BACKGROUND AND OBJECTIVES: Rectal cancer management increasingly relies on watch-and-wait strategies after neoadjuvant chemoradiotherapy (nCRT). Accurate, non-invasive prediction of pathological complete response (pCR) remains elusive. Emerging evidence suggests that gut-microbiome composition modulates radio-chemosensitivity. We systematically reviewed primary studies that correlated baseline or on-treatment gut-microbiome features with nCRT response in locally advanced rectal cancer (LARC).

METHODS: MEDLINE, Embase and PubMed were searched from inception to 30 April 2025. Eligibility required (i) prospective or retrospective human studies of LARC, (ii) faecal or mucosal microbiome profiling by 16S, metagenomics, or metatranscriptomics, and (iii) response assessment using tumour-regression grade or pCR. Narrative synthesis and random-effects proportion meta-analysis were performed where data were homogeneous.

RESULTS: Twelve studies (n = 1354 unique patients, median sample = 73, range 22-735) met inclusion. Four independent machine-learning models achieved an Area Under the Receiver Operating Characteristic curve AUROC ≥ 0.85 for pCR prediction. Consistently enriched taxa in responders included Lachnospiraceae bacterium, Blautia wexlerae, Roseburia spp., and Intestinimonas butyriciproducens. Non-responders showed over-representation of Fusobacterium nucleatum, Bacteroides fragilis, and Prevotella spp. Two studies linked butyrate-producing modules to radiosensitivity, whereas nucleotide-biosynthesis pathways conferred resistance. Pooled pCR rate in patients with a "butyrate-rich" baseline profile was 44% (95% CI 35-54) versus 21% (95% CI 15-29) in controls (I[2] = 18%).

CONCLUSIONS: Despite heterogeneity, convergent functional and taxonomic signals underpin a microbiome-based radiosensitivity axis in LARC. Multi-centre validation cohorts and intervention trials manipulating these taxa, such as prebiotics or live-biotherapeutics, are warranted before clinical deployment.},
}

@article {pmid40559193,
year = {2025},
author = {Anselmo, A and Rizzo, F and Gervasi, E and Corrent, L and Ciammaruconi, A and Fillo, S and Fortunato, A and Marella, AM and Costantini, S and Baldassari, L and Lista, F and Ciervo, A},
title = {Tropheryma whipplei and Giardia intestinalis Co-Infection: Metagenomic Analysis During Infection and the Recovery Follow-Up.},
journal = {Infectious disease reports},
volume = {17},
number = {3},
pages = {},
pmid = {40559193},
issn = {2036-7430},
support = {B1519 ESM4 GP//Italian General Secretariat of Defense and the National Armaments Directorate within the "Eu-ropean Biodefence Laboratory Network 2 (EBLN2) project",/ ; },
abstract = {BACKGROUND: Whipple's disease (WD) is a rare infection caused by Tropheryma whipplei. Diagnosis is challenging and requires a combination of several data sets, such as patient history, clinical and laboratory investigations, and endoscopy with histology analyses. While persistent diarrhea is a common symptom, WD can affect multiple organs.

CASE DESCRIPTION: We present the case of a 66-year-old immunocompetent patient with WD and a history of Helicobacter pylori infection who developed chronic diarrhea. Colonoscopy and histopathological analysis revealed the presence of foamy macrophages with periodic acid-Schiff-positive particles. Subsequently, molecular methods confirmed the clinical WD diagnosis and metagenomic analyses further identified a co-infection with Giardia intestinalis. The patient fully recovered after 14 months of antibiotic therapy. During pharmacological treatment, clinical and laboratory follow-ups were conducted at 6 and 12 months, and microbiome profiles were also analyzed to identify the most abundant species in the samples.

CONCLUSION: The metagenomic analyses showed the eradication of the two pathogens and a progressive restoration to a healthy/balanced status after antibiotic therapy.},
}

@article {pmid40559130,
year = {2025},
author = {Chaple-Gil, AM and Santiesteban-Velázquez, M and Urbizo Vélez, JJ},
title = {Association Between Oral Microbiota Dysbiosis and the Risk of Dementia: A Systematic Review.},
journal = {Dentistry journal},
volume = {13},
number = {6},
pages = {},
pmid = {40559130},
issn = {2304-6767},
abstract = {Background/Objectives: Growing evidence suggests that oral microbiota dysbiosis may contribute to the development of systemic conditions, including neurodegenerative diseases. This dysregulation promotes immunoinflammatory responses that are increasingly associated with dementia. This systematic review aimed to evaluate the association between oral microbiota dysbiosis and the risk of dementia in older adults. Methods: Eligible studies evaluated oral microbial composition using validated methods such as genetic sequencing, bacterial culture, or metagenomic analysis. Following PRISMA guidelines and a PICO framework, the review included cohort, case-control, and cross-sectional studies. Searches were conducted across PubMed, Scopus, Web of Science, Embase, and Cochrane Library. Two independent reviewers screened and selected studies, resolving disagreements through a third evaluator. Results: This systematic review revealed that Tannerella forsythia, Fusobacterium nucleatum, Porphyromonas, Prevotella, Leptotrichia, Fusobacteriota, Peptostreptococcaceae, and Candida spp. were consistently associated with Alzheimer's disease and mild cognitive impairment, indicating their potential role in neurodegeneration. In contrast, Streptococcus gordonii, Gemella haemolysans, Rothia, Neisseria, and Haemophilus were reduced in cognitively impaired individuals, suggesting a link with healthy cognition. Studies also showed decreased microbial diversity in Alzheimer's disease and the possible modifying effect of the APOE4 allele. Oral health interventions improved microbial composition and slowed cognitive decline, supporting the diagnostic and therapeutic potential of oral microbiota modulation. Conclusions: The findings suggest that oral microbiota dysbiosis may not only result from cognitive decline but also contribute to its pathogenesis. Future studies with larger and more diverse cohorts are recommended to validate these associations.},
}

@article {pmid40558984,
year = {2025},
author = {Crane, YM and Crane, CF and Subramanyam, S and Schemerhorn, BJ},
title = {Shotgun Metagenome Analysis of Two Schizaphis graminum Biotypes over Time With and Without Carried Cereal Yellow Dwarf Virus.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
pmid = {40558984},
issn = {2075-4450},
support = {5020-21000-000-D//USDA-ARS Research Project/ ; },
abstract = {The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes.},
}

@article {pmid40558870,
year = {2025},
author = {Abreu, CM and Carneiro, GHF and Costa, MRD and Barroso, GM and Duque, TS and Silva, JMS and Santos, JBD},
title = {Avena sativa as a Multifunctional Tool for Phytoremediation and Bioenergy Production in Sulfentrazone Contaminated Soils.},
journal = {Journal of xenobiotics},
volume = {15},
number = {3},
pages = {},
pmid = {40558870},
issn = {2039-4713},
support = {APQ 01151-23; APQ 00694-23 and, APQ 004955-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 001//National Council for Scientific and Technological Development/ ; },
abstract = {Phytoremediation using Avena sativa offers a sustainable strategy for mitigating sulfentrazone contamination while integrating bioenergy production. This study proposes an analysis of the bioenergy potential and the microbial metagenomic profile associated with Avena sativa in the presence and absence of sulfentrazone, aiming at the synergistic bioprospecting of microbial communities capable of biodegradation and remediation of contaminated environments. Using a randomized block design, we evaluated the bioenergy potential and rhizospheric microbial dynamics of A. sativa in soils with and without sulfentrazone (600 g ha[-1]). Herbicide residues were quantified via UHPLC-MS/MS, and metagenomic profiles were obtained through 16S rRNA gene and ITS region sequencing to assess shifts in rhizospheric microbiota. Microbial diversity was analyzed using the Shannon and Gini-Simpson Indices, complemented by Principal Component Analysis (PCA). Bioenergy yields (biogas and ethanol) were estimated based on plant biomass. Over 80 days, the cultivation of A. sativa promoted a 19.7% dissipation of sulfentrazone, associated with rhizospheric enrichment of plant growth-promoting taxa (Bradyrhizobium, Rhodococcus, and Trichoderma), which increased by 68% compared to uncontaminated soils. Contaminated soils exhibited reduced microbial diversity (Gini-Simpson Index = 0.7), with a predominance of Actinobacteria and Ascomycota, suggesting adaptive specialization. Despite herbicide-induced stress (39.3% reduction in plant height and 60% reduction in grain yield), the biomass demonstrated considerable bioenergy potential: 340.6 m[3] ha[-1] of biogas and 284.4 L ha[-1] of ethanol. The findings highlight the dual role of A. sativa in soil rehabilitation and renewable energy systems, supported by plant-microbe synergies. Scalability challenges and regulatory gaps in ecotoxicological assessments were identified, reinforcing the need to optimize microbial consortia and implement region-specific management strategies. These results support the integration of phytoremediation into circular bioeconomy models, balancing ecological recovery with agricultural productivity. Future research should focus on microbial genetic pathways, field-scale validation, and the development of regulatory frameworks to advance this green technology in global soil remediation efforts.},
}

@article {pmid40558084,
year = {2025},
author = {Brumfield, KD and Enke, S and Swan, BK and Carrasquilla, L and Lee, MD and Stern, DB and Gieser, L and Hasan, NA and Usmani, M and Jutla, AS and Huq, A and Caviness, K and Goodrich, JS and Bull, R and Colwell, RR},
title = {Hybridization capture sequencing for Vibrio spp. and associated virulence factors.},
journal = {mBio},
volume = {},
number = {},
pages = {e0051625},
doi = {10.1128/mbio.00516-25},
pmid = {40558084},
issn = {2150-7511},
abstract = {Proliferation of Vibrio spp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundance Vibrio spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 Vibrio spp. and 162 Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic Vibrio spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific Vibrio spp., yielded significantly greater metagenomic insight, notably a variety of other Vibrio spp., including detection of Vibrio cholerae, Vibrio fluvialis, and Vibrio aestuarianus, in addition to Vibrio parahaemolyticus and Vibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios.IMPORTANCEThe increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundance Vibrio spp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing of Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples. Results suggest pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.},
}

@article {pmid40558050,
year = {2025},
author = {Phan, J and Jain, S and Nijkamp, JF and Sasidharan, R and Agarwal, A and Bird, JK and Spooren, A and Wittwer Schegg, J and Ver Loren van Themaat, E and Mak, TN},
title = {Gut health predictive indices linking gut microbiota dysbiosis with healthy state, mild gut discomfort, and inflammatory bowel disease phenotypes using gut microbiome profiling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0027125},
doi = {10.1128/spectrum.00271-25},
pmid = {40558050},
issn = {2165-0497},
abstract = {Despite the complexity of the gut microbiome, several scores that use taxonomic characteristics exist that attempt to identify a healthy gut or gastrointestinal disease. Two systems in use are the metagenomic aerotolerant predominance index (MAPI) and keystone scores. The aim of this analysis was to compare different gut microbiome scores, specifically MAPI and a keystone species score, on two cross-sectional data sets and to investigate correlations of these scores with self-reported gut discomfort and gastrointestinal disease. The first data set is a commercial data set (Sun Genomics data set) with whole-genome shotgun sequencing samples from 5,372 customers. The second data set is curated from publicly available data (public data set) with 2,415 samples from participants in human studies with gut-related taxonomic profiles. MAPI scores and keystone species scores were calculated using standard methodology. The MAPI score was significantly lower in men for the public data set. There was a graded response for both the MAPI and keystone scores between healthy subjects, subjects with mild gastrointestinal discomfort, and patients with gastrointestinal disease: the MAPI score was higher, and the keystone score was lower in subjects with gastrointestinal discomfort or with inflammatory bowel disease patients. The keystone and MAPI scores have the potential to help identify factors associated with gut microbial dysbiosis and gastrointestinal discomfort or disease. Furthermore, given the functional link of the MAPI score to oxidative stress in the microbiome, the scores can help to identify conditions where oxidative stress is one of the hallmarks of dysbiosis.IMPORTANCEGut bacteria play a role in both mild gastrointestinal discomfort, which includes bloating and constipation, and inflammatory bowel disease. There are many different types of bacteria in the gut, and gut microbiome composition differs greatly between different people. Therefore, it is difficult to predict who has a gut microbiome associated with a healthy gut and who might develop disease or experience gut discomfort. Several scoring systems have been developed to categorize gut health states. This analysis compared two different scoring systems using data from two different sources to see how well they could identify people with gastrointestinal disease, gastrointestinal complaints, or a healthy gut. The scoring systems showed similar trends according to gut health status: groups of people with gut bacteria imbalance or gut disease had a different score than groups of people with healthy gut bacteria.},
}

@article {pmid40557789,
year = {2025},
author = {Jones, KS and Pilliod, DS and Aunins, AW},
title = {Metabarcoding Analysis of Arthropod Pollinator Diversity: A Methodological Comparison of eDNA Derived From Flowers and DNA Derived From Bulk Samples of Insects.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70003},
doi = {10.1111/mec.70003},
pmid = {40557789},
issn = {1365-294X},
support = {//U.S. Bureau of Land Management/ ; //U.S. Geological Survey/ ; },
abstract = {Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators-especially bees-are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.},
}

@article {pmid40557508,
year = {2025},
author = {Schroeder, TH and Vanwynsberghe, M and Dervishi, A and Stäudle, H},
title = {Detection of pathogenic microorganisms using metagenomic next generation sequencing for patients with suspected infection presenting in the emergency department.},
journal = {European journal of emergency medicine : official journal of the European Society for Emergency Medicine},
volume = {32},
number = {4},
pages = {288-290},
doi = {10.1097/MEJ.0000000000001239},
pmid = {40557508},
issn = {1473-5695},
}

@article {pmid40557420,
year = {2025},
author = {Girard, M and Vandamme, L and Cazaux, B and Limasset, A},
title = {OReO: optimizing read order for practical compression.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf128},
pmid = {40557420},
issn = {2635-0041},
abstract = {MOTIVATION: Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and managing the rapidly growing volume of read datasets. Although more than 50 specialized compression tools have been developed, employing methods such as reference-based approaches, customized generic compressors, and read reordering, many users still rely on common generic compressors (e.g. gzip, zstd, xz) for convenience, portability, and reliability, despite their low compression ratios. Here, we introduce Optimizing Read Order (OReO), a simple read-reordering framework that achieves high compression performance without requiring specialized software for decompression. By grouping overlapping reads together before applying generic compressors, OReO exploits inherent redundancies in sequencing data and achieves compression ratios on par with state-of-the-art tools. Moreover, because it relies only on standard decompressors, OReO avoids the need for dedicated installations and maintenance, removing a key barrier to practical adoption.

RESULTS: We evaluated OReO on both Oxford Nanopore Technologies (ONT) and HiFi genomic and metagenomic datasets of varying sizes and complexities. Our results demonstrate that OReO provides substantial compression gains with comparable resource usage and outperforms dedicated methods in decompression speed. We propose that future compression strategies should focus on reordering as a means to let generic compression tools fully exploit data redundancy, offering an efficient, sustainable, and user-friendly solution to the growing challenges of sequencing data storage.

The OReO code is open source and available at github.com/girunivlille/oreo.},
}

@article {pmid40557317,
year = {2025},
author = {Ding, Y and Jing, C and Wei, J and Wang, D and Li, W and Wang, M and Zhou, J and Qian, Q and Sun, W},
title = {Comparison of the diagnostic capabilities of tNGS and mNGS for pathogens causing lower respiratory tract infections: a prospective observational study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1578939},
pmid = {40557317},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Prospective Studies ; Female ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Sensitivity and Specificity ; Aged ; Adult ; China ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/isolation & purification/genetics/classification ; Fungi/isolation & purification/genetics ; *Molecular Diagnostic Techniques/methods ; },
abstract = {AIMS: Pathogens in lower respiratory tract infections(LRTI) are complex. Conventional microbiological testings(CMTs) are time-consuming and inaccurate. mNGS is widely used to overcome these issues. tNGS, as an emerging NGS technology, has uncertain diagnostic efficacy.

MATERIALS AND METHODS: 136 suspected LRTI patients were included from January 2022 to February 2024 from the Department of Respiratory and Critical Care Medicine at Jiangsu Province People's Hospital,China.We simultaneously submitted the bronchoalveolar lavage fluids (BALFs) for mNGS, tNGS and conventional microbial testing (CMTs) and compared the pathogen diagnostic efficacy of mNGS, and tNGS.

RESULTS: A total of 136 patients were included, and there was no statistically significant difference in the detection sensitivity(74.75% VS 78.64%, p>0,05) and specificity(81.82% vs 93,94%,p>0.05) between mNGS and tNGS. However, tNGS has a higher sensitivity(27.94% vs 17.65%,p=0.043)and specificity(88.78% vs 84.82%,p=0.048) for fungi. According to our diagnostic criteria, tNGS successfully identified 3 cases of Pneumocystis jirovecii(P. jirovecii) individually. In addition, both tNGS and mNGS detected chlamydia psittaci whereas CMTs were unable to detect it.

CONCLUSIONS: tNGS demonstrates diagnostic efficacy for pathogens in lower respiratory tract infections that is comparable to mNGS. However, tNGS has specific advantages in the detection of fungi. Considering the cost-effectiveness of tNGS, it is recommended to implement tNGS clinically for patients with lower respiratory tract infections.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology
Male
Prospective Studies
Female
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology/virology
Sensitivity and Specificity
Aged
Adult
China
*High-Throughput Nucleotide Sequencing/methods
Bacteria/isolation & purification/genetics/classification
Fungi/isolation & purification/genetics
*Molecular Diagnostic Techniques/methods

@article {pmid40557154,
year = {2025},
author = {Bai, X and Raju, SC and Knudsen, AD and Thudium, RF and Arentoft, NS and Gelpi, M and Heidari, SL and Kunisaki, KM and Kristiansen, K and Hov, JR and Nielsen, SD and Trøseid, M},
title = {Microbiome profiling reveals gut bacterial species associated with rapid lung function decline in people with HIV.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1555441},
pmid = {40557154},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *HIV Infections/microbiology/complications/physiopathology ; Middle Aged ; Dysbiosis ; *Lung/physiopathology ; *Bacteria/genetics/classification ; Adult ; *Lung Diseases/microbiology ; Respiratory Function Tests ; Aged ; },
abstract = {BACKGROUND: People with HIV (PWH) have an increased risk of pulmonary comorbidities compared to people without HIV. The gut microbiome regulates host immunity and is altered in PWH. This study aims to determine potential associations between gut microbiome, lung function decline, and airflow limitation in PWH.

METHODS: PWH from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study with available lung function testing and microbiome data were included (n=385). The gut microbiome was characterized using shotgun metagenomic sequencing. Associations between gut microbiome, rapid lung function decline, and airflow limitation were analysed in multivariable logistic regressions adjusted for traditional and HIV-associated risk factors for lung disease.

RESULTS: Several bacterial species were significantly enriched in PWH with rapid lung function decline, including opportunistic pathogenic bacterial species Bacteroides coprophilus, Klebsiella michiganensis, and Clostridium perfringens. A gut microbial dysbiosis index based on compositional changes was associated with rapid lung function decline (adjusted odds ratio (aOR) 1.18, 95% confidence interval (CI) [1.11-1.27], p<0.001), and airflow limitation (aOR 1.16, 95% CI [1.04-1.29], p=0.007) in adjusted multivariable logistic regression analyses.

CONCLUSION: Associations between the gut dysbiosis index and rapid lung function decline and airflow limitation suggest a potential role of certain gut bacterial species in the pathogenesis of pulmonary comorbidities in PWH.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*HIV Infections/microbiology/complications/physiopathology
Middle Aged
Dysbiosis
*Lung/physiopathology
*Bacteria/genetics/classification
Adult
*Lung Diseases/microbiology
Respiratory Function Tests
Aged

@article {pmid40556944,
year = {2025},
author = {Chen, Y and Fan, B and Zeng, J and Zou, Y and Tao, C and Chen, C and Zhang, P and Liang, J and Qi, F and Tang, H and Lu, L},
title = {Single-Cell RNA Transcriptomics and Multi-omics Analyses Reveal the Clinical Effects of Acupuncture on Methadone Reduction.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0741},
pmid = {40556944},
issn = {2639-5274},
abstract = {Opioid use disorders (OUDs) pose a substantial global health burden, with methadone maintenance treatment (MMT) widely adopted as an intervention; however, MMT is associated with immunosuppression, metabolic disturbances, and dysbiosis of the gut microbiota. Despite the potential of acupuncture in reducing methadone dosages and opioid addiction, the underlying biological mechanisms remain unclear. Therefore, we aimed to integrate clinical trial data with multi-omics analysis, including single-cell sequencing, transcriptomics, metabolomics, and metagenomics, to evaluate the effects of acupuncture in patients undergoing MMT. We collected peripheral blood mononuclear cells, plasma, and fecal samples from 48 MMT participants in a randomized, placebo-controlled trial. Participants were divided into acupuncture (n = 25) and sham-acupuncture (n = 23) groups. After 8 weeks of intervention, 84% of patients in the acupuncture group achieved ≥20% reduction in methadone dosage, compared to 39% in the sham-acupuncture group (P < 0.01). Our findings revealed that acupuncture may activate the defense response to viruses, with altered immune cell functions in classical monocytes correlating with clinical responses to reduced methadone doses. Acupuncture might ameliorate intestinal microbial disruptions caused by OUD by up-regulating Bilophila and modulating bile acid metabolism. Furthermore, acupuncture up-regulated galectin-9 (LGALS9)-mediated intercellular communication between classical monocytes and other immune subsets. To further validate the mechanistic link between bile acid metabolism and immune regulation, we conducted in vitro experiments using THP-1 monocytes treated with cholic acid. The results showed that bile acid exposure suppressed galectin-9 and IFN-γ expression, while low-dose bile acid (simulating acupuncture effects) partially reversed this effect. These findings support a bile acid-galectin-interferon axis that may be modulated by acupuncture in OUD. Collectively, our results provide clinical and mechanistic evidence supporting acupuncture as a potential adjunct therapy to mitigate the adverse effects of long-term opioid use.},
}

@article {pmid40556900,
year = {2025},
author = {Zhang, Q and Wang, X and Cheng, P and Huo, S and Liu, C and Yu, Z},
title = {Editorial: Recent advances in agricultural waste recycling by microorganisms and their symbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1631828},
doi = {10.3389/fmicb.2025.1631828},
pmid = {40556900},
issn = {1664-302X},
}

@article {pmid40556899,
year = {2025},
author = {Ning, T and Zheng, X and Liang, J and Wang, W and Zhang, G and Wei, X and Tan, L},
title = {Effect of different bulking agents on the quality, microbial community structure and metabolic functions during human feces composting in foam composting device.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1556537},
pmid = {40556899},
issn = {1664-302X},
abstract = {Aerobic composting represents an efficacious strategy for the disposal of human feces, yet investigations into the effects of different bulking agents on this process remain limited. This study investigated the effects of composting human feces with four types of bulking agents-wheat straw, corn straw, millet straw, and sawdust-in a foam composting device, as well as the impacts of the process on the microbial community structure and metabolic functions adopting sequencing data analysis and metagenomic analysis. The results demonstrate that aerobic composting can safely treat human feces, resulting in a mature compost product. Comparative assessments of compost quality and microbial profiles with various bulking agents indicated superior performance of corn straw compost, surpassing those produced with wheat straw, millet straw, and sawdust in terms of humification level (HA/FA = 2.9), peak temperature reached (71.2°C), composting duration (20 days), and nutrient composition (TN 42.87 g/kg). Additionally, the diversity and dominance of certain microbial colonies (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidota) were significantly higher in composts formulated with corn straw. The metagenomic data analysis reveals significant differences in the abundance of "carbon metabolism" and "microbial metabolism" among different groups, further indicating that the addition of different bulking agents affects the utilization of metabolic products, amino acids, and carbohydrates as carbon sources by microbes in human feces compost. Consequently, leveraging corn straw as a bulking agent, given its abundant availability, could potentially improve the efficiency and outcome of the human feces composting process.},
}

@article {pmid40556897,
year = {2025},
author = {Lu, L and Huang, X and Zheng, P and Wei, S and Jiao, N and Zhang, R and Li, X and Yang, Y},
title = {Two novel phages infecting Erythrobacter isolated from the epipelagic ocean.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592355},
pmid = {40556897},
issn = {1664-302X},
abstract = {Erythrobacter, an aerobic anoxygenic photoheterotrophic bacterial genus, plays a vital role in carbon and energy cycling in marine environments. However, their phage predators remain poorly understood, with only two strains previously reported. This study isolated and characterized a novel Erythrobacter phage, vB_EauS-R34L1 (R34L1), and its sub-strain vB_EauS-R34L2 (R34L2), from coastal seawater. Both phages exhibit long-tailed, icosahedral morphologies and relatively narrow but slightly different host ranges. One-step growth curve analysis revealed a 160-min latent period and burst sizes of 81 and 91 PFU/cell for R34L1 and R34L2, respectively. Genomic analysis showed that the phages possess dsDNA genomes of 56,415 bp (R34L1) and 54,924 bp (R34L2), with G + C contents of 61.60 and 61.19%, respectively. Both phages harbor a suite of unique genes, including GapR and GH19, which are crucial for host interaction and ecological functionality. Blastn analysis indicated a 99.73% genome similarity between them. Taxonomic and phylogenetic analyses positioned them in a novel viral genus cluster, Eausmariqdvirus, under the family Casjensviridae, indicating a distant evolutionary relationship with known phages. Metagenomic queries suggested that R34L1- and R34L2-like phages are exclusively abundant in temperate and tropical epipelagic zones. This study expands our understanding of Erythrobacter phages and provides insights into their ecological roles in marine ecosystems.},
}

@article {pmid40556523,
year = {2025},
author = {Huang, J and Liang, W and Zhang, R and Zhao, Y and Shi, R and Chen, X and Zheng, Y and Li, X and Liu, D and Wang, H and Liu, J and Liao, Y and Zhang, X and Jiang, Z and Fu, C and Huang, T and Shan, X and Wang, W and Bu, J and Peng, T and Shen, E},
title = {Pou2af1 Deficiency Aggravates DSS-Induced Colitis via Impaired Germinal Center Responses and Altered Gut Microbiota.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf089},
pmid = {40556523},
issn = {1536-4844},
support = {//The Affiliated Qingyuan Hospital/ ; 202301-316//Guangzhou Medical University/ ; JCXKJS2021C11//Discipline from School of Basic Medicine of Guangzhou Medical University/ ; 2021KTSCX090//Department of Education of Guangdong Province/ ; //Guangzhou Medical University 2022 Student Innovation Ability Improvement Program/ ; },
abstract = {BACKGROUND: Bob1 plays a critical role in immune system regulation, particularly in the function of B cells. Its deficiency in the context of colitis remains underexplored. This study investigates the effects of Bob1 (Pou2af1) deficiency on colitis, particularly focusing on immune responses and gut microbiota alterations in a murine model.

METHODS: In this study, we employed Pou2af1 knockout (KO) and wild-type (WT) mice to investigate the role of Bob1 in dextran sodium sulfate (DSS)-induced colitis. Colitis was induced by administering 2.5% DSS in drinking water for 7 days. Mice were monitored daily for weight loss, stool consistency, and rectal bleeding to calculate the disease activity index (DAI). Colon length was measured, and colon tissues were collected for histological analysis using hematoxylin and eosin (H&E) staining. Flow cytometry was performed to assess germinal center responses as well as the proportion of T helper (Th)1 and Th17 cells in the colonic lamina propria. Metagenomic sequencing was conducted on fecal samples to evaluate gut microbiota composition.

RESULTS: Pou2af1-deficient mice exhibited significantly exacerbated colitis compared to WT mice. This was evidenced by greater weight loss, elevated disease activity index, reduced colon length, and more severe pathological changes. Immune analysis revealed an impaired germinal center response, diminished generation of IgA⁺ plasma cells, and decreased Th17 cells in the colonic lamina propria in Pou2af1-deficient mice. Additionally, microbiota analysis indicated dysbiosis in the Pou2af1-deficient group, with a notable decrease in Bacteroides species and an increase in pro-inflammatory microbes.

DISCUSSION: The findings suggest that Pou2af1 deficiency exacerbates DSS-induced colitis by impairing immune responses, particularly the germinal center reaction, and altering gut microbiota composition. These alterations contribute to increased disease severity, highlighting the importance of Pou2af1 in maintaining intestinal immune homeostasis.},
}

@article {pmid40556381,
year = {2025},
author = {Zhao, S and Xu, Q and Li, M and Chen, J and Francis, F and Dai, X and Tan, J and Kong, Z},
title = {Exploring the Impact of Dinotefuran Residue on Microbial Community and Flavor Generation in Huangjiu Fermentation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c02308},
pmid = {40556381},
issn = {1520-5118},
abstract = {Pesticide residues create food safety hazards while negatively affecting the quality of fermented foods, but the mechanisms of the deterioration response have been a mystery. In this study, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and metagenomics sequencing analyses were employed to investigate the effect of dinotefuran residue on the aroma profile and microbial community of Huangjiu. The presence of dinotefuran led to a reduction in the overall concentration of volatile compounds, and some floral, fruity, and sweet aromas such as piperitenol, citronellyl isobutyrate, and trans-2-decenal were no longer detected. Meanwhile, the levels of certain acidic volatiles, including formic acid, propionic acid, and heptanoic acid, increased and contributed to off-flavors. Dinotefuran affected the Huangjiu flavor by modifying the abundance and structure of key genera such as Saccharomyces, Lactococcus, and Cyberlindnera. These changes were associated with disturbances in 16 KEGG tertiary metabolic pathways, including glycolysis, pyruvate metabolism, and amino acid biosynthesis. These results provided some reference for further studies on how pesticide residues affect the flavor and microbial characteristics of traditional fermented beverages like Huangjiu.},
}

@article {pmid40555957,
year = {2025},
author = {Gonçalves, OS and Fernandes, AS and de Sousa, TGG and Santana, MF and Barreto, CC},
title = {From cultivation challenges of Acidobacteriota to biotechnological promises - unveiling what is needed to fully harness their potential.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {208},
pmid = {40555957},
issn = {1573-0972},
support = {00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 5.10/2022//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 402644/2021-2//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-02381-21//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Biotechnology/methods ; Biodegradation, Environmental ; Genome, Bacterial ; Industrial Microbiology ; Genomics ; },
abstract = {Acidobacteriota are currently well-known for their ubiquity and metabolic versatility. Their environmental importance is the subject of many studies, but their biotechnological applications still need to be explored. Although they are considered hard-to-culture bacteria, many genomes are available, which reveals promising biotechnological potential. Despite these promising features, the application of Acidobacteriota in biotechnology remains underexplored. In this context, we review key findings regarding the potential applications of Acidobacteriota, emphasizing advancements derived from genomic, metagenomic, and culture-based studies. We specifically focus on their ability to produce enzymes and other bioactive molecules, their antimicrobial properties, and their potential applications in agriculture and bioremediation. Furthermore, we discuss strategies to overcome the challenges associated with culturing and manipulating these bacteria, such as heterologous expression and other emerging techniques related to -omics and computational approaches. These strategies could provide deeper insights into Acidobacteriota's metabolism, including their biosynthetic pathways and interactions within microbial consortia. Ultimately, this understanding could lead to broader applications of Acidobacteriota in environmental and industrial biotechnology.},
}

*Biotechnology/methods
Biodegradation, Environmental
Genome, Bacterial
Industrial Microbiology
Genomics

@article {pmid40555791,
year = {2025},
author = {Lin, S and Sun, Z and Zhu, X and Wang, M and Zhang, Q and Qian, J and Zhang, H and Mei, Z and Pu, Y and Kong, M and Guo, P and Zhou, X and Li, J and Sun, X and Ma, L and Zhang, X and Zhao, F and Nie, J and Hong, S and Chen, J and Wang, X and Li, X and Zheng, Y},
title = {Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40555791},
issn = {2058-5276},
abstract = {Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analysed gut metagenome data from 1,550 older individuals (aged 65-93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions.},
}

@article {pmid40555747,
year = {2025},
author = {Jarman, JB and Torres, PJ and Stromberg, S and Sato, H and Stack, C and Ladrillono, A and Pace, S and Jimenez, NL and Haselbeck, RJ and Insel, R and Van Dien, S and Culler, SJ},
title = {Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {867},
pmid = {40555747},
issn = {2399-3642},
mesh = {Humans ; *Bifidobacterium/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Dysbiosis/epidemiology/microbiology ; Infant ; United States/epidemiology ; Female ; Male ; Infant, Newborn ; Metagenomics ; },
abstract = {The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.},
}

Humans
*Bifidobacterium/isolation & purification/genetics
*Gastrointestinal Microbiome
*Dysbiosis/epidemiology/microbiology
Infant
United States/epidemiology
Female
Male
Infant, Newborn
Metagenomics

@article {pmid40555322,
year = {2025},
author = {Ying, S and Zhang, Z and Xiang, R},
title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.06.009},
pmid = {40555322},
issn = {2213-7173},
abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.

METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.

RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.

CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.},
}

@article {pmid40555025,
year = {2025},
author = {Lin, Z and Pang, S and Wu, Y and Xu, T and Zhou, YL and Li, H and Zhang, C and Qian, PY and Zhang, S},
title = {Biodiversity and nitrogen metabolism in the plastisphere impacted by urban nitrogen loading from a coastal mega-city.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139012},
doi = {10.1016/j.jhazmat.2025.139012},
pmid = {40555025},
issn = {1873-3336},
abstract = {The plastisphere, recognized for vast biomass and critical role in nitrogen cycling, is becoming a pertinent component of marine ecosystems. The relationship between plastisphere and increased nitrogen inputs from urban wastewater in coastal zones remains poorly understood. Through metagenomics, metatranscriptomics and metabolomics, this research sought to elucidate the plastisphere's reaction to elevated nitrogen loading and pinpoint key microbial resources that can be harnessed. Although the archaeal community composition within the plastisphere remains largely unchanged by nitrogen loading, bacterial diversity experiences a substantial boost, which is inversely correlated with fungal diversity. Furthermore, such conditions are associated with reduced intricate microbial interactions. Moreover, the plastisphere subjected to nitrogen loading shows an enrichment of genera and genes implicated in ammonium assimilation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Metabolomics analysis highlighted the plastisphere's accumulation of L-glutathione oxidized (GSSG) in response to nitrogen loading. The research further highlighted a quartet of microbial phyla-Actinomycetota, Bacteroidota, Cyanobacteriota, and Pseudomonadota-that not only thrive but also constitute pivotal microbial resources within the plastisphere when confronted with strong nitrogen loading. In essence, this investigation illuminates the plastisphere's biodiversity dynamics and nitrogen metabolic adjustments during augmented nitrogen loading and offers novel perspectives on taking advantage of the plastisphere's untapped microbial potential.},
}

@article {pmid40554894,
year = {2025},
author = {Zheng, SJ and Gao, XY and Diao, XH and Chen, ND},
title = {Dendrobium huoshanense improves atherosclerosis in high-fat-induced ApoE mice by regulating gut microbiota and serum metabolite profiles.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156964},
doi = {10.1016/j.phymed.2025.156964},
pmid = {40554894},
issn = {1618-095X},
abstract = {BACKGROUND: Cardiovascular diseases, particularly atherosclerosis (AS), remain leading causes of mortality, with limited effective treatments available. Dendrobium huoshanense, a traditional medicinal herb, has shown promising anti-inflammatory and antioxidant effects, but its cardiovascular protective potential remains underexplored.

PURPOSE: This study aimed to explore the protective effects of Dendrobium huoshanense polysaccharides (DHP) against AS and elucidate the underlying mechanisms involved.

METHODS: An ApoE(-/-) mice model of AS was established, and DHP was administered at different concentrations via gavage. After 14 weeks, serum and fecal samples were collected. The effects of DHP on lipid profiles, aortic plaques, matrix metalloproteinases (MMP-2 and MMP-9), and the Nrf2/HO-1 pathway were assessed. Additionally, metagenomic sequencing of fecal samples and untargeted metabolomics of serum were conducted and correlations between these findings were explored.

RESULTS: DHP improved lipid profiles, reduced reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and enhanced superoxide dismutase (SOD) activity. It stabilized aortic plaques, suppressed MMP-2 and MMP-9 overexpression, and activated the Nrf2/HO-1 pathway. DHP also promoted gut microbiota balance, increasing Mucispirillum, Bifidobacterium, and Faecalibaculum while decreasing Desulfovibrionaceae and Eubacterium. Metabolomics revealed alterations in metabolites, including taurochenodeoxycholic acid and ursocolic acid, influencing amino acid, glycerophospholipid, and bile acid metabolism.

CONCLUSIONS: DHP effectively lowers lipid levels, stabilizes aortic plaques, restores gut microbiota balance, and corrects metabolic disturbances, thereby inhibiting the progression of atherosclerosis. These findings provide a scientific basis for the clinical use of DHP in AS prevention and treatment.},
}

@article {pmid40554566,
year = {2025},
author = {Calderón-Ezquerro, MC and Brunner-Mendoza, C and Guerrero-Guerra, C and Sanchez-Flores A, A and Salinas-Peralta, I and Toriello, C and Ponce-de León, A and Ortega-Rosas C I, CI},
title = {Genetic sequencing of the airborne fungal spectrum and air quality at a public hospital in Mexico City.},
journal = {PLOS global public health},
volume = {5},
number = {6},
pages = {e0004784},
pmid = {40554566},
issn = {2767-3375},
abstract = {Hospital bioaerosols represent significant risks for nosocomial infections, contributing to patient morbidity and mortality. Exposure to these particles, particularly airborne fungal spores or propagules, can trigger adverse effects on the immune system and cause respiratory diseases. This study evaluated the airborne fungal community in a public hospital in Mexico City using a metagenomic approach, two types of aerobiological samplers as well as temperature, humidity, and suspended particle analysis. Sampling was carried out in three areas within the hospital: and outside the hospital. Airborne sampling was performed for three consecutive days, except in the EU. The results showed that using two different samplers revealed fungal diversity and composition variations. Specifically, the Cμ-Sampler captured a higher abundance and diversity of fungi than the AVPS, with Total Taxonomy Annotations at a Genus level of 626 in F1, 632 in F2, 485 in EU and 617 in OH). In the analysis of fungal presence, Ascomycota and Basidiomycota were identified as dominant phyla. Using the AVPS sampler, Ascomycota showed an overwhelming presence of 90% to 100% inside and outside the hospital, while Basidiomycota was found in a range of 1% to 10%. Using the CμS-Sampler, Ascomycota was observed to vary between 39% and 72% in areas F1 and F2 of the hospital and from 73% to 82% outside it. On the other hand, Basidiomycota presented values between 54% and 61% in F1 and from 18% to 27% outside the hospital. The predominant genera were Aspergillus, Penicillium, Cladosporium and Alternaria. The identification of twenty-seven fungal species, including opportunistic pathogens such as Aspergillus fumigatus, Penicillium chrysogenum, P. expansum, Cladosporium and Alternaria alternata, is a significant result of this study. The results revealed the diversity of fungi in the hospital environment. The proposed complementary use of different samplers could significantly optimise current surveillance methods.},
}

@article {pmid40554279,
year = {2025},
author = {Zhang, Z and Liu, C and Chen, T and Liu, F and Luo, S and Ye, J},
title = {Microorganisms and characteristic volatile flavor compounds in Luocheng fermented rice noodles.},
journal = {Food chemistry},
volume = {490},
number = {},
pages = {145133},
doi = {10.1016/j.foodchem.2025.145133},
pmid = {40554279},
issn = {1873-7072},
abstract = {The association between the appealing flavors of Luocheng fermented rice noodles (LCFN) and microbial succession during long-term fermentation is poorly understood. This study aims to elucidate the mechanism of flavor formation in LCFN during fermentation over a 30-day period. The electronic nose results showed that the LCFN underwent a flavor shift in 7-10 days with maturation in 15-30 days. This transformation was associated with the formation of characteristic flavors of (E)-2-decenal, 2-undecenal, (E, E)-2,4-decadienal, (E)-2-octenal, (E)-2-heptenal, hexanal, nonanal, and 2-pentyl furan, which had significant positive correlation with palmitic acid, oleic acid, and linoleic acid. Changes in lipase activity and the analysis of metagenomics, suggested that the characteristic flavors may be produced by Lactobacillaceae and Geotrichum via lipid metabolism. This study provides theoretical guidance for the screening of safe and efficient microorganisms for the production of flavorful rice noodles.},
}

@article {pmid40554148,
year = {2025},
author = {Xiang, J and Zhou, Z and Liu, Z and Ren, C and Xu, Y},
title = {Constructing simplified microbial consortia that couple lactic acid and ethanol utilization to highly produce caproic acid from liquor-making wastewater.},
journal = {Water research},
volume = {284},
number = {},
pages = {123973},
doi = {10.1016/j.watres.2025.123973},
pmid = {40554148},
issn = {1879-2448},
abstract = {Converting biodegradable carbon in wastewater into medium-chain fatty acids (MCFAs) through stable microbiota is highly attractive. In this study, we utilized a top-down approach for constructing MCFA-producing microbial consortia. Specifically, an enrichment and plating-screening strategy employing lactic acid and ethanol as selective carbon sources was applied to isolate simplified caproic acid-producing microbial consortia from liquor-making pit mud. The representative microbial consortium SimpCom3 demonstrated high level of caproic acid production (14.62 ± 0.48 g/L) in a semi-synthetic medium, significantly outperforming consortium SimpCom1 (5.96 ± 0.11 g/L) and consortium SimpCom2 (9.63 ± 0.16 g/L). This performance of microbial consortium SimpCom3 was attributed to its ability to co-utilize lactic acid and ethanol, produce fewer odd-chain fatty acids byproducts, and maintain pH self-regulation between 6.45 and 8.29. Metagenomic analyses revealed the dominance of Clostridium kluyveri (30.69 %-50.46 %), C. butyricum (6.71 %-13.98 %) and C. tyrobutyricum (37.11 %-58.07 %) in consortium SimpCom3, which synergistically converted lactic acid and ethanol to caproic acid via reverse β-oxidation. Stable performance over 56 days of cyclic-batch fermentation processes confirmed the robustness of consortium SimpCom3. When applying consortium SimpCom3 to unsterilized liquor-making wastewater in a fermenter with a fed-batch approach, 22.13 g/L caproic acid was produced with 66.38 % selectivity, and microbial dynamics analysis demonstrated the consortium's high adaptability to real wastewater. Metabolic analysis based on high-quality assembly metagenomes (HQ-MAGs) revealed a novel cooperative metabolism: cross-feeding between Clostridium kluyveri (which utilizes ethanol and produces caproic acid) and lactate-utilizing butyrate producers maintained consortium stability and enhanced caproic acid production. Crucially, the decarboxylation of lactic acid counteracted acidification caused by ethanol-driven caproic acid synthesis, enabling self-regulated pH stability within the simplified microbiome system. Together, this study presents a simplified microbial consortium construction method for caproic acid production from liquor-making wastewater, overcoming the limitations of synthetic co-cultures and enhancing the viability of chain-elongation biorefineries in wastewater treatment.},
}

@article {pmid40554092,
year = {2025},
author = {Choi, BS and Holm, JB and Brejnrod, A and Fjære, E and Xia, Z and Allingbjerg, ML and Larsen, IS and Kristensen, DM and Dall, M and Myrmel, LS and Koch, J and Danneskiold-Samsøe, NB and Kalliokoski, O and Treebak, JT and Xiao, L and Hansen, AK and Sørensen, H and Madsen, L and Arumugam, M and Kristiansen, K and Jensen, BAH},
title = {Housing matters: experimental variables shaping metabolism in obese mice.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102190},
doi = {10.1016/j.molmet.2025.102190},
pmid = {40554092},
issn = {2212-8778},
abstract = {Diet-induced obesity in mice is an important model for investigating host-diet interactions as well as dietary and pharmacological treatments of metabolic diseases. Experimental reproducibility is, however, a recurrent challenge. To determine key controllable experimental drivers of mouse metabolism, we distributed 338 C57BL/6JBomTac mice (males and females) into six research units across two countries, divided them into a variety of housing conditions (i.e., diets, cage types, temperatures, group-housing vs. single-housing) and kept 26 reference mice at the vendor. We applied linear mixed models to rank the influence of each variable on metabolic phenotype (i.e., body weight gain, glucose intolerance, liver, and visceral adipose tissue weight). Group-housing was the most potent driver of metabolic dysfunction apart from sex and diet. Accordingly, single-housed mice exhibited reduced weight gain (∼50%), increased energy expenditure, and diminished respiratory exchange ratio concomitant with improved glucose tolerance (∼20%) compared to their group-housed counterparts. Our results may aid in clarifying the impact of experimental design and promote rational, transparent reporting to increase reproducibility.},
}

@article {pmid40554085,
year = {2025},
author = {Chen, H and Ruan, F and Wu, W and Liu, J and Wang, Z and Xu, X and Liu, Y and Wu, S and Zhou, J and Ma, J},
title = {Pulmonary fungal infection caused by Rhizopus microsporus in type II diabetic patient:A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116953},
doi = {10.1016/j.diagmicrobio.2025.116953},
pmid = {40554085},
issn = {1879-0070},
abstract = {Pulmonary fungal infections are invasive fungal diseases with high mortality, particularly in immunocompromised patients. This case report describes a patient with type II diabetes mellitus who developed a pulmonary fungal infection. The patient presented with a one-week history of paroxysmal cough and expectoration of yellowish-white, purulent sputum following exposure to cold temperatures. Initial empirical antiviral therapy failed to yield any clinical improvement Subsequent chest computed tomography (CT) scans revealed irregular areas of increased density in the left lower lung, while metagenomic next-generation sequencing (mNGS) identified the infection as caused by Rhizopus microspores. The patient was treated with intravenous amphotericin B and showed clinical improvement without side effects during follow-up. This case highlighted the potential of mNGS as an adjunctive diagnostic tool for rare pathogen infections, especially in immunocompromised patients where conventional microbiological methods may be inconclusive.},
}

@article {pmid40554061,
year = {2025},
author = {Yang, W and Zou, P and He, S and Cui, H and Yang, Z and An, H and Chen, Q and Huang, W and Guo, H and Liu, J and Ling, X and Cao, J and Ao, L},
title = {Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.06.037},
pmid = {40554061},
issn = {2090-1224},
abstract = {INTRODUCTION: Perfluorooctane sulfonic acid (PFOS) as a global contaminant is ubiquitously presented in the environmental media and human body. The association between PFOS exposure and reduced male fertility has been recently discovered. However, the relevant mechanism remains unexplored.

OBJECTIVES: Our study aimed to investigate the effect and mechanism of PFOS exposure on male reproductive function.

METHODS: In a murine PFOS exposure model, single-nucleus transcriptome sequencing was performed to delineate the transcriptomic landscape of mouse testes at the single-cell resolution. We examined the serum metabolomic profile and conducted in-depth analysis of hepatic transcriptome datasets to explore the metabolic connections between liver and testis under PFOS exposure. Through integrating chenodeoxycholic acid intervention, fecal microbiota transplantation (FMT), metagenomic sequencing, testicular metabolome, Ligilactobacillus murinus (L. murinus) metabolome, and administration of L. murinus, we confirmed the role of the liver-gut microbiota-testis axis and screened the critical gut microbiota involved in PFOS-mediated spermatogenic disorders.

RESULTS: The results showed that PFOS exposure led to spermatogenic arrest and abnormal spermatogenic microenvironment in the mouse testis. The PFOS-repressed hepatic chenodeoxycholic acid (CDCA) synthesis contributed to the reduced serum/testicular levels of essential fatty acid (linoleic acid) and lipid-soluble vitamins (retinol, vitamin D3), which was responsible for the spermatogenic arrest. Beyond this, PFOS-mediated impaired CDCA production decreased the abundance of gut L. murinus, which affected spermatogenesis through the potential involvement of aspartic acid metabolism. For the first time to our knowledge, we comprehensively assessed the effects of PFOS exposure on the spermatogenic process and elucidated the unrecognized role of liver-gut microbiota-testis axis in PFOS-induced abnormal spermatogenesis.

CONCLUSIONS: The unveiled organ crosstalks provide new insights into the metabolism-disrupting properties, hepatotoxicity, and reproductive toxicity of PFOS, which may facilitate the development of molecule-, metabolite-, and microbe-based strategies for PFOS-induced metabolic diseases and reproductive disorders.},
}

@article {pmid40553742,
year = {2025},
author = {Frutkoff, YA and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D},
title = {Whole food diet induces remission in children and young adults with mild-moderate Crohn's disease and is more tolerable than exclusive enteral nutrition: a randomized controlled trial.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.06.011},
pmid = {40553742},
issn = {1528-0012},
abstract = {BACKGROUND: Tasty&Healthy (T&H) is a whole-food diet for Crohn's disease (CD), which excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized-controlled trial comparing tolerability and effectiveness of T&H vs. exclusive enteral nutrition (EEN).

METHODS: Patients with biologic-naive mild-moderate CD aged 6-25 years were randomized to either T&H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Non-Invasive (MINI) index, calprotectin, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Fecal microbiome was analyzed by metagenomics at baseline, week-4 and week-8. Data were analyzed by the intention-to-treat approach unless specified otherwise.

RESULTS: Among 83 included patients (41 T&H, 42 EEN; mean age 14.5±3.7 years), 88% tolerated T&H vs. 52% for EEN (aOR 7.7 [95%CI 2.4-25]; p<0.001). Calprotectin, CRP and ESR decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of T&H group vs. 38% of the EEN group (aOR 2.5 [0.98-6.3], p=0.1; per-protocol: 67% vs. 76%; p=0.47). Calprotectin <250μg/g was achieved in 34% vs. 33% (aOR 0.97 [0.37-2.6], p=0.84) and MINI<8 in 44% vs. 31% (aOR 1.8 [0.7-4.5]; p=0.33). Microbiome α-diversity improved in the T&H arm and declined in the EEN arm, showing superior species richness at both week-4 and week-8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&H and increased in EEN (q<0.001).

CONCLUSIONS: T&H demonstrated better tolerability than EEN for inducing remission in mild-to-moderate CD, while positively affecting the microbiome (TASTI-MM, NCT#04239248).},
}

@article {pmid40553325,
year = {2025},
author = {Mukhopadhyay, S and Ulaganathan, N and Dumpuri, P and Aich, P},
title = {Integrative AI-Based Approaches to Connect the Multiome to Use Microbiome-Metabolome Interactive Outcome as Precision Medicine.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2952},
number = {},
pages = {15-37},
pmid = {40553325},
issn = {1940-6029},
mesh = {Humans ; *Precision Medicine/methods ; *Metabolomics/methods ; *Metabolome ; Metagenomics/methods ; *Microbiota ; *Artificial Intelligence ; Computational Biology/methods ; Gastrointestinal Microbiome ; },
abstract = {In the era of Genome-Wide Association Studies (GWAS), biologists have unprecedented access to vast datasets, mirrored in the wealth of information from various omics studies, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics. Integrating diverse data sources has emerged as crucial in unravelling the intricacies of biological processes. This chapter delves into our method for merging various omics methodologies, emphasizing metabolomics and metagenomics data. A powerful strategy addresses data processing challenges and opens new avenues for personalized microbiome-based interventions. The combined analysis of host and microbial metabolomics and metagenomics data has significantly advanced our understanding in diagnosing and treating conditions such as inflammatory bowel disease and irritable bowel syndrome. Metabolic signatures in biological fluids and their microbial counterparts serve as indicators, differentiating health from disease. The sheer volume of data demands sophisticated automated tools for processing and interpretation. Recognizing this need, integrating artificial intelligence (AI) and data science has become increasingly prominent. In this chapter, we combine microbiome and metabolome analyses through publicly available models to elucidate the correlations between microbial and metabolic profiles. By harnessing AI models across various omics data sources, this chapter bridges the gap between data acquisition and clinical applications, paving the way for personalized interventions and optimizing individual health.},
}

Humans
*Precision Medicine/methods
*Metabolomics/methods
*Metabolome
Metagenomics/methods
*Microbiota
*Artificial Intelligence
Computational Biology/methods
Gastrointestinal Microbiome

@article {pmid40552763,
year = {2025},
author = {Claypool, J and Lindved, G and Myers, PN and Ward, T and Nielsen, HB and Blount, KF},
title = {Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrent Clostridioides difficile infection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520412},
doi = {10.1080/19490976.2025.2520412},
pmid = {40552763},
issn = {1949-0984},
mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; *Clostridioides difficile/physiology ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Recurrence ; Aged ; },
abstract = {Live microbiota therapies have shown promise in many gastrointestinal diseases, including in the prevention of recurrent Clostridioides difficile infections (rCDI); however, frameworks for their pharmacokinetic and pharmacodynamic analysis are not fully established. Fecal microbiota, live-jslm (RBL) is the first microbiota-based product approved by the US Food and Drug Administration for the prevention of rCDI and was superior to placebo in the PUNCH™ CD3 phase 3 clinical trial (NCT03244644). In this analysis, deep shotgun metagenomic sequencing was used to assess changes in gut microbiome compositions of participants and engraftment of bacterial clonal populations (i.e. strains) from RBL to recipients. Among RBL responders, gut microbiota shifted toward compositions that resembled healthy donors as early as 1 week after RBL administration; the resulting microbiota compositions included clonal populations that engrafted from RBL to recipients. Engraftment was higher in RBL responders compared with non-responders, and many clonally engrafted populations persisted for ≥ 6 months. Bacteroidia species were among the most effectively engrafted species from RBL. This study utilizes data from a large clinical trial to establish a method with high specificity for exploring clonal engraftment from microbiota-based treatments to facilitate future pharmacokinetic and pharmacodynamic analyses.Clinicaltrials Registration: NCT03244644.},
}

Humans
*Clostridium Infections/therapy/microbiology
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
*Feces/microbiology
Male
*Clostridioides difficile/physiology
Female
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Adult
Recurrence
Aged

@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}

@article {pmid40551486,
year = {2025},
author = {Yan, F and Wu, SM and Yuan, WQ and Yang, YH and Zhu, H and Cui, DJ},
title = {Thermophiles, Thick-Walled Bacteria, and Pseudomonads in High-Altitude Gut Microbiota.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.17032},
pmid = {40551486},
issn = {1440-1746},
support = {qiankehe2018-5764-11//Cultivation Fund of National Natural Science Foundation/ ; gzwkj2025-268//Science and Technology Fund of Guizhou provincial health committee/ ; },
abstract = {BACKGROUND AND AIM: High-altitude environments are characterized by low oxygen and reduced low pressure, which impose significant physiological challenges on organisms. Among various adaptive systems, the intestinal flora plays a crucial role in maintaining gut health and barrier integrity function under such conditions. This study aimed to elucidate the regulatory mechanisms of intestinal flora in high-altitude environments, focusing on downregulating intracellular Bone Morphogenetic Protein 4 (BMP4) to influence glycolysis metabolism, thereby affecting intercellular communication of the intestinal mucosal barrier and matrix remodeling.

METHODS: High-altitude mouse intestinal flora composition and function were analyzed using 16S rRNA and metagenomic sequencing. Additionally, single-cell sequencing was employed to examine cell population communication and gene expression differences between normal and high-altitude mouse intestinal tissues.

RESULTS: Single-cell sequencing showed significantly reduced interactions between intestinal fibroblasts and epithelial cells in high-altitude mice, accompanied by a marked increase in BMP4 expression. Overexpression of BMP4 was found to activate the glycolysis pathway. Gut microbiota metabolites, including secondary bile acids, lactic acid, and butyrate, exhibited protective effects on hypoxia-induced intestinal mucosal barrier injury, with butyrate showing the most prominent effect. Under hypoxic conditions, butyrate suppressed the BMP4/glycolysis pathway, thereby alleviating hypoxia-induced intestinal mucosal barrier damage.

CONCLUSION: This study uncovered a novel mechanism by which the gut microbiota in high-altitude environments modulate glycolysis metabolism through BMP4 downregulation, thereby affecting intercellular communication and matrix remodeling within the intestinal mucosal barrier.},
}

@article {pmid40551155,
year = {2025},
author = {Mizsei, E and Sos, T and Móré, A and Wenner, B and Rák, G and Mebert, K},
title = {Restriction times on the rise: mechanistic modelling of activity time of grassland vipers (Vipera spp.) in the face of climate change.},
journal = {Frontiers in zoology},
volume = {22},
number = {1},
pages = {10},
pmid = {40551155},
issn = {1742-9994},
support = {LIFE18 NAT/HU/000799//LIFE programme/ ; },
abstract = {Climate change threatens species adapted to cool alpine environments, particularly ectotherms like reptiles. Small-sized grassland specialist vipers inhabit such environments in Eurasia and are highly susceptible to overheating and dehydration as global temperature rises. This study modelled activity restriction times, defined as hours when environmental temperatures exceed the thermal tolerance (i.e. not available for essential activities) of the species, for 20 grassland viper taxa to assess climate change impacts. Under future conditions, hours of activity restriction are projected to increase by 21% by the SSP1-2.6 scenario, and by 52.1% by the SSP5-8.5 scenario. Elevation and latitude significantly influenced restriction time changes, with high-altitude and northern populations predicted to be most affected. The taxa Vipera graeca and Vipera ursinii moldavica are expected to experience the greatest increase in restriction times. Despite warmer conditions potentially increasing hours within preferred thermal ranges, vipers are unlikely to exploit lower-elevation habitats due to competition and ecological constraints. These findings emphasise the urgent need for conservation strategies, including habitat preservation and connectivity, to mitigate the adverse effects of climate change on grassland vipers, particularly the most vulnerable populations.},
}

@article {pmid40550680,
year = {2025},
author = {Lin, M and Hu, L and Hao, L and Wang, Z},
title = {[Microbiome and its genetic potential for carbon fixation in small urban wetlands].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2415-2431},
doi = {10.13345/j.cjb.240399},
pmid = {40550680},
issn = {1872-2075},
mesh = {*Wetlands ; *Microbiota/genetics ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; China ; Cities ; Geologic Sediments/microbiology ; Archaea/genetics/metabolism/classification ; Metagenomics ; Metagenome ; },
abstract = {Small urban wetlands are widely distributed and susceptible to human activities, serving as important sources and sinks of carbon. Microorganisms play a crucial role in carbon cycle, while limited studies have been conducted on the microbial diversity in small urban wetlands and the functions of microbiome in carbon fixation and metabolism. To probe into the microbiome-driven carbon cycling in small urban wetlands and dissect the composition and functional groups of microbiome, we analyzed the relationships between the microbiome structure, element metabolism pathways, and habitat physicochemical properties in sediment samples across three small wetlands in Huzhou City, and compared them with natural wetlands in the Zoige wetland. High-throughput sequencing of 16S rRNA gene amplicons and metagenomics was employed to determine the species and functional groups. Sixty medium to high-quality metagenome-assembled genomes (MAGs) were constructed, including 55 bacterial and 5 archaeal taxa, and their potential in driving elemental cycles were analyzed, with a focus on carbon fixation. Several bacterial species were found to encode a nearly complete carbon fixation pathway, including the Calvin cycle, the reductive tricarboxylic acid cycle, the Wood-Ljungdahl pathway, and the reductive glycine pathway. There were several potential novel carbon-fixing bacterial members, such as those belonging to Syntrophorhabdus (Desulfobacterota) and UBA4417 (Bacteroidetes), which had high relative abundance in the wetland microbiome. Unveiling the genetic potential of these functional groups to facilitate element cycling is of great scientific importance for enhancing the carbon sequestration capacity of small urban wetlands.},
}

*Wetlands
*Microbiota/genetics
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification
RNA, Ribosomal, 16S/genetics
China
Cities
Geologic Sediments/microbiology
Archaea/genetics/metabolism/classification
Metagenomics
Metagenome

@article {pmid40550672,
year = {2025},
author = {Wang, X and Wang, S and Yang, K and Tang, Y and Xu, Y and Shen, Q and Wei, Z},
title = {[Methodological breakthroughs and challenges in research of soil phage microecology].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2310-2323},
doi = {10.13345/j.cjb.250258},
pmid = {40550672},
issn = {1872-2075},
mesh = {*Bacteriophages/genetics/isolation & purification/physiology ; *Soil Microbiology ; Ecosystem ; Microbiota ; Metagenomics/methods ; },
abstract = {Phages, as obligate bacterial and archaeal parasites, constitute a virus group of paramount ecological significance due to their exceptional abundance and genetic diversity. These biological entities serve as critical regulators in Earth's ecosystems, driving biogeochemical cycles, energy fluxes, and ecosystem services across terrestrial and marine environments. Within soil microbiomes, phages function as microbial "dark matter," maintaining the soil-plant system balance through precise modulation of the microbial community structure and functional dynamics. Despite the growing research interests in soil phages in recent years, the proportion of such studies in environmental virology remains disproportionately low, which is primarily attributed to researchers' limited familiarity with the research methodologies for phage microecology, incomplete technical frameworks, and inherent challenges posed by soil environmental complexity. To address these challenges, this review synthesizes cutting-edge methodologies for soil phage investigation from four aspects: (1) tangential flow filtration (TFF)-based phage enrichment strategies; (2) integrated quantification approaches combining double-layer agar plating, epifluorescence microscopy, and flow cytometry; (3) multi-omics analytical pipelines leveraging metagenomics and viromics datasets; and (4) computational frameworks merging machine learning algorithms with eco-evolutionary theory for deciphering phage-host interaction networks. Through comparative analysis of methodological principles, technical merits, and application scopes, we establish a comprehensive workflow for soil phage research. Future research in this field should prioritize: (1) construction of soil phage resource libraries, (2) exploration of RNA phages based on transcriptomes, (3) functional characterization of unknown genes, and (4) deep integration and interaction validation of multi-omics data. This systematic methodological synthesis provides critical technical references for addressing fundamental challenges in characterizing soil phages regarding the community structure, functional potential, and interaction mechanisms with hosts.},
}

*Bacteriophages/genetics/isolation & purification/physiology
*Soil Microbiology
Ecosystem
Microbiota
Metagenomics/methods

@article {pmid40550235,
year = {2025},
author = {Howard-Jones, AR and Mahar, JE and Proudmore, K and Butel-Simoes, GI and Eden, JS and Neave, MJ and Mileto, P and Hueston, L and Freeman, K and Ellem, J and Caly, L and Sikazwe, C and Levy, A and Thomas, A and Taylor, C and Kurucz, N and Smyth, K and Jennison, A and Moore, P and Wright, R and Mee, PT and Brischetto, A and Feldman, R and Dwyer, DE and O'Sullivan, MV and Mahony, AA and Warner, MS and Papanicolas, LE and Schlebusch, S and Lim, CK and Baird, R and Speers, D and Williams, DT and Currie, BJ and Kok, J},
title = {Diagnostic and phylogenetic perspectives of the 2023 Murray Valley encephalitis virus outbreak in Australia: an observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101089},
doi = {10.1016/j.lanmic.2025.101089},
pmid = {40550235},
issn = {2666-5247},
abstract = {BACKGROUND: An outbreak of Murray Valley encephalitis virus (MVEV), the largest since 1974, was observed in Australia between Jan 1 and July 31, 2023. This study aims to characterise the utility of diagnostic platforms, testing algorithms, and genomic characteristics of MVEV to facilitate a comprehensive framework for MVEV testing and surveillance in the outbreak setting.

METHODS: In this observational study, we assessed flavivirus diagnostics for all patients with suspected Murray Valley encephalitis in Australia from Jan 1 to July 31, 2023. We included all patients with confirmed Murray Valley encephalitis, probable Murray Valley encephalitis, or acute unspecified flavivirus infection using the Communicable Diseases Network Australia case definition. Cases were excluded if an alternative diagnosis was identified. We collected blood, serum, cerebrospinal fluid, brain tissue, urine, or a combination of these samples, as appropriate and at the discretion of the treating clinician. We conducted multimodal diagnostic testing, which included flavivirus-specific serological and nucleic acid amplification testing. Metagenomic next-generation sequencing, including next-generation deep sequencing, target-enrichment, and targeted amplification, was conducted on human and representative mosquito-derived samples obtained from established mosquito population surveillance programmes for phylogenetic analysis.

FINDINGS: 27 patients with encephalitis were assessed for MVEV between Jan 1, 2023, and July 31, 2023, 23 (85%) of whom fulfilled national case definitions for confirmed Murray Valley encephalitis. Patient ages ranged from 6 weeks to 83 years (median 62·0 years [IQR 31·0-67·5]) and patients were mostly male (21 [78%] male patients and six [22%] female patients). Incidence varied widely by geographical region and was highest in the Northern Territory (32·0 per 1 000 000 population). Diagnostic specimen collection generally occurred promptly (median 6·0 days [IQR 4·0-14·5] from symptom onset to diagnostic specimen collection). In seven patients, case assignation relied on convalescent serum samples to assess for seroconversion or an appropriate rise in antibody titre (to four times the initial value or greater), or both. MVEV-specific IgM was detectable in serum samples of 17 (81%) of 21 patients tested by day 7 and MVEV IgG or total antibody (TAb) were detected in 18 (100%) of 18 patients tested by day 30. MVEV-specific IgM (or TAb) and MVEV RNA were detected in cerebrospinal fluid collected within 14 days of symptom onset in nine (39%) of 23 patients and seven (28%) of 25 patients, respectively. Phylogenetic analysis revealed two circulating MVEV genotypes, G1A and G2, in mosquitoes and humans in 2023. In southeast Australia, only G1A was detected and probably introduced from enzootic foci in northern Australia.

INTERPRETATION: This study provides a comprehensive overview of the diagnostic workflows and phylogenetic evaluations used during the 2023 MVEV outbreak in Australia, emphasising the importance of a multimodal approach for accurate and timely confirmation of flavivirus infection. Further One Health surveillance for MVEV and other zoonotic flaviviruses is key, given potential expanded ecological niches in the context of episodic climatic events.

FUNDING: None.},
}

@article {pmid40549455,
year = {2025},
author = {Goryanin, I and Sorokin, A and Seitov, M and Emilov, B and Iskakov, M and Goryanin, I and Osmonov, B},
title = {Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.},
journal = {Journal of integrative bioinformatics},
volume = {},
number = {},
pages = {},
pmid = {40549455},
issn = {1613-4516},
abstract = {This study investigates the gut microbiome and metabolome of asthma patients treated with inhaled corticosteroids (ICS), some of whom experience adverse side effects. We analyzed stool samples from 24 participants, divided into three cohorts: asthma patients with side effects, those without, and healthy controls. Using next-generation sequencing and LC-MS/MS metabolomics, we identified significant differences in bacterial species and metabolites. Multi-Omics Factor Analysis (MOFA) and Global Sensitivity Analysis-Partial Rank Correlation Coefficient (GSA-PRCC) provided insights into key contributors to side effects, such as tryptophan depletion and altered linolenate and glucose-1-phosphate levels. The study proposes dietary or probiotic interventions to mitigate side effects. Despite the limited sample size, these findings provide a basis for personalized asthma management approaches. Further studies are required to confirm initial fundings.},
}

@article {pmid40549420,
year = {2025},
author = {Podowski, JC and Forrester, S and Yaqub, T and Aqel, A and Abu Lubad, M and Mukhtar, N and Waqar Aziz, M and Sardar, N and Bin Aslam, H and Pervaiz, H and Wolfe, AJ and Schabacker, DS},
title = {Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan.},
journal = {Microbial genomics},
volume = {11},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001422},
pmid = {40549420},
issn = {2057-5858},
mesh = {*Bacillus anthracis/genetics/classification/isolation & purification ; Pakistan ; *Anthrax/microbiology/epidemiology ; Animals ; *Genome, Bacterial ; Humans ; Genomics/methods ; Phylogeny ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.},
}

*Bacillus anthracis/genetics/classification/isolation & purification
Pakistan
*Anthrax/microbiology/epidemiology
Animals
*Genome, Bacterial
Humans
Genomics/methods
Phylogeny
Computational Biology/methods
High-Throughput Nucleotide Sequencing

@article {pmid40548737,
year = {2025},
author = {Ren, G and Ma, L and Yan, C and Xue, Q and Zhang, H and Wang, W and Ren, X and Lei, Y and Li, S and Liu, Y and Zheng, Q and Wei, S and Zhang, Y and Wang, X},
title = {Application of targeted metagenomic next-generation sequencing in pneumonia patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0171324},
doi = {10.1128/spectrum.01713-24},
pmid = {40548737},
issn = {2165-0497},
abstract = {After the coronavirus disease 2019 (COVID-19) pandemic, the incidence rate of mixed infections, especially in critically ill patients with severe pneumonia, increases due to the immunity gap and has also been proven to be associated with mortality, increasing the difficulty in accurate and rapid diagnoses. Here, we evaluated the performance of targeted metagenomic next-generation sequencing (mNGS), including capture hybridization-based mNGS (chNGS) and multiplex PCR-based targeted mNGS (tNGS), in diagnosing pneumonia. Patients admitted to the Pulmonary and Critical Care Medicine, Beijing Aerospace General Hospital, and diagnosed as suspected pulmonary infections from April 2022 to March 2024 were retrospectively evaluated, and 110 patients were finally enrolled. According to the final comprehensive clinical diagnoses, there were 99 patients diagnosed with definite infectious diseases. Single infections accounted for 58.6% of these patients (58/99), while mixed infections occurred in about half of these patients (41.4%, 41/99) and were found in most of the death cases. Pseudomonas aeruginosa (n = 22), Pneumocystis jirovecii (n = 15), and severe acute respiratory syndrome coronavirus 2 (n = 13) were found to be the most common bacterial, fungal, and viral pathogens, respectively. Taking final comprehensive clinical diagnoses as the reference standard, the total coincidence rate (TCR) of chNGS can reach up to 64.1% (95% confidence interval [CI], 54.8%-73.3%), while the TCR of conventional methods was only 39.8% (95% CI, 30.4%-49.3%). The performance of tNGS was slightly superior to that of chNGS, while chNGS yielded more false-negative results, especially for viral detection. Additionally, chNGS combined with tNGS can improve the TCR to 81.3% (95% CI, 62.1%-100.0%).IMPORTANCEThis is the first report on evaluating the performance of capture hybridization-based metagenomicnext-generation sequencing (chNGS), multiplex PCR-based targeted mNGS (tNGS), and conventional methods in diagnosing pneumonia. Our findings emphasized the importance of chNGS and tNGS in diagnosing, managing, and ruling out infections, and an era of widespread application of regional tNGS in monitoring and diagnosing infections with high sensitivity and low economic burden on patients can be expected.},
}

@article {pmid40548531,
year = {2025},
author = {Zhang, J and Li, Y and Zheng, J and Ding, X},
title = {Metagenomic Next-Generation Sequencing Provides a Reliable Method for Early Diagnosis of Pneumocystis jirovecii Pneumonia After Kidney Transplant: A Single-Center Retrospective Cohort Study.},
journal = {Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation},
volume = {23},
number = {5},
pages = {334-341},
doi = {10.6002/ect.2024.0250},
pmid = {40548531},
issn = {2146-8427},
mesh = {Humans ; Retrospective Studies ; *Pneumonia, Pneumocystis/diagnosis/microbiology/epidemiology/immunology ; *Pneumocystis carinii/genetics/pathogenicity/isolation & purification ; Female ; Male ; *Kidney Transplantation/adverse effects ; Middle Aged ; Predictive Value of Tests ; Adult ; *High-Throughput Nucleotide Sequencing ; Early Diagnosis ; China/epidemiology ; *Metagenomics ; Time Factors ; Risk Factors ; Treatment Outcome ; Incidence ; },
abstract = {OBJECTIVES: Pneumocystis jirovecii pneumonia, a common pulmonary infection after kidney transplant, cannot be detected by conventional culture methods, and limitations have been shown with lung tissue biopsy, sputum collection, and sample smear staining. Early diagnosis is key as long-term survival is decreased in patients with Pneumocystis jirovecii pneumonia who are not treated in a timely and effective manner.

MATERIALS AND METHODS: From January 2018 to January 2023, our study enrolled 110 patients with pulmonary infection seen at the First Affiliated Hospital of Xi'an Jiaotong University (China). Of these patients, 46 had confirmed Pneumocystis jirovecii pneumonia per metagenomic next-generation sequencing or conventional detection methods. We compared percentages of positive tests, other pathogen species, and other factors between the 2 test methods. Clinical characteristics of patients with (n = 46) and without (n = 64) Pneumocystis jirovecii were analyzed retrospectively.

RESULTS: Overall incidence of PJP was 2.3% (46/1977). Among 46 patients diagnosed with Pneumocystis jirovecii pneumonia, average time of onset post-transplant was 7.21 ± 2.55 months; 42 patients were cured, and 4 patients died. Thirty-three patients had mixed pulmonary infections, with Pneumocystis jirovecii and human cytomegalovirus being the most common pathogen combination, and 13 patients had monotypic pulmonary infections. Sixteen patients were Pneumocystis jirovecii positive according to conventional pathogen detection, for a detection rate of 34.8% (16/46), with significant difference shown between detection methods (χ2 = 92.0, P < .01). Patients who were treated with tacrolimus had insufficient use of sulfamethoxazole-trimethoprim and previous cytomegalovirus infection, and patients with acute rejection were more likely to develop Pneumocystis jirovecii pneumonia (P < .05).

CONCLUSIONS: Metagenomic next-generation sequencing showed more advantages in early diagnosis of Pneumocystis jirovecii pneumonia. Precision medicine can be adopted to reduce costs and improve cure rates based on results of metagenomic next-generation sequencing.},
}

Humans
Retrospective Studies
*Pneumonia, Pneumocystis/diagnosis/microbiology/epidemiology/immunology
*Pneumocystis carinii/genetics/pathogenicity/isolation & purification
Female
Male
*Kidney Transplantation/adverse effects
Middle Aged
Predictive Value of Tests
Adult
*High-Throughput Nucleotide Sequencing
Early Diagnosis
China/epidemiology
*Metagenomics
Time Factors
Risk Factors
Treatment Outcome
Incidence

@article {pmid40548332,
year = {2025},
author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {283},
pmid = {40548332},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).},
}

@article {pmid40548295,
year = {2025},
author = {Diwan, A and Harke, S and Panche, AN},
title = {Exploration of novel bioactive compounds from the microbiome of fish and shellfish as an alternative to replace antibiotic drugs in aquaculture farming.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e8},
pmid = {40548295},
issn = {2632-2897},
abstract = {The use of antibiotics in fish and shrimp aquaculture all over the world was found to be only partially successful in preventing infectious diseases. However, their overuse has resulted in the contamination of closed aquatic ecosystems, reduced antibiotic resistance in organisms that fight infectious diseases, and compromised the effectiveness of various antibiotic medications in controlling diseases. Excessive use of antibiotics damages aquaculture species and impacts human health, also rendering the most potent antibiotics increasingly ineffective, with limited alternatives. Therefore, intensive research efforts have been made to replace antibiotics with other protocols and methods like vaccines, phage therapy, quorum quenching technology, probiotics, prebiotics, chicken egg yolk antibody (IgY), and plant therapy," etc. Though all these methods have great potential, many of them are still in the experimental stage, except for fish vaccines. All these alternative technologies need to be carefully standardized and evaluated before implementation. In recent times, after realizing the importance of the gut microbiome community in maintaining the health of animals, efforts have been made to use the microbiome strains for the prevention of pathogenic bacterial and viral infections. Now it has been experimentally proven that animals should possess a healthy microbiome community in their gut tract to strengthen the immune system and prevent the entry of harmful pathogens. Investigations are now being carried out on the derivation of various bioactive compounds from the gut microbiome strains and their structural profile and functionality using the molecular tools of metagenomics and bioinformatics. Such newly discovered compounds from microbiomes can be used as potential alternatives to replace antibiotic drugs in the aquaculture industry. These alternatives are likely to emerge as breakthroughs in animal health management and farming, with effects on cost efficiency, species health, productivity, and yield enhancement. Therefore, introducing new micro-innovative technologies into an overall health management plan will be highly beneficial.},
}

@article {pmid40547922,
year = {2025},
author = {Yuan, B and Jiang, T and Han, J and Wang, M},
title = {Neurobrucellosis with negative serological examination: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1583891},
pmid = {40547922},
issn = {2296-858X},
abstract = {Neurobrucellosis is an uncommon occurrence that can arise as a consequence of brucellosis. However, its clinical symptoms are severe and have the potential to be life-threatening. Timely detection, prompt diagnosis, and early treatment are crucial factors. Clinically, the gold standard for diagnosing pathogenic microorganisms is through culture. However, this method is hindered by its lengthy culture duration, low rate of positive results, and the absence of typical clinical signs of neurobrucellosis. Consequently, misdiagnosis and delayed treatment are common. Metagenomics next-generation sequencing (mNGS) technology is a novel approach in microbiological diagnosis that enables the simultaneous detection of all microorganisms present in a sample, including viruses, bacteria, fungus, and parasites. This method holds significant diagnostic significance for viral disorders affecting the central nervous system. This paper reports a case of neurobrucellosis detected by mNGS after a negative serological test, as well as a review of the relevant literature.},
}

@article {pmid40547485,
year = {2025},
author = {Su, C and Zhu, M and Guo, Y and Sun, J and Liu, M and Ma, Y and Xu, Y and Bai, Y and Che, X and Zhang, N},
title = {DMAHDM@MPC nanoparticles in orthodontic adhesive inhibit cariogenic bacteria and sugar metabolism to prevent enamel demineralization.},
journal = {Materials today. Bio},
volume = {33},
number = {},
pages = {101969},
pmid = {40547485},
issn = {2590-0064},
abstract = {During orthodontic treatment, poor oral hygiene often facilitates the proliferation of cariogenic bacteria, particularly Streptococcus mutans, leading to lactic acid accumulation and subsequent enamel demineralization. To mitigate this issue, Dimethylaminohexadecyl methacrylate (DMAHDM) was incorporated onto the protein-repellent surface of 2-Methacryloyloxyethyl phosphorylcholine (MPC), resulting in the formation of a DMAHDM@MPC composite. This composite was then integrated into resin-modified glass ionomer cement (RMGIC) to develop an antimicrobial orthodontic adhesive, termed RMGIC + MPC + DMAHDM (RMD). This study demonstrated that DMAHDM@MPC nanoparticles self-assembled into a core-shell structure, thereby enhancing the antimicrobial activity. A six-month randomized controlled trial (RCT) involving 29 orthodontic patients, along with metagenomic and metabolomic analyses, revealed that RMD significantly reduced plaque accumulation by selectively inhibiting pathogenic bacteria while preserving beneficial microbiota. Additionally, MPC was shown to competitively bind to sucrose-6-phosphatase (SPP) in pathogenic bacteria, inhibiting sucrose synthesis and carbohydrate metabolism, thus reducing the production of organic acids. In conclusion, RMD effectively prevents enamel demineralization by selectively targeting cariogenic bacteria and their associated sugar metabolism pathways during orthodontic treatment.},
}

@article {pmid40546666,
year = {2025},
author = {Jeyaraman, N and Jeyaraman, M and Dhanpal, P and Ramasubramanian, S and Nallakumarasamy, A and Muthu, S and Santos, GS and da Fonseca, LF and Lana, JF},
title = {Integrative review of the gut microbiome's role in pain management for orthopaedic conditions.},
journal = {World journal of experimental medicine},
volume = {15},
number = {2},
pages = {102969},
pmid = {40546666},
issn = {2220-315X},
abstract = {The gut microbiome, a complex ecosystem of microorganisms, has a significant role in modulating pain, particularly within orthopaedic conditions. Its impact on immune and neurological functions is underscored by the gut-brain axis, which influences inflammation, pain perception, and systemic immune responses. This integrative review examines current research on how gut dysbiosis is associated with various pain pathways, notably nociceptive and neuroinflammatory mechanisms linked to central sensitization. We highlight advancements in meta-omics technologies, such as metagenomics and metaproteomics, which deepen our understanding of microbiome-host interactions and their implications in pain. Recent studies emphasize that gut-derived short-chain fatty acids and microbial metabolites play roles in modulating neuroinflammation and nociception, contributing to pain management. Probiotics, prebiotics, synbiotics, and faecal microbiome transplants are explored as potential therapeutic strategies to alleviate pain through gut microbiome modulation, offering an adjunct or alternative to opioids. However, variability in individual microbiomes poses challenges to standardizing these treatments, necessitating further rigorous clinical trials. A multidisciplinary approach combining microbiology, immunology, neurology, and orthopaedics is essential to develop innovative, personalized pain management strategies rooted in gut health, with potential to transform orthopaedic pain care.},
}

@article {pmid40544959,
year = {2025},
author = {Lin, T and Liu, X and Wu, L and Wu, Q and Zeng, H and Li, W and Tang, H and Zhao, J and Ding, Z},
title = {Clinical efficacy of metagenomic Next-Generation Sequencing for Pathogen Detection in Septic Patients based on Blood Samples in Intensive Care Units.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {100897},
doi = {10.1016/j.ijmmb.2025.100897},
pmid = {40544959},
issn = {1998-3646},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is considered superior to traditional culture for pathogen detection. However, its utility in septic patients based on blood samples remains limited.

METHODS: This research aimed to compare mNGS and culture-based diagnostics in 78 septic patients, with 25 with sepsis and 53 with septic shock.

RESULTS: Among 68 cases with matching sample types, pathogens of 38 cases were solely identified through mNGS, and in contrast, 2 cases had their pathogens detected by microbiological culture only. Moreover, 17 of 63 cases (26.98%) were found to be positive by both mNGS and culture, and 6 of 63 cases (9.52%) came negative under both diagnostic methods. Regardless of prior antibiotic exposure, the positive rate of mNGS, which was 80.77%, was significantly higher than that of culture (37.18%). Significantly, among the 38 septic patients diagnosed solely by mNGS, 23 patients achieved a favorable outcome after physicians adjusted the treatment based on the mNGS findings.

CONCLUSION: In conclusion, mNGS offered a swift and accurate means for pathogen identification, and thus making this approach as a promising technology for detecting sepsis.},
}

@article {pmid40544684,
year = {2025},
author = {Eckermann, C and Klein, CJ and Schäfer, F and Thiel, M and Weiss, AV and Motz, C and Lienkamp, K and Hannig, M and Schneider, M},
title = {Probiotics-embedded polymer films for oral health: Development, characterization, and therapeutic potential.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {255},
number = {},
pages = {114886},
doi = {10.1016/j.colsurfb.2025.114886},
pmid = {40544684},
issn = {1873-4367},
abstract = {The oral microbiome plays a crucial role in maintaining homeostasis, and microbial imbalances contribute to diseases such as periodontitis. Probiotic strains such as Lactobacillus rhamnosus and Lactobacillus reuteri have shown potential in restoring microbial balance in the oral cavity. However, their application remains challenging due to limited survival and adherence under intraoral conditions. Thus, we aimed to develop and evaluate mucoadhesive polymer films for local probiotic delivery. L. rhamnosus and L. reuteri were microencapsulated via spray drying and embedded in films composed of hydroxypropyl methylcellulose-polyvinyl alcohol (HPMC-PVA) and foamed polyvinyl alcohol (PVA). The films were characterized in terms of bacterial viability, tensile strength, folding endurance, and mucoadhesive properties. A proof-of-concept in vivo study was conducted by intraorally exposing enamel samples to two volunteers for eight hours, followed by confocal imaging and morphological analysis of adherent bacteria. Microencapsulation preserved high bacterial viability. The resulting films exhibited suitable mechanical properties and strong mucoadhesion. Biological evaluation revealed clear effects: films containing microencapsulated bacteria led to a statistically significant increase in adherent rod-shaped lactobacilli and a consistent reduction in coccoid bacteria associated with dysbiosis. The foamed PVA formulation showed the most pronounced modulation of the enamel-associated microbiota. These findings demonstrate that probiotic films can enable both bacterial stabilization and effective oral delivery. The system enhances colonization by beneficial bacteria while reducing potentially pathogenic cocci. This approach presents a promising strategy for microbiome-based prevention of oral diseases and merits further clinical investigation.},
}

@article {pmid40544677,
year = {2025},
author = {Bortoluzzi, C and Watson, M and Iuspa, MA and Lumpkins, B and Mathis, G and Jones, M and Hofacre, C},
title = {Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105454},
doi = {10.1016/j.psj.2025.105454},
pmid = {40544677},
issn = {1525-3171},
abstract = {Precision biotics (PB) are innovative feed additives designed to influence key metabolic pathways in the microbiome, particularly those involved in short-chain fatty acid (SCFA) production. These SCFAs are crucial for the healthy development and functionality of the gastrointestinal tract (GIT) in chickens. Our hypothesis was that adding a glycan-based PB to the diet would steer microbial metabolism towards increased SCFA production in the ceca, thereby reducing the adverse effects of necrotic enteritis (NE) in chickens. These studies evaluated the supplementation of PB on the cecal microbiome and growth performance in broiler chickens exposed to a necrotic enteritis (NE) challenge. Experiment 1: Day-old chicks were assigned to three treatment groups: a control, a challenged control, and a challenged group supplemented with PB. The birds were vaccinated for coccidiosis at day 0 and challenged with Clostridium perfringens. Cecal content was collected from one bird per pen on days 22 and 42 for microbiome analysis. Experiment 2: Day-old chicks were again assigned to three treatments: control, challenged control, and challenged with PB. All birds were vaccinated for coccidiosis and challenged with Eimeria maxima on day 14 and later with C. perfringens. On day 21, birds were euthanized for NE lesion scoring. In Exp. 1, the supplementation of PB significantly improved (P < 0.05) the growth performance of the challenged birds. An increased relative abundance of species related to SCFA production was observed on day 42, including several Faecalibacterium species (P < 0.05). This was paired with an increased relative abundance of both propionate (P<0.05) and butyrate pathways in birds with PB supplementation. In Exp. 2, on day 21, the challenge impaired growth performance, but the supplementation of PB counteracted this effect (P < 0.05). On day 42, the supplementation of PB improved BW by 10 % (P < 0.0001), and the FCR by 8.4 % (P < 0.0001) when compared to the challenged group. The supplementation of PB reduced NE associated mortality (5.5 vs 0.5 %; P = 0.002) and reduced the lesions characteristic of NE (P < 0.0001). Taken together, the microbiome metabolic shift observed with the supplementation of PB explains the improvement in growth performance, resilience to enteric stress and faster recovery of the intestine, which consequently improves welfare and the sustainability of poultry production.},
}

@article {pmid40544571,
year = {2025},
author = {Cao, J and Xu, Y and Zhang, C and Li, X and Liu, R and Wang, X and Dai, X},
title = {Enhancing the participation of water in the anaerobic digestion of sewage sludge for highly efficient methanogenesis.},
journal = {Water research},
volume = {284},
number = {},
pages = {124047},
doi = {10.1016/j.watres.2025.124047},
pmid = {40544571},
issn = {1879-2448},
abstract = {Water is widely present in sewage sludge, in which it constitutes the largest proportion; however, its participation in the methanogenesis of sludge has been overlooked. Here we revealed the mechanisms enhancing the participation of water in methanogenesis of sludge. Through stable isotope tracing experiments, we observed that isoelectric point pretreatment significantly enhanced the participation of water in CO2-reduction methanogenesis. Experimental results show that solid-liquid non-covalent interactions and interfacial water ordering in sludge were significantly enhanced. The former outcome drove electron transfer, while the latter provided an efficient proton channel. Combined with hydrogen/deuterium kinetic isotope effect (KIE) tests, it demonstrated that the water-mediated proton-coupled electron transfer (PCET) in the sludge were enhanced, accompanied by possible quantum tunnelling effect (KIE >> 10). Variations in the concentrations of key enzymes indicated that enhancing water-mediated PCET promoted both intracellular and extracellular electron-proton flow and accelerated the efficiency of mutual conversion between NADH and NAD[+], strongly driving ATP synthesis. Further genome-centric metagenomic analysis and reaction thermodynamic calculations revealed that enhancing water-mediated PCET triggered enrichment of CO2-reduction methanogenic consortia and effectively bypassed the limitation of H2 partial pressure, providing a thermodynamic advantage to promote collaborative methanogenic metabolisms. These findings provide a theoretical basis for regulating the methanogenesis of perishable organic solid waste by water.},
}

@article {pmid40544520,
year = {2025},
author = {Zhang, E and Gong, GA and Huang, S and Bao, Y and Ji, L and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Zhang, W},
title = {Viral Metagenomics of the Bharal (Pseudois nayaur) within the Qinghai-Tibet Plateau Revealed Diverse Viruses.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {143-152},
doi = {10.33073/pjm-2025-012},
pmid = {40544520},
issn = {2544-4646},
mesh = {Animals ; *Metagenomics ; Phylogeny ; Genome, Viral ; Tibet ; Feces/virology ; *Viruses/genetics/classification/isolation & purification ; Genetic Variation ; },
abstract = {The Qinghai-Tibetan Plateau (QTP) provides a home to diverse flora and fauna, and its ecosystems are unique worldwide. The study focused on the bharal, an endemic species found in the QTP and adjacent regions. We applied viral metagenomics technology to extract samples from the feces of 10 wild bharal. Viral nucleic acids were isolated, enriched, and sequenced from these samples, revealing the presence of a novel strain of Astroviridae virus. Phylogenetic analysis and sequence comparison identified this virus as part of the Mamastro-virus, forming a cluster with other Mamastrovirus species. Recombination analysis confirmed a multiple recombination event, suggesting that the new strain may be a potential recombinant. Additionally, nearly complete genome sequences of viruses belonging to the family Circoviridae were characterized, and a phylogenetic tree was constructed based on genotyping and predicted amino acid sequence analysis of the rep protein. Overall, this study helps us better understand the viral communities in the gut microbiome of the rare bharal. Moreover, the new recombinant discovered in this study will provide insights into the origin, genetic diversity, and evolution of bharal from the QTP and play a crucial role in future research on its presence in the intestinal ecology of sheep.},
}

Animals
*Metagenomics
Phylogeny
Genome, Viral
Tibet
Feces/virology
*Viruses/genetics/classification/isolation & purification
Genetic Variation

@article {pmid40544519,
year = {2025},
author = {Yu, X and Liang, J and Yang, R and Gai, W and Zheng, Y},
title = {Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {192-205},
doi = {10.33073/pjm-2025-016},
pmid = {40544519},
issn = {2544-4646},
mesh = {Humans ; Infant ; *High-Throughput Nucleotide Sequencing ; Male ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; Intensive Care Units, Pediatric ; *Trachea/microbiology ; *Pneumonia/microbiology/diagnosis/virology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation & purification ; Coinfection/microbiology ; },
abstract = {Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.},
}

Humans
Infant
*High-Throughput Nucleotide Sequencing
Male
Child, Preschool
Female
*Metagenomics/methods
Child
Intensive Care Units, Pediatric
*Trachea/microbiology
*Pneumonia/microbiology/diagnosis/virology
Microbiota/genetics
Bacteria/genetics/classification/isolation & purification
Coinfection/microbiology

@article {pmid40544513,
year = {2025},
author = {Muccee, F and Mohiuddin, F and Shahab, A and Almajwal, A and Afsar, T and Amor, H and Razak, S},
title = {Whole Genome Shotgun Sequencing-Based Insights into the Benzene and Xylene Degrading Potentials of Bacteria.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {244-261},
doi = {10.33073/pjm-2025-020},
pmid = {40544513},
issn = {2544-4646},
mesh = {*Xylenes/metabolism ; *Benzene/metabolism ; Biodegradation, Environmental ; Whole Genome Sequencing ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Genome, Bacterial ; Soil Microbiology ; Phylogeny ; Soil Pollutants/metabolism ; DNA, Bacterial/genetics ; Shotgun Sequencing ; },
abstract = {Due to their hazardous effects on human health and air quality, benzene and xylene constitute the primary pollutants. Coupling the physicochemical strategies with bacterial bioremediation is an emerging mode of decontamination. Considering the limited understanding of benzene and xylene degradation pathways in the genus Bacillus, failure of earlier documented bacteria to degrade these compounds due to poor optimization and complicated real-world contamination scenarios, we initiated the current project. It is an attempt to explore the gene repertoire and pathways associated with the bioremediation of benzene and xylene in new and efficient bacteria. Eleven bacteria were isolated from tannery industry soil in a previous study. Bacterial DNA was extracted by the organic method. To prepare a sample for whole genome sequencing (WGS) analysis, a mixture of genomic DNA was made by adding DNA from each isolate in equimolar concentration (100 ng). The sample was subjected to WGS. Results obtained as FASTq files were submitted to Sequence Read Archives (SRA), NCBI, to get the accession number assigned. Taxonomic profiling revealed that the sample was composed of phyla Proteobacteria (76%), Firmicutes (16%) and unclassified phyla (8%). Functional annotation unraveled the presence of benzoate, m-, p- and o-xylene isomers, benzene, aminobenzoate, 2-, 3- and 4-fluorobenzoate, toluene, chloroalkane and chloroalkene, naphthalene, polycyclic aromatic hydrocarbons (PAHs), dioxin, caprolactum, atrazine, styrene, and chlorobenzene and chlorocyclohexane degradation enzymes and pathways. It is the first ever study documenting the benzene degradation pathway similar to Gram-negative bacteria, in the genus Bacillus, inhabiting the tannery soil and coexistence of metabolic pathways for multiple organic pollutants.},
}

*Xylenes/metabolism
*Benzene/metabolism
Biodegradation, Environmental
Whole Genome Sequencing
*Bacteria/metabolism/genetics/classification/isolation & purification
*Genome, Bacterial
Soil Microbiology
Phylogeny
Soil Pollutants/metabolism
DNA, Bacterial/genetics
Shotgun Sequencing

@article {pmid40544449,
year = {2025},
author = {Yew, WC and Young, GR and Cheung, W and Nelson, A and Berrington, JE and Smith, DL},
title = {Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk.},
journal = {STAR protocols},
volume = {6},
number = {3},
pages = {103917},
doi = {10.1016/j.xpro.2025.103917},
pmid = {40544449},
issn = {2666-1667},
abstract = {Bacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomics approaches, respectively. We describe steps for extracting phages and lipids in low-volume milk, characterizing phageome using an in-house bioinformatic pipeline, and statistical analysis to correlate the phageome and lipidome. Finally, we detail an in vitro assay to examine the associations between fatty acid chain length and phage morphotype. For complete details on the use and execution of this protocol, please refer to Yew et al.[1].},
}

@article {pmid40544407,
year = {2025},
author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and de Barros, MP and Spilki, FR},
title = {SARS-CoV-2 Spillback in Opossums, Southern Brazil.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {40544407},
issn = {1612-9210},
abstract = {This study focuses on monitoring of SARS-CoV-2 in free-living animals in the Vale dos Sinos region, Rio Grande do Sul, Brazil, aiming to verify the presence of this emerging virus using next-generation sequencing (NGS) technique. Rectal and oral swab samples were collected from 52 white-eared opossums (Didelphis albiventris) and submitted to metagenomics and subsequently directed SARS-CoV-2 genome sequencing. Five positive samples were found to originate from these animals' contact with human waste or contaminated water bodies, indicating the spillover of SARS-CoV-2 to D. albiventris.},
}

@article {pmid40544290,
year = {2025},
author = {Chege, MN and Ferretti, P and Webb, S and Macharia, RW and Obiero, G and Kamau, J and Alberts, SC and Tung, J and Akinyi, MY and Archie, EA},
title = {Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {70},
pmid = {40544290},
issn = {2524-4671},
support = {R01 AG071684/NH/NIH HHS/United States ; R01 AG071684/NH/NIH HHS/United States ; DEB 1840223//National Science Foundation/ ; },
abstract = {BACKGROUND: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characterize bacterial communities in animal microbiota, these methods are less often applied to gut eukaryotic composition. Here we used shotgun metagenomic sequencing to characterize eukaryotic diversity in the microbiomes of wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, sequencing depth, and season of sample collection.

RESULTS: We analyzed a total of 75 fecal samples collected in 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of all samples, respectively (percentages indicate the percent of samples in which each kingdom was observed). Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effects of season, host age, or host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).

CONCLUSIONS: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is important for primate health monitoring and management strategies.},
}

@article {pmid40544256,
year = {2025},
author = {Mannavola, CM and De Maio, F and Marra, J and Fiori, B and Santarelli, G and Posteraro, B and Sica, S and D'Inzeo, T and Sanguinetti, M},
title = {Bloodstream infection by Lactobacillus rhamnosus in a haematology patient: why metagenomics can make the difference.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {47},
pmid = {40544256},
issn = {1757-4749},
support = {PE00000007, INF-ACT//EU funding for the MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; },
abstract = {BACKGROUND: Bloodstream infections (BSIs) pose a persistent threat to hospitalized patients, particularly those who are immunocompromised and susceptible to infections caused by anaerobic or facultative anaerobic bacteria. Alterations in gut microbiota composition can predispose individuals to intestinal domination by one or more pathobionts, increasing the risk of bacterial translocation into the bloodstream and subsequent bacteremia.

CASE PRESENTATION: We report the case of a 20-year-old female with multiple relapsed/refractory Philadelphia-negative B-cell acute lymphoblastic leukemia, initially referred to our hematology center for CAR-T cell therapy. The patient ultimately underwent allogeneic hematopoietic stem cell transplantation, which was complicated by infections, moderate-to-severe graft-versus-host disease, hepatic sinusoidal obstruction syndrome, and transplant-associated thrombotic microangiopathy, all contributing to a fatal outcome. Blood cultures obtained in the final week before the patient succumbed to multi-organ toxicity grew Lactobacillus rhamnosus. A fecal sample collected concurrently for intestinal microbiota characterization revealed a marked predominance of Bacillota (98.5%), with Lacticaseibacillus dominating at 47.9%, followed by Pediococcus (18.59%) and Staphylococcus (3.5%) at the genus level. We performed genomic comparison between the L. rhamnosus isolated from blood cultures and the best-matched strain detected in the intestinal microbiota.

CONCLUSIONS: We report the isolation of L. rhamnosus from blood cultures in a patient post hematopoietic cell transplantation, with genomic similarity to a gut-dominant L. rhamnosus strain. This case highlights the potential link between intestinal domination and subsequent bloodstream infection, supporting the value of gut microbiota profiling as an adjunctive tool for monitoring high-risk patients, such as hematopoietic cell transplant recipients.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13099-025-00722-3.},
}

@article {pmid40543872,
year = {2025},
author = {Yu, PF and Wang, D and Ma, XG and Fu, YB and Han, LY and Wang, A and Jiang, DL and Sun, HW and Li, DX and Jin, X and Yang, KD and Zhang, LC and Tang, YL},
title = {System characteristics of integrated continuous flow simultaneous partial Nitrification, Anammox and Denitrification (SNAD) for NH4[+]-rich wastewater: performance, sludge evolution, metagenomic sequencing analysis.},
journal = {Environmental research},
volume = {283},
number = {},
pages = {122175},
doi = {10.1016/j.envres.2025.122175},
pmid = {40543872},
issn = {1096-0953},
abstract = {The integrated process of simultaneous partial nitrification, anammox, and denitrification (SNAD) is designed to achieve efficient nitrogen removal and carbon reduction. This study details the design and successful implementation of an innovative, single-piece continuous flow SNAD system for treating high concentration NH4[+] wastewater. The system leverages simultaneous anammox and denitrification (SAD) granular sludge and employs a strategy of dosing partial nitrification sludge, alongside meticulous control of pH, dissolved oxygen (DO), free ammonia (FA), and free nitrous acid (FNA) was applied to initiate the SNAD process. The spectral analysis results suggest a marginal reduction in the stability and flocculation properties of the SNAD granular sludge. Molecular analysis via 16S rRNA gene sequencing revealed ammonia-oxidizing bacteria, anaerobic ammonia-oxidizing bacteria, and denitrifying bacteria as the predominant microbial populations within the SNAD system. A marked increase in the abundance of related functional genes was observed, alongside a reduction in quorum sensing (QS) and ATP-Binding Cassette (ABC) transporter proteins. These findings suggest a possible attenuation in the secretion of native signaling proteins within the SNAD system.},
}

@article {pmid40543557,
year = {2025},
author = {Nunley, BE and Weixler, A and Kim, HG and Xie, H and Sereewit, J and Hajian, P and Ellis, S and Mills, MG and Pérez-Osorio, AC and Goya, S and Gov, J and Dewar, R and Fernandes, G and Templeton, KE and Maloney, DM and Greninger, AL and Roychoudhury, P},
title = {Clinical performance evaluation of a tiling amplicon panel for whole genome sequencing of respiratory syncytial virus.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmoldx.2025.05.005},
pmid = {40543557},
issn = {1943-7811},
abstract = {Accurate genomic characterization of respiratory syncytial virus (RSV) is crucial for studies of epidemiology and viral evolution, including monitoring potential escape from newly authorized vaccines and prophylactic monoclonal antibodies. We adapted a viral genome tiling amplicon panel (UW-ARTIC) and developed a custom bioinformatic pipeline for high-throughput, cost-effective sequencing of both RSV-A and RSV-B subgroups. We established genome acceptability criteria and determined the performance characteristics of the panel including assay sensitivity, specificity, breadth of genome recovery, accuracy, and precision using contrived and remnant clinical specimens. High-quality genomes (>95% genome completeness; >500X and >1000X average depth for whole genome and fusion gene respectively) were recovered from samples with Ct ≤ 30 (∼594 and 2,004 copies per reaction for RSV-A and RSV-B respectively). Minor variants were accurately identified at >5% allele frequency. The assay showed high accuracy when compared to Sanger, shotgun metagenomic, and hybridization capture-based sequencing, as well as high repeatability and reproducibility. The UW-ARTIC RSV panel has utility for cost-effective RSV genome recovery in public health, clinical, and research applications. It has been used to generate FDA-reportable data for clinical trials of RSV antiviral products, with robust performance in global samples from as recently as the 2023/24 season. Continued genomic surveillance and future updates to primers will be essential for continued recovery of genomes as RSV continues to evolve.},
}

@article {pmid40543442,
year = {2025},
author = {Li, Y and Liu, J and Huang, G and Chen, Z and Ma, X and Huang, L},
title = {Metagenomic diagnosis of congenital tuberculosis with coinfections in an extremely preterm infant conceived via in vitro fertilization.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116960},
doi = {10.1016/j.diagmicrobio.2025.116960},
pmid = {40543442},
issn = {1879-0070},
abstract = {We describe a case of congenital tuberculosis in an extremely preterm infant (24 weeks' gestation, 800 g) conceived via in vitro fertilization, complicated by cytomegalovirus and Klebsiella pneumoniae coinfections. Diagnosis was confirmed by metagenomic next-generation sequencing after conventional tests were inconclusive. Management included anti-tuberculosis, antiviral, and antibacterial therapy, as well as surgical correction of a patent ductus arteriosus. The infant demonstrated significant clinical recovery, with resolution of pulmonary, splenic, and cardiac abnormalities. This case underscores the value of advanced molecular diagnostics and multidisciplinary care in managing life-threatening neonatal infections.},
}

@article {pmid40543441,
year = {2025},
author = {Hong, WL and Yao, LY and Zhong, Z and Meng, FJ and Zhang, WY and Lu, K and She, ZY},
title = {Successful management of Nocardia farcinica brain abscess in an immunocompetent adult with trimethoprim/sulfamethoxazole hypersensitivity: A case report and review.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116954},
doi = {10.1016/j.diagmicrobio.2025.116954},
pmid = {40543441},
issn = {1879-0070},
abstract = {BACKGROUND: Nocardia farcinica brain abscesses are rare in immunocompetent individuals. Trimethoprim/sulfamethoxazole (TMP/SMX) is first-line therapy, but hypersensitivity reactions necessitate alternative regimens. This report details successful management in a TMP/SMX-allergic patient.

CASE REPORT: A 38-year-old immunocompetent male presented with recurrent seizures. MRI revealed expanding left frontal lobe lesions. Surgical excision and metagenomic next-generation sequencing (mNGS) confirmed N. farcinica. Due to hypersensitivity to TMP/SMX, an alternative antibiotic regimen consisting of intravenous imipenem/cilastatin for 18 days and amikacin for 7 days was administered, followed by oral amoxicillin for 435 days and minocycline for 252 days. This therapeutic approach resulted in effective infection control, as evidenced by sustained clinical improvement over a 28-month follow-up period.

CONCLUSION: N. farcinica brain abscess can occur in immunocompetent adults, posing therapeutic challenges with TMP/SMX intolerance. This case demonstrates that alternative regimens-imipenem/cilastatin, amikacin, amoxicillin, and minocycline-can achieve sustained remission. Individualized therapy based on drug susceptibility and patient factors is critical.},
}

@article {pmid40543402,
year = {2025},
author = {Aziz, T and Shabbir, MA and Sarwar, A and Khan, AA and Zhao, L and Yang, Z and Shami, A and Alwethaynani, MS and Al-Asmari, F and Alghamdi, AM and Al-Joufi, FA},
title = {Exploring the multifaceted probiotic potential of Lactiplantibacillus plantarum NMGL2, investigating its antimicrobial resistance profiles and bacteriocin production.},
journal = {Journal of microbiological methods},
volume = {236},
number = {},
pages = {107178},
doi = {10.1016/j.mimet.2025.107178},
pmid = {40543402},
issn = {1872-8359},
abstract = {BACKGROUND: Lactiplantibacillus plantarum is widely recognized for its probiotic and antimicrobial properties, making it a valuable candidate for food and clinical applications. Genomic characterization provides deeper insight into its potential health benefits and safety profile.

AIM: This study aimed to sequence and analyze the genome of L. plantarum NMGL2 to evaluate its antimicrobial resistance, probiotic potential, and genetic suitability for biotechnological applications.

METHODS: The genomic DNA of L. plantarum NMGL2 was extracted and sequenced using Illumina technology. Genome assembly and annotation were performed, followed by gene prediction using Prokka and identification of antimicrobial resistance genes, virulence factors, and probiotic markers via BLAST. Metagenomic analysis of gut microbiota samples and phylogenetic analysis were conducted to assess strain relationships with other L. plantarum isolates.

RESULTS: The genome analysis revealed approximately 3000 protein-coding genes, including those encoding bile salt hydrolase, antimicrobial peptides, and antibiotic resistance determinants. Phylogenetic analysis showed that NMGL2 is closely related to other probiotic L. plantarum strains, supporting its probiotic characteristics and its potential role in combating pathogens.

CONCLUSION: L. plantarum NMGL2 demonstrates promising probiotic traits and carries genes that support its application in food safety and clinical contexts. Further, in vivo studies are needed to validate its health benefits and ensure safety, particularly in treating gastrointestinal disorders.},
}

@article {pmid40543345,
year = {2025},
author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y},
title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138980},
doi = {10.1016/j.jhazmat.2025.138980},
pmid = {40543345},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.},
}

@article {pmid40543204,
year = {2025},
author = {Yang, J and Kim, JS and Jeon, HW and Lee, J and Seo, JH},
title = {Integrated culture-based and metagenomic profiling of airborne and surface-deposited bacterial communities in residential environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126703},
doi = {10.1016/j.envpol.2025.126703},
pmid = {40543204},
issn = {1873-6424},
abstract = {Indoor environments host diverse microbial communities, where airborne and surface-deposited bacteria contribute to human exposure and potential health risks. This study applies metagenomic analysis to examine bacterial diversity in residential apartments, focusing on four key indoor spaces: kitchens, living rooms, toilets, and bedrooms. Airborne bacteria were collected using a culture-based air sampler and surface-deposited bacteria were collected via swabbing of high-contact areas; both were analyzed through 16S rRNA gene sequencing and bioinformatics processing. Airborne bacterial communities were primarily composed of Staphylococcus, Bacillus, and Enhydrobacter, whereas surface-deposited bacteria varied by location, with Streptococcus and Staphylococcus being most common on high-contact surfaces. Overall, surface-deposited bacterial diversity was greater than that of airborne communities, highlighting their distinct but interconnected roles in indoor microbial ecosystems. Functional pathway analysis suggested that indoor bacterial communities may harbor metabolic functions, as well as antibiotic resistance and virulence-related pathways, pointing to potential health concerns. Principal component analysis (PCA) showed clear distinctions between airborne and surface-deposited bacterial communities. These findings highlight the need for space-specific microbial management strategies, such as improved ventilation and surface hygiene, to reduce exposure risks and promote healthier indoor environments.},
}

@article {pmid40542451,
year = {2025},
author = {Ji, S and Ahmad, F and Peng, B and Yang, Y and Su, M and Zhao, X and Vatanen, T},
title = {Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {149},
pmid = {40542451},
issn = {2049-2618},
support = {U22A20365//Joint Funds of National Natural Science Foundation of China/ ; T2341019//National Natural Science Foundation of China/ ; 2023A1515012429//Natural Science Foundation of Guangdong Province/ ; 2024B03J1343//Guangzhou Science and Technology Plan Project/ ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear.

METHODS: The gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis.

RESULTS: Gut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages.

CONCLUSIONS: FMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes. Video Abstract.},
}

@article {pmid40542420,
year = {2025},
author = {Yu, M and Chu, Y and Wang, Y and Mo, L and Tan, X and Guo, S and Yuan, S and Ma, Y},
title = {Metagenomic analysis reveals gut phage diversity across three mammalian models.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {146},
pmid = {40542420},
issn = {2049-2618},
support = {2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; B2302023//Shenzhen Medical Research Fund/ ; B2302023//Shenzhen Medical Research Fund/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; },
abstract = {BACKGROUND: The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown.

RESULTS: We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (> = 60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota.

CONCLUSIONS: Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.},
}

@article {pmid40542368,
year = {2025},
author = {Liu, F and Zhuang, Y and Huang, X and Papazian, L and Cai, H and Shao, H and Chen, Q and Xie, C and Tang, K and Li, K and Wang, M and Xu, Y and Shen, P and Wang, Q and He, X and Wang, N and Wang, H and Dai, M and Xiong, Y and Zhong, L and Pan, Y and Chu, L and Yang, B and Zhang, G and Zhou, H and Xu, J and Jiang, C and Huang, L},
title = {The Landscape of lower respiratory tract herpesviruses in severe pneumonia patients: a multicenter, retrospective study with prospective validation.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {254},
pmid = {40542368},
issn = {1466-609X},
support = {82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
abstract = {OBJECTIVE: Herpesviruses are widely distributed in the lower respiratory tract, yet no study has comprehensively characterized their clinical features and prognostic impact in severe pneumonia.

METHOD: In this multicenter, retrospective study, we included severe pneumonia patients who underwent bronchoalveolar lavage fluid (BALF) metagenomic testing in intensive care units across 17 medical centers from January 2019 to June 2023. Based on metagenomic results, patients were categorized into herpesvirus-negative, HSV-1, EBV, CMV, HHV-6B, and HHV-7 groups. Propensity score matching and multivariable Cox regression were used to compare mortality between herpesvirus-positive and -negative patients. Interaction analyses were conducted to assess the impact of co-detection of different herpesviruses. Besides, main findings were validated using data from a prospective multicenter cohort.

RESULTS: Among 1,737 enrolled patients, the 28-day mortality rate was 41.3% (718/1,737). Herpesviruses were detected in 828 patients. Detection frequencies were: HSV-1 (26.8%), CMV (17.8%), EBV (16.6%), HHV-7 (5.3%), HHV-6B (2.2%), and VZV (0.5%). Clinical characteristics varied across herpesvirus groups. No single herpesvirus was independently associated with increased mortality compared to the negative group. However, co-detection of HSV-1 and CMV was significantly associated with higher 28-day mortality (vs. both negative: adj-HR = 1.439, 95% CI: 1.093-1.894, P = 0.009). This finding was validated in a prospective cohort (adj-HR = 1.656, 95% CI: 1.061-2.585, P = 0.026).

CONCLUSIONS: Herpesviruses are frequently detected in the lower respiratory tract of patients with severe pneumonia, with distinct clinical features across virus types. Co-detection of HSV-1 and CMV was associated with increased 28-day mortality.},
}

@article {pmid40542287,
year = {2025},
author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C},
title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40542287},
issn = {2058-5276},
support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; },
abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.},
}

@article {pmid40541587,
year = {2025},
author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TTY and Dawson, HD},
title = {Broccoli consumption alters microbial diversity, metatranscriptome and host transcriptome in mice fed a Total Western Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.05.041},
pmid = {40541587},
issn = {1541-6100},
abstract = {BACKGROUND: Cruciferous vegetables (CV) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent CV compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) are unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.

OBJECTIVE: We investigated the effects of a broccoli powder-supplemented Total Western Diet (TWD) on changes in the gut microbiome, the host transcriptome and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.

METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for six weeks followed by supplementation with 0, 0.5, 1 or 2.5% broccoli powder (BP) (reflecting a human intake from ¼ -1 cup per day) for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S rRNA amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess functionality of the microbial communities. The host cecal transcriptome was also assessed.

RESULTS: Beta diversity was significantly higher (p = 1.20E-03) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial RNA transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.

CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.},
}

@article {pmid40541578,
year = {2025},
author = {Tian, J and Hu, J and Xiong, Y and Deng, X and Fang, Y and Wang, G and Chi, R and Xiao, C},
title = {Metagenomic and metabolomic insights into microalgal-bacterial symbiosis under low carbon-to-nitrogen ratios.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132849},
doi = {10.1016/j.biortech.2025.132849},
pmid = {40541578},
issn = {1873-2976},
abstract = {Microalgal-bacterial symbiotic system (MBSS) is expected to efficiently treat ammonia nitrogen (NH4[+]-N) wastewater at low carbon-to-nitrogen ratio (CNR). In this study, MBSS was constructed and operated at CNRs of 0, 2, and 4 for 36 days, named as L (low CNR), M (medium CNR), and H (high CNR). Microbial interaction mechanisms were explored through metagenomics and non-targeted metabolomics. The average NH4[+]-N removal efficiencies of L, M, and H were 9.2 ± 4.3 %, 33.6 ± 10.9 %, and 51.6 ± 14.1 %, respectively. CNR significantly influenced NH4[+]-N removal. Metagenomics and metabolomics showed that bacteria dominate MBSS, with phylum Pseudomonadota having a large advantage. Addition of simple organic carbon sources may inhibit the generation of complex organic compounds by microalgae, consequently leading to bacteria utilizing simple carbon sources. Certain key microorganisms, genes, and metabolites respond to different CNRs to regulate MBSS performance. This study provides new insights into MBSS nitrogen removal at low CNR.},
}

@article {pmid40541123,
year = {2025},
author = {Jiao, Y and Xiao, D and Li, X and Jiang, M and Li, H},
title = {Integrative fMRI and multiomics reveal neuroprotective mechanisms of Astragalus membranaceus in sleep deprivation-induced depression.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156959},
doi = {10.1016/j.phymed.2025.156959},
pmid = {40541123},
issn = {1618-095X},
abstract = {BACKGROUND: Sleep deprivation (SD) is a significant public health concern and a risk factor for neuropsychiatric disorders, including depression. SD disrupts the gut-brain axis, causing dysbiosis and neuroinflammation. Astragalus membranaceus (AST) exhibits antidepressant and anti-inflammatory properties, including modulation of the gut microbiota; however, its neuroprotective effects on SD-induced neuropsychiatric disturbances remain largely unexplored. This study investigates the potential of AST using an innovative integrative multiomics approach.

PURPOSE: This study was conducted to investigate the neuroprotective effects of AST against SD-induced depression-like behavior and to explore the mechanism underlying its regulatory effects on the gut-brain axis.

METHODS: We established a chronic SD mouse model that was subjected to AST intervention and employed a pioneering integrative multiomics approach-combining resting-state functional magnetic resonance imaging for brain function, metagenomics for microbiota profiling, metabolomics for metabolic alterations, and transcriptomics for gene expression in key brain regions. Behavioral tests and cytokine assays complemented these analyses to comprehensively evaluate the therapeutic effects of AST.

RESULTS: SD induced depression-like behavior, neuroinflammation (IL-1β, IL-6, and TNF-α secretion), gut dysbiosis (Proteobacteria expansion, loss of beneficial microbes), and disrupted metabolic pathways. AST alleviated behavioral deficits, normalized brain connectivity, and reduced the levels of proinflammatory cytokines. It also reshaped microbiota, enriching Muribaculum and Butyricicoccus, and restored metabolic profiles, increasing the levels of short-chain fatty acids and promoting bile acid pathways. Integrated analysis linked microbiota restoration to reduced neuroinflammation and improved neuroprotection.

CONCLUSION: AST modulates the gut-brain axis to counteract SD-induced dysbiosis, neuroinflammation, and metabolic imbalance, alleviating depression-like symptoms. These findings offer novel mechanistic insights into the therapeutic potential of AST for SD-related neuropsychiatric conditions.},
}

@article {pmid40540838,
year = {2025},
author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO},
title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128260},
doi = {10.1016/j.micres.2025.128260},
pmid = {40540838},
issn = {1618-0623},
abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.},
}

@article {pmid40540566,
year = {2025},
author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ},
title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadq5232},
pmid = {40540566},
issn = {2375-2548},
abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.},
}