@article {pmid41862790,
year = {2026},
author = {Amir, A and Zhong, J and Yao, Y and Chen, T and Li, M and Yan, H},
title = {Seasonal diet shifts alter the gut microbiome and resistome of captive geriatric giant pandas (Ailuropoda melanoleuca).},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41862790},
issn = {1471-2180},
support = {2024CPB-B18//Chengdu Research Base of Giant Panda Breeding/ ; 2024CPB-B18//Chendu Research Base of Giant Panda Breeding/ ; },
abstract = {UNLABELLED: The nutritional changes of giant pandas (Ailuropoda melanoleuca) in response to the seasonal variations from bamboo shoots (rich in proteins) to fibrous leaves trigger significant alterations in the structure and functions of the gut microbiome. However, the effect these dietary changes have on the gut resistome, especially in older adults, is not well characterized. In this study, shotgun metagenomic sequencing and quantitative PCR (qPCR) were used to investigate the microbial composition, functional potential, and profiles of antibiotic- and metal-resistance genes (ARG and MRG) in feces of adult (n = 11) and geriatric captive pandas (n = 11) that were fed on bamboo shoots or leaves. The microbes varied considerably among diet and age groups, with diet becoming the main source of taxonomic and functional disparity (P < 0.05). Shoot-fed pandas exhibited higher alpha diversity at the genus level and distinct clustering in principal coordinate analyses, whereas leaf-fed groups showed enrichment of taxa associated with fiber degradation and stress tolerance (P < 0.05). Functional annotation of bacterial responses to diet showed changes in carbohydrate processing pathway, carbohydrate transport, and cellular process pathways by changes in the KEGG pathway (P < 0.05). Changes depending on diet were also identified with significant changes in carbohydrate-active enzyme (CAZy) family during changes in the composition of the bamboo parts. Metagenomics and qPCR revealed that several antibiotic resistance genes, such as aac(3)-Xa, bcrA, tet44, sul2 and macB, were highly interacting between diet and age and the most diverse resistome was found in geriatric pandas (P < 0.05). Correlation analysis demonstrated that there is a positive co-occurrence pattern of Enterobacteriaceae and several ARGs. Collectively, our findings demonstrate that seasonal dietary shifts and host aging jointly restructure the gut microbiome and resistome of giant pandas, suggesting diet-mediated modulation of microbial adaptation, resistance dissemination, and ecological resilience in captivity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04966-0.},
}

@article {pmid41872905,
year = {2026},
author = {Zhao, H and Hua, J and Lu, W and Lv, X and Chen, C and Liang, Y},
title = {Rubber seed cake supplementation alters meat quality, intestinal health, and gut microbiota in Hu sheep.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41872905},
issn = {2524-4671},
support = {880698//Key Technology Integration and Application of Standardized Rearing Management for Meat Sheep in Agricultural Areas/ ; },
abstract = {UNLABELLED: This study aimed to investigate the effects of rubber seed cake (RSC) supplementation on slaughter performance, intestinal health, and gut microbiota in Hu sheep. Forty-eight Hu sheep (17.01 ± 0.57 kg; 3 months old) were randomly allocated to four dietary treatments: 0% (CON), 6% (R6), 12% (R12), and 18% (R18) RSC. Following an 80-day feeding trial, six sheep per group were randomly selected for slaughter. Samples of the longissimus dorsi, small intestine, and intestinal mucosa were collected for meat quality, morphological, and intestinal health analyses. Additionally, ileal contents were harvested and frozen for metagenomic sequencing. Dietary supplementation with RSC reduced the shear force of the longissimus dorsi muscle (P = 0.043) and lowered meat color L* (P = 0.044) and b* (P = 0.035) values in the R6 group compared to the CON group. Quadratic effects were observed for the villus height to crypt depth (VH/CD) ratio in the duodenum (P = 0.006), jejunum (P = 0.006), and ileum (P = 0.001) with increasing RSC supplementation, and the VH/CD ratio was significantly increased in the R6 and R12 groups (P < 0.05). Ileal pro-inflammatory cytokine concentrations, including tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and interleukin-6 (IL-6), decreased both linearly and quadratically with increasing RSC supplementation (P < 0.05). Quadratic effects (P < 0.05) were observed for the concentrations of mucin 2 (MUC2) and tight junction proteins such as zonula occludens-1 (ZO-1), occludin, and claudin in the jejunal and ileal mucosa with increasing RSC supplementation. Specifically, the concentrations of MUC2 and tight junction proteins in the jejunum, as well as MUC2 and ZO-1 in the ileum, were significantly higher in the R6 group (P < 0.05). RSC supplementation significantly altered the relative abundance of specific taxa, including Stenotrophomonas, Piromyces, Lichinomycetes, and Syntrophobacteria, as well as CAZyme gene sequences such as GH119, GT39, and GH13-8 (P < 0.05). In conclusion, these findings indicate that a 6% dietary supplementation of RSC is optimal in Hu sheep, as it improves meat quality and intestinal health by modulating the ileal microbiota composition and CAZyme abundance, thereby strengthening mucosal barrier function and alleviating inflammation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00556-7.},
}

@article {pmid42010622,
year = {2026},
author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M},
title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42010622},
issn = {1756-994X},
support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; },
abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood.

METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages.

RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution.

CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01646-6.},
}

@article {pmid42057074,
year = {2026},
author = {de Oliveira, LG and Lopes Mechler-Dreibi, M and Storino, GY and Moreira Petri, FA and Carvalho Abreu Fantini, M and Silva Martins, T},
title = {Respiratory microbiota dynamics in piglets under nanotechnology-based and conventional vaccination protocols against Mycoplasma hyopneumoniae.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05458-z},
pmid = {42057074},
issn = {1746-6148},
abstract = {Mycoplasma hyopneumoniae is a key pathogen in porcine enzootic pneumonia (PEP) and plays an important role in the porcine respiratory disease complex (PRDC). Understanding how vaccination strategies relate to the respiratory microbiota in piglets may provide insights into host-microbiota interactions and vaccine performance. This study evaluated the temporal dynamics of the respiratory microbiota in piglets subjected to different vaccination protocols, including a nanotechnology-based oral vaccine formulated with mesoporous silica (SBA-15), alone or combined with a commercial vaccine, on the respiratory microbiota of piglets. Forty-eight piglets from M. hyopneumoniae-free sows were divided into four experimental groups receiving different vaccination protocols: CV + SBA received the pure silica-based adjuvant (SBA-15) orally and a commercial vaccine at 24 days of life; OV3 + CV received an oral vaccine (OV) at 3 days and an intramuscular commercial vaccine at 24 days; CV received only the intramuscular commercial vaccine at 24 days; and OV + CV received both the oral and commercial vaccines at 24 days. Microbiota composition was assessed at 3, 41, and 71 days of life using 16S rRNA gene sequencing from nasal swabs and bronchoalveolar lavage fluid (BALF). Significant differences in nasal microbiota diversity were observed at early life stages. At D3, CV exhibited the highest diversity, while OV3 + CV had the lowest (Shannon index, p < 0.05 between CV and OV3 + CV). At D41, microbiota differences between groups had diminished, with only OV + CV showing higher richness compared with OV3 + CV (Chao1 index, p < 0.05). At D71, no significant differences were observed in overall diversity or bacterial composition among groups. As no treatment had been administered prior to sampling, these differences likely reflect baseline variability between groups. Additionally, no consistent associations were detected between microbiota diversity patterns and vaccination outcomes assessed by lung lesion scores and bacterial DNA load. These findings indicate that early-life differences in nasal microbiota were observed, but these were not sustained over time, and the respiratory microbiota converged toward a more stable community structure regardless of vaccination protocol.},
}

@article {pmid42057154,
year = {2026},
author = {Mahmud, MR and Uddin, MK and Kareljärvi, P and Jalasvuori, M and Peräkylä, J and Eklund, T and Biström, M and Hasan, S and Vatanen, T and Kiljunen, S and Oliviero, C},
title = {Impact of phage therapy in post-weaning piglets challenged with ETEC strain in a controlled minitrial.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00516-2},
pmid = {42057154},
issn = {2055-5660},
abstract = {Enterotoxigenic Escherichia coli (ETEC) is a pathogen responsible for post-weaning diarrhea (PWD) in piglets, which results in economic losses in pig production. The rise of antibiotic-resistant ETEC strains together with restrictions on addition of zinc oxide in pig feed require alternative management approaches. Our research examines bacteriophage therapy as a solution to control ETEC infections in newly weaned piglets. A cocktail of phages targeting a strain of ETEC F4LT1ST2 was identified and subsequently multiplicated in laboratory. We conducted a trial including nine piglets divided into three groups. The negative control group was exposed to the phage cocktail by administration with the bedding material (saw dust) on the floor of their pen. The treatment group was exposed to the ETEC strain and to the phage cocktail, and the positive control group was exposed to the ETEC strain only. Shotgun metagenomic sequencing was performed on fecal samples to characterize bacterial and phage dynamics. Throughout a 10-day period we monitored daily the rectal temperature and the diarrheal score of piglets. Subsequently we evaluated phage and bacterial counts in fecal samples to determine phage therapy effect on gut microbiota dynamics and piglet health. The PHAGE+ETEC group showed 19.2% lower cumulative diarrhea burden (p = 0.044) and 61.9% higher average daily gain (p = 0.065). Rectal temperature correlated significantly with diarrhea severity (per-piglet Spearman's ρ = 0.727, p = 0.027). Alpha diversity did not differ between treatment groups across timepoints, suggesting that phage administration did not cause major shifts in microbial diversity. Metagenomic analyses showed significant reduction of E. coli abundance in PHAGE+ETEC group compared to PHAGE groups (p = 0.009). Consistent with these observations, plaque assay results confirmed active phage-bacteria interactions: no plaque formation was detected in the feces of the ETEC-only group, whereas the PHAGE+ETEC group showed phage replication, reaching 10[6] PFU/ml. This pilot study highlights the potential of phage therapy as an alternative to antibiotics for ETEC infections in piglets. Additional research with larger pig population and longer duration is required to confirm these findings and develop optimal phage application methods for swine production.},
}

@article {pmid42057164,
year = {2026},
author = {Cabello, AM and Salles, S and Domínguez-Huerta, G and Capo, E and Camarena-Gómez, MT and García-Gómez, C and Sánchez, A and Mangot, JF and Cerezo, I and Bautista, R and Pérez, P and García, R and Ruiz, JM and Mercado, JM and Ferrera, I},
title = {Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00893-9},
pmid = {42057164},
issn = {2524-6372},
abstract = {BACKGROUND: Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics (petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages.

RESULTS: Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short‑term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine‑scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics.

CONCLUSIONS: The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non‑equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem's complexity. This study highlights the importance of incorporating microbial community analyses into long‑term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.},
}

@article {pmid42057198,
year = {2026},
author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J},
title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01660-8},
pmid = {42057198},
issn = {1756-994X},
support = {09150162410022/ZONMW_/ZonMw/Netherlands ; 2021-01637//Vetenskapsrådet/ ; 967569//Västerbotten Läns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; },
abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.

METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.

RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value = 0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.

CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.},
}

@article {pmid42057295,
year = {2026},
author = {Klaps, J and Lemey, P and Bletsa, M and , and Kafetzopoulou, LE},
title = {nf-core/viralmetagenome: A Novel Pipeline for Untargeted Viral Genome Reconstruction.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag187},
pmid = {42057295},
issn = {1367-4811},
abstract = {MOTIVATION: Reconstructing eukaryotic viral genomes from metagenomic data is challenging due to their extensive diversity and potential genome segmentation. Current approaches often rely on labor-intensive manual curation for reference selection and scaffolding, limiting scalability for large studies or rapid outbreak response. We address the critical need for an automated, scalable pipeline for efficient viral metagenomic analysis without manual intervention.

RESULTS: We present nf-core/viralmetagenome, a comprehensive Nextflow pipeline for the untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation capture enriched samples. The pipeline automates the entire process from read preprocessing to consensus generation, integrating multiple de novo assemblers, automated reference selection, and iterative consensus refinement. It features robust quality control, extensive documentation, and seamless portability via Docker and Singularity. We validated the pipeline on diverse simulated and real datasets, demonstrating its ability to recover high-quality genomes from complex metagenomic samples and resolve co-infections, making it a powerful tool for viral surveillance.

AVAILABILITY: nf-core/viralmetagenome is freely available at https://github.com/nf-core/viralmetagenome with comprehensive documentation at https://nf-co.re/viralmetagenome. Archival code repository snapshots are published at zenodo with doi: https://doi.org/10.5281/zenodo.17524074.

SUPPLEMENTARY INFORMATION: Supplementary data are available at https://github.com/Joon-Klaps/nf-core-viralmetagenome-manuscript online.},
}

@article {pmid42057740,
year = {2026},
author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM},
title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17636},
pmid = {42057740},
issn = {1520-5118},
abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.},
}

@article {pmid42057783,
year = {2026},
author = {Harshvardhan, and Kaur, M and Grover, V and Pinnaka, AK and Korpole, S},
title = {Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799124},
pmid = {42057783},
issn = {1664-302X},
abstract = {INTRODUCTION: Subgingival microbial dysbiosis is one of the key reasons behind periodontitis, a chronic inflammatory disease, which is further get severe in the presence of type 2 diabetes mellitus (T2D). Although changes in taxonomic composition have been well established, the functional interactions and metagenomic profiles across different stages of the disease remain unclear.

METHODS: A shotgun metagenomic analysis was performed on subgingival dental plaque samples from 16 individuals, divided into healthy, staged periodontitis, and diabetic periodontitis groups. Group-wise DNA pooling was done for maximum DNA yield. Further, Alpha/beta diversity, taxonomic profiling, pathogen-probiotic ratios, and metabolic pathway abundance were analyzed and studied.

RESULTS: The healthy group showed the highest alpha diversity, especially in the core biosynthetic pathways. On the other hand, the earlier stages of periodontitis showed a unique community structure and the lowest alpha diversity. Early periodontitis also showed the highest abundance of commensals like Actinomyces and Bifidobacterium, along with increased UMP/guanosine and L-arginine biosynthesis pathways. The advanced periodontitis group had an increase of red complex bacteria and loss of probiotics. An increase of the degradative pathways, such as L-histidine degradation, had also been observed in this stage. The diabetic periodontitis group had a distinct microbial profile that included Capnocytophaga and a considerable metabolic shift toward lipid metabolism and glycolysis, with higher overall microbial diversity than the other periodontitis groups.

CONCLUSION: The results clearly show that the subgingival microbial and functional patterns are different across the stages of the disease and metabolic status, which can be developed for underscoring the importance of targeting early metabolic shifts to prevent dysbiosis.},
}

@article {pmid42057917,
year = {2026},
author = {Szentiványi, T and Bruszniczky, B and Biró, Z and Katona, K and Klein, Á and Bende, A and Bánáti, L and Vass, G and Lehotzky, P and Kovács, D and Földvári, G and Csivincsik, Á and Nagy, G and Nagy, RR and Miklós, M and Szabadi, KL and Szabó, ÉS and Garamszegi, LZ},
title = {Unwelcome guests: Nematodes of zoonotic and animal health importance in native and invasive carnivores of Hungary.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {9},
number = {},
pages = {100380},
pmid = {42057917},
issn = {2667-114X},
abstract = {Wild carnivores are important reservoirs of parasitic nematodes, several of which have veterinary and zoonotic significance. In Europe, the role of invasive carnivores in parasite circulation remains poorly understood. Here, we screened 371 individuals of six wild carnivore species from Hungary (red foxes, badgers, golden jackals, raccoons, raccoon dogs, and beech martens), using molecular markers (cox1 and S12), and detected five nematode parasites: Dirofilaria immitis, Crenosoma vulpis, Angiostrongylus vasorum, Thelazia callipaeda, and Spirocerca lupi. The highest prevalence was observed in badgers (32.0%) and red foxes (15.7%), while invasive raccoons also showed a relatively high infection rate (13.2%). Dirofilaria immitis was one of the most common nematode species detected: it was found in four host species, including the first confirmed cases in Hungarian badgers and invasive raccoons, extending the known host range of this parasite in central Europe. Importantly, T. callipaeda was recorded in red foxes and an invasive raccoon dog, representing the first invasive host records of this zoonotic eyeworm in Hungary. Crenosoma vulpis was identified in raccoons, suggesting invasive species may act as incidental carriers of endemic parasites. Both C. vulpis and D. immitis showed low host specificity. These findings indicate that invasive carnivores, particularly raccoons, may harbour unexpectedly high prevalence and play a greater role in local parasite networks than previously assumed. Our results highlight the epidemiological significance of both native and invasive carnivores in sustaining nematodes of zoonotic and veterinary importance in central Europe, stressing the need for continued surveillance in wild carnivores.},
}

@article {pmid42058175,
year = {2026},
author = {Zhong, H and Sun, C and Lu, Y and Cai, X and Cao, M and Wang, L and Feng, C and Song, M and Sun, W and Shi, M and Tao, Y and Zhou, J and Chen, C and Lu, X and Li, Y and Ni, Y and Cai, Y and Zhong, J and Li, Y and Wu, W and Shi, Y and Wang, M and Su, X},
title = {The clinical value of metagenomic next generation sequencing in the diagnosis of non-neutropenic invasive pulmonary aspergillosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1731736},
pmid = {42058175},
issn = {2235-2988},
mesh = {Humans ; Male ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sputum/microbiology ; Mannans/analysis/blood ; Aged ; Sensitivity and Specificity ; Adult ; *Aspergillus/genetics/isolation & purification/classification ; Galactose/analogs & derivatives ; },
abstract = {BACKGROUND: This study aims to explore the performance of metagenomic next generation sequencing (mNGS) in the diagnosis of non-neutropenic invasive pulmonary aspergillosis (IPA) and its clinical application value.

METHODS: This multi-center study enrolled 293 suspected IPA patients who conducted mNGS from October 2020 to February 2024. These cases were classified into IPA group and non-IPA group according to IPA diagnostic criteria. We analyzed the diagnostic value of mNGS by comparing with sputum culture, BALF culture, serum and BALF GM test.

RESULTS: A total of 118 IPA patients (4 proven/113 probable/1 possible diagnosis) were included in our study. The most common Aspergillus species was A. fumigatus (63.4%), followed by A. flavus (23.2%), A. oryzae (7.1%), A. niger (3.6%) and A. terreus (2.7%). The sensitivity of bronchoalveolar lavage fluid (BALF) mNGS was significantly higher than BALF culture (81.9% vs. 27.0%, p<0.001) and BALF galactomannan (GM) (81.9% vs. 55.8% (GM≥1.0 cutoff value), p<0.001). The specificity of BALF mNGS was 92.2%, which was similar with BALF culture (98.5%) and BALF GM (94.7%). The combination of BALF mNGS and GM could increase the sensitivity to 88.7%, and had great negative predictive value (NPV, 92.3%). The sensitivity of blood mNGS was significantly higher than serum GM (58.8% vs. 16.7%, p<0.001). And the sensitivity of sputum mNGS was 66.7%, which was significantly higher than sputum culture (30.0%, p=0.025).

CONCLUSION: mNGS demonstrated significant diagnostic value for IPA, exhibiting significantly higher sensitivity compared to current conventional microbiological tests while maintaining equivalent specificity. The combination of BALF mNGS with GM performed great sensitivity and negative predictive value. BALF specimens seemed to be superior to blood and sputum samples. However, for patients unable to undergo bronchoscopy, sputum and blood mNGS were still superior to other methods.},
}

Humans
Male
*Invasive Pulmonary Aspergillosis/diagnosis/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Sputum/microbiology
Mannans/analysis/blood
Aged
Sensitivity and Specificity
Adult
*Aspergillus/genetics/isolation & purification/classification
Galactose/analogs & derivatives

@article {pmid42058649,
year = {2026},
author = {Kwarteng, A and Amedorme, D and Addy, HPK and Amewu, EKA and Osei-Poku, P and Larbi, A},
title = {Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {6677609},
pmid = {42058649},
issn = {1687-918X},
abstract = {Brukina, a traditional fermented beverage smoothie made from milk and millet, is popular in Ghana and other West African countries due to its tasty flavor, high nutritional content, and affordability. Despite its widespread consumption, the nature of its production through artisanal fermentation processes presents concerns regarding microbial consistency, nutritional optimization, and food safety. This literature review explores the potential of metagenomic approaches to uncover microbial diversity, functional capacity, and safety profiles of Brukina. By integrating insights from amplicon-targeted and shotgun whole-genome sequencing studies on fermented foods, we highlight how next-generation sequencing technologies can characterize lactic acid bacteria, yeast, and other microorganisms that drive fermentation. Additionally, we discuss how metagenomics can identify functional genes influencing carbohydrate metabolism, flavor and aroma generation, and production of antimicrobial resistance compounds. Thus, metagenomics provides a powerful framework for assessing public health risks and nutritional benefits. Bioinformatic tools have also been highlighted, and their relevant application in analyzing sequenced data to achieve taxonomic classification, identification of biochemical pathways, and functional profiling of microbial ecology of fermented foods. This review outlines key research gaps and recommends future directions, including starter culture development, standardization of Brukina production, multi-omics integration in metagenomics, and microbiome-informed food safety standards. Metagenomic profiling of Brukina holds promise for improving product quality, consumer safety, and scientific understanding of traditional fermented foods. By tackling the challenges raised, metagenomic techniques can be extremely helpful in maximizing Brukina fermentation, guaranteeing food safety, and maintaining the customs that give this product its distinctive character.},
}

@article {pmid42058681,
year = {2026},
author = {Budai, M and Rák, G and Wenner, B and Móré, A and Bancsik, B and Nagy, B and Kovács, G and Szabolcs, M and Ladnyik, Z and Molnár, C and Guller, ZE and Lengyel, A and Vadász, C and Mizsei, E},
title = {The Influence of Plant Species Composition on an Endangered Grassland Specialist Reptile, the Hungarian Meadow Viper.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73579},
pmid = {42058681},
issn = {2045-7758},
abstract = {The Hungarian meadow viper (Vipera ursinii rakosiensis) is one of the most threatened vertebrates in Hungary, whose populations are not growing significantly despite enormous conservation efforts. Previous studies suggested an influence of vertical vegetation structure on habitat use, while the role of horizontal vegetation structure is still poorly understood. In the present study, we used vegetation survey data to investigate the effects of variables related to the horizontal structure and functional composition of vegetation on the occupancy and density of the Hungarian meadow viper. During a spring survey period, we collected viper occurrence data in 59 sampling quadrats alongside plant community samples, then used single-season occupancy models and N-mixture models for analysis. After model selection, the best models included the moisture-related vegetation gradient, species richness, graminoid-forb ratio, and height of plants as explanatory variables for both occupancy and density. Wetter meadows with fewer plant species, a higher graminoid/forb ratio, and habitats with characteristically lower-growing plant species were more probable to be used by the vipers. Our results suggest that the horizontal structure of the vegetation influences the habitat use of vipers and also draw attention to the threats posed by more frequent droughts and heatwaves.},
}

@article {pmid42059272,
year = {2026},
author = {Damian, R and Katarzyna, J and Sebastian, W and Piotr, J and Joanna, G and Małgorzata, C and Monika, H and Edyta, K},
title = {Native Aquatic Plastispheres in a River-Wastewater Catchment: Carbapenem-Resistant Bacteria Isolation and Microscopy-Based Structural Analysis.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70312},
doi = {10.1111/1462-2920.70312},
pmid = {42059272},
issn = {1462-2920},
support = {2021/43/B/ST10/01076//Narodowe Centrum Nauki/ ; },
mesh = {*Rivers/microbiology ; *Biofilms/growth & development ; *Wastewater/microbiology ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/isolation & purification/drug effects/genetics/classification ; Drug Resistance, Bacterial ; Plastics ; *Carbapenem-Resistant Enterobacteriaceae/isolation & purification ; },
abstract = {Plastispheres, microbial biofilms formed on plastic surfaces, are increasingly recognised as ecological niches capable of transporting pollutants and antibiotic-resistant microorganisms. However, mechanistic insights into antimicrobial resistance (AMR) dynamics in natural plastispheres remain limited, particularly for priority pathogens such as carbapenem-resistant Enterobacterales (CRE). Here, we evaluated plastispheres as environmental reservoirs and vectors of carbapenem-resistant bacteria, comparing wastewater (secondary settling tanks, representing the final stage before environmental discharge) and riverine environments. Using a combined SEM-CFM approach, we resolved plastic surface topography and the spatial organisation of biofilm-associated bacteria. Although CRE were not detected, carbapenem-resistant bacteria constituted a stable fraction of heterotrophic communities in both environments and were primarily associated with intrinsic resistance mechanisms. Carbapenem-resistant isolates included Aeromonas spp. (blaCphA), Stenotrophomonas maltophilia (blaL1), and Pseudomonas putida (efflux-based resistance). Microscopy revealed dense bacterial clusters on plastic surfaces, suggesting microenvironments that may facilitate cell-cell interactions, including horizontal gene transfer. These findings highlight plastispheres not only as vectors of AMR but also as potential evolutionary hotspots shaping resistance persistence and dissemination in aquatic systems. Future integrating metagenomic and genomic data on resistance gene mobility with spatially resolved microbial community structure will provide critical insights into the mechanisms and risks of AMR dissemination in plastisphere environments.},
}

*Rivers/microbiology
*Biofilms/growth & development
*Wastewater/microbiology
*Carbapenems/pharmacology
*Anti-Bacterial Agents/pharmacology
*Bacteria/isolation & purification/drug effects/genetics/classification
Drug Resistance, Bacterial
Plastics
*Carbapenem-Resistant Enterobacteriaceae/isolation & purification

@article {pmid42059388,
year = {2026},
author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA},
title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0360225},
doi = {10.1128/spectrum.03602-25},
pmid = {42059388},
issn = {2165-0497},
abstract = {The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology. Self-collected vaginal swabs and questionnaires on dietary, menstrual, and health information were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Medication regimen, along with disease activity and severity, was captured for the RA cohort. Vaginal swabs were subjected to long-read 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, C-reactive protein, and anti-citrullinated protein antibodies (ACPAs). Vaginal microbial richness and Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal interleukin (IL)-18 and epidermeal growth factor (EGF) levels were increased in the RA group; IL-18 correlated with multiple microbial features, whereas EGF levels were not associated with bacterial composition or other host factors. When faceted by diet and menopausal status, several immune markers were increased in the RA vaginal environment. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines. We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, and disease activity and severity. This work opens a new avenue in the multidisciplinary approach to RA patient care.IMPORTANCERheumatoid arthritis (RA) is a debilitating autoimmune disease that disproportionately impacts women. Although it is widely recognized that microbial factors can trigger or aggravate RA symptoms and alter disease progression, it is unknown whether RA impacts the microbiota and immune responses within the vaginal tract. In this study, we compare the vaginal microbial communities and immune (cytokine) profiles in women with RA and healthy controls. Within RA patients, we also evaluate how these factors relate to clinical RA symptoms, RA biomarkers, and RA-related medications. Overall, we found that RA was associated with increased microbial diversity and multiple inflammatory markers, some of which were also associated with RA biomarkers and disease activity. These findings suggest that the vaginal tract may be an additional tissue impacted by RA disease, and further research is needed to understand mechanisms and potential for therapeutic intervention.},
}

@article {pmid42059394,
year = {2026},
author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS},
title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0251025},
doi = {10.1128/spectrum.02510-25},
pmid = {42059394},
issn = {2165-0497},
abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.},
}

@article {pmid42059571,
year = {2026},
author = {Čepić, A and Rausch, P and Geese, T and Dempfle, A and Grassl, GA and Baines, JF},
title = {Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related B4galnt2 gene.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0164025},
doi = {10.1128/msystems.01640-25},
pmid = {42059571},
issn = {2379-5077},
abstract = {UNLABELLED: The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of B4galnt2, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of B4galnt2[+/-] and B4galnt2[-/-] mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that B4galnt2[-/-] mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their B4galnt2[+/-] counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as Blautia, Dorea, and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes aadA and aadE. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the B4galnt2-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.

IMPORTANCE: Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.},
}

@article {pmid42059616,
year = {2026},
author = {Moidu Jameela, R and Kedare, MM and Khan, R and Dhankad, N and Sinha, RK and Zade, A and Shah, S and Chatterjee, A},
title = {Whole genome sequence of Tsukamurella tyrosinosolvens extracted from metagenome of human pleural fluid enriched in Mycobacteria Growth Indicator Tube.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0151825},
doi = {10.1128/mra.01518-25},
pmid = {42059616},
issn = {2576-098X},
abstract = {Misdiagnosis of emerging pathogen Tsukamurella tyrosinosolvens is common due to phenotypic similarity with Mycobacterium tuberculosis (MTB). We report a high-quality, near-complete genome of T. tyrosinosolvens from pleural fluid enriched in Mycobacteria Growth Indicator Tube. The genome of this clinically successful strain can be studied to understand pathogenesis and diagnostic challenges.},
}

@article {pmid42059625,
year = {2026},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0362625},
doi = {10.1128/spectrum.03626-25},
pmid = {42059625},
issn = {2165-0497},
abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.

IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.},
}

@article {pmid42059663,
year = {2026},
author = {Liu, C and Mao, Z and Yu, F and Ni, J and Bao, J and Qu, W and Huang, M and Shen, Y and Zheng, S and Chen, Y},
title = {Integrative multi-omics analysis reveals microbiota alterations and clinical indicators predictive of pulmonary fibrosis progression following SARS-CoV-2 infection.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag173},
pmid = {42059663},
issn = {1477-4054},
support = {82300005//National Natural Science Foundation of China/ ; 82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *COVID-19/complications/virology/microbiology ; Male ; *SARS-CoV-2 ; Female ; Middle Aged ; Disease Progression ; *Pulmonary Fibrosis/microbiology/etiology/virology/pathology ; *Microbiota ; Aged ; Gastrointestinal Microbiome ; Bronchoalveolar Lavage Fluid/microbiology ; Transcriptome ; Metagenomics ; Multiomics ; },
abstract = {Pulmonary fibrosis (PF) following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a life-threatening complication. Despite growing concerns about PF after SARS-CoV-2 infection, early recognition remains challenging. Additionally, the role of changes in respiratory and intestinal microbiota in PF progression remains insufficiently understood. To address this gap, this study uses a multi-omics approach to analyze microbiota and clinical changes in PF patients following SARS-CoV-2 infection, developing a predictive model for PF progression with risk stratification to enable early interventions and improve outcomes. A total of 68 patients with confirmed SARS-CoV-2 infection were included in the study, divided into two subgroups: patients with PF (COVID-PF) and patients without PF (COVID-non PF). Metagenomic sequencing of bronchoalveolar lavage fluid (BALF) and fecal specimens was performed to profile respiratory and intestinal microbiota. Peripheral blood mononuclear cells (PBMCs) were collected for transcriptome sequencing. A random forest classifier was developed to predict PF risk based on integrated respiratory-intestinal microbiota profiles as well as clinical indicators. Our findings suggest that there are significant differences in the respiratory and intestinal microbiota between COVID-non PF and COVID-PF patients. Transcriptomic analysis of PBMCs revealed significant activation of immunomodulatory pathways associated with PF development. The machine learning model further allowed early PF risk stratification, demonstrating that changes in both microbiomes, along with clinical indicators, can predict the progression and prognosis of PF. Overall, these results offer new insights into disease and suggest options for early detection and personalized treatment strategies for PF in SARS-CoV-2-infected patients.},
}

Humans
*COVID-19/complications/virology/microbiology
Male
*SARS-CoV-2
Female
Middle Aged
Disease Progression
*Pulmonary Fibrosis/microbiology/etiology/virology/pathology
*Microbiota
Aged
Gastrointestinal Microbiome
Bronchoalveolar Lavage Fluid/microbiology
Transcriptome
Metagenomics
Multiomics

@article {pmid42059780,
year = {2026},
author = {Wolfe, BE},
title = {Metagenomes enriched with Virgibacillus are associated with a pink paste defect in an unpasteurized blue cheese.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0002726},
doi = {10.1128/mra.00027-26},
pmid = {42059780},
issn = {2576-098X},
abstract = {Shotgun metagenomes were used to identify microbes associated with a pink discoloration of an unpasteurized blue cheese made in the United States. Taxonomic assessments of individual reads and metagenome-assembled genomes revealed that the genus Virgibacillus was present in the pink paste, but not in unaffected paste.},
}

@article {pmid42059891,
year = {2026},
author = {Pang, H and Peng, B and Yan, X and Wang, J and Lu, Y and Yuan, X and Zhang, Y and Zhang, L and Huang, J and Zhang, Y and Yang, R and Ma, X and Wang, X and Fan, C and Zhang, L and Song, W and Cheng, Y and Liang, S and Wang, Y and Zheng, W and Li, G},
title = {Pregnancy-induced hypertension are preceded by prenatal perturbations of the gut microbiome and metabolome.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-026-06221-1},
pmid = {42059891},
issn = {1420-9071},
support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; No. Lingjunrencai-02-02//High-level construction project of public health technical personnel in Beijing Municipal Health System/ ; },
}

@article {pmid42060200,
year = {2024},
author = {Demirci, T},
title = {Highlighting the Microbial Community of Kuflu Cheese, an Artisanal Turkish Mold-Ripened Variety, by High-Throughput Sequencing.},
journal = {Food science of animal resources},
volume = {44},
number = {2},
pages = {390-407},
doi = {10.5851/kosfa.2023.e59},
pmid = {42060200},
issn = {2636-0780},
abstract = {Kuflu cheese, a popular variety of traditional Turkish mold-ripened cheeses, is characterized by its semi-hard texture and blue-green color. It is important to elucidate the microbiota of Kuflu cheese produced from raw milk to standardize and sustain its sensory properties. This study aimed to examine the bacteria, yeasts, and filamentous mold communities in Kuflu cheese using high-throughput amplicon sequencing based on 16S and ITS2 regions. Lactococcus, Streptococcus, and Staphylococcus were the most dominant bacterial genera while Bifidobacterium genus was found to be remarkably high in some Kuflu cheese samples. Penicillium genus dominated the filamentous mold biota while the yeasts with the highest relative abundances were detected as Debaryomyces, Pichia, and Candida. The genera Virgibacillus and Paraliobacillus, which were not previously reported for mold-ripened cheeses, were detected at high relative abundances in some Kuflu cheese samples. None of the genera that include important food pathogens like Salmonella, Campylobacter, Listeria were detected in the samples. This is the first experiment in which the microbiota of Kuflu cheeses were evaluated with a metagenomic approach. This study provided an opportunity to evaluate Kuflu cheese, which was previously examined for fungal composition, in terms of both pathogenic and beneficial bacteria.},
}

@article {pmid42060748,
year = {2026},
author = {Xie, F and Jiang, C and Li, Z and Feng, J and Yan, X and Hu, C and He, J and Chai, X and Huang, Z and Xu, Q and Wang, Y and Xiao, Y and Chen, K and Qin, W and Xiao, Y and Zhang, J and Wang, G and Jin, W and Guo, K and Lin, L and Liu, Y and Gao, X and Zheng, L and Shu, X and Wang, R and Wang, M and Si, H and Du, R and Zhu, W and Guan, LL and Wang, W and Qiu, Q and Mao, S and Xiong, J and Miao, W},
title = {Rumen ciliates modulate methane emissions in ruminants.},
journal = {Science (New York, N.Y.)},
volume = {392},
number = {6797},
pages = {eadv4244},
doi = {10.1126/science.adv4244},
pmid = {42060748},
issn = {1095-9203},
mesh = {Animals ; *Methane/biosynthesis/metabolism ; *Rumen/parasitology/metabolism ; *Ciliophora/genetics/classification/metabolism/ultrastructure/enzymology/physiology ; Hydrogen/metabolism ; Cattle/parasitology ; Hydrogenase/metabolism/genetics ; Oxygen/metabolism ; },
abstract = {Rumen ciliates are major contributors to enteric methane emissions from ruminant animals, yet the underlying mechanisms remain poorly understood. We present a catalog of 450 rumen ciliate genomes, with 87% newly generated. Using this resource, we quantified methane emissions from 100 cows and analyzed 1877 rumen metagenomic and metatranscriptomic datasets, which revealed correlations among ciliate abundance, methanogen abundance, and methane emissions. We further demonstrated that taxon-specific effects of rumen ciliates on methane production arise from a single-membrane, hydrogen-producing organelle called the hydrogenobody (HB), which is distinct from canonical hydrogenosomes in other protists. HBs are positioned near ciliary basal bodies and harbor specific hydrogenases and oxygen reductases. We found that Vestibuliferida ciliates, which have more abundant HBs than do Entodiniomorphida, exhibit enhanced hydrogen production and oxygen-scavenging capacity, thereby strongly promoting methanogenesis.},
}

Animals
*Methane/biosynthesis/metabolism
*Rumen/parasitology/metabolism
*Ciliophora/genetics/classification/metabolism/ultrastructure/enzymology/physiology
Hydrogen/metabolism
Cattle/parasitology
Hydrogenase/metabolism/genetics
Oxygen/metabolism

@article {pmid42060822,
year = {2026},
author = {Poretsky, RS and Dhiman, VK and Hendricks, DL and Lin, CY and Sanchez Gonzalez, D and Greenwald, S and Owens, SM and Williams, CH and Leslie, MT and Bemis, K and Frias, M and Kaufman, JT and O'Connor, DH and Johnson, MC},
title = {Detection of a Single Measles Infection Using Untargeted Ultra-Deep Metagenomic Sequencing of Wastewater in Cook County, Illinois.},
journal = {NEJM evidence},
volume = {},
number = {},
pages = {EVIDpha2600079},
doi = {10.1056/EVIDpha2600079},
pmid = {42060822},
issn = {2766-5526},
abstract = {AbstractMeasles is a contagious, vaccine-preventable viral disease that can be shed into wastewater by infected individuals. In September 2025, as part of an ongoing, nontargeted, ultra-deep metagenomic sequencing effort of wastewater in Cook County, Illinois, we detected measles reads from a facility serving more than 1 million people. Out of more than 900 million reads sequenced from wastewater collected on September 14, 2025, 43 matched measles virus genotype B3. Subsequent genomic analysis linked these reads to a confirmed measles infection that was present in the community on that day, demonstrating that untargeted metagenomics appeared to detect a single measles infection in a large municipal wastewater stream.},
}

@article {pmid42060994,
year = {2026},
author = {Huang, D and Sun, X and Lin, W and Lan, X and Tan, Z and Ren, Y and Huang, Y and Cao, Y and Sun, W},
title = {Hydrogen oxidation coupled to dissimilatory arsenate reduction: A potentially widespread pathway associated with arsenic mobility in anoxic sediments.},
journal = {Water research},
volume = {301},
number = {},
pages = {125984},
doi = {10.1016/j.watres.2026.125984},
pmid = {42060994},
issn = {1879-2448},
abstract = {In aquatic environments, the arsenic (As) mobilization from anoxic sediments is an important process affecting water quality and associated health risks, as sediment-bound As can serve as a persistent secondary source to overlying waters and groundwater systems. Dissimilatory arsenate reduction (DAsR) is a key microbial process releasing dissolved As(III), yet the role of inorganic electron donors in this pathway remains poorly constrained. Although hydrogen (H2) is thermodynamically favorable for arsenate respiration, its role in arsenate reduction in natural sediments remains insufficiently resolved. In this study, hydrogen oxidation coupled to arsenate reduction (HOAsR) was investigated using sediments from an As-contaminated, mining-impacted river system. Microcosm incubations showed that H2 amendment stimulated As(V) reduction under anoxic conditions. DNA-stable isotope probing combined with metagenomics identified Sulfuritalea, Dechloromonas, and a Moorellia-related lineage as putative HOAsR-associated populations. Corresponding metagenome-assembled genomes encoded both H2 uptake [NiFe]-hydrogenases and the dissimilatory arsenate reductase gene (arrA). Comparative genome analysis further revealed that ∼75% of arrA-containing genomes harbor H2 uptake [NiFe]-hydrogenases, suggesting that H2 oxidation represents a phylogenetically widespread metabolic trait among DAsR bacteria. Analysis of public riverine metagenomes further indicated that HOAsR-associated genetic configurations are broadly distributed across sediment microbial communities. Together, these results indicated that HOAsR is a biologically plausible and geographically widespread potential pathway contributing to arsenic mobilization in anoxic sediments.},
}

@article {pmid42061080,
year = {2026},
author = {Chen, C and Hao, H and Hao, R and Yu, N and Li, X},
title = {Microbial driving mechanisms of sludge reduction in modular wastewater treatment systems under surplus aeration regulation.},
journal = {Journal of environmental management},
volume = {406},
number = {},
pages = {129816},
doi = {10.1016/j.jenvman.2026.129816},
pmid = {42061080},
issn = {1095-8630},
abstract = {The treatment and disposal of residual sludge pose a critical bottleneck to the sustainable development of wastewater treatment plants (WWTPs). Modular wastewater treatment systems have garnered significant interest due to their high efficiency and operational flexibility, making them well-suited for small-scale community applications. This study aims to investigate the microbial driving mechanisms underlying sludge reduction in such field-based systems under surplus aeration regulation. By comparing treatment performance, microbial community structure, and metabolic functions between the Surplus Aeration (SA) group and the Conventional (Conv.) group-coupling 16S rRNA high-throughput sequencing and metagenomic analysis -the microbiological basis of sludge reduction was systematically elucidated. Results demonstrated that the SA group achieved a 63.7% reduction in residual sludge while maintaining compliant effluent quality (GB 18918-2002), with COD and NH4[+]-N removal rates both reaching more than 85%. 16S rRNA profiles indicated higher alpha diversity in the SA group and clear community separation from the Conv. group (PERMANOVA, p < 0.001). The SA group was enriched in taxa with documented extracellular polymeric substance (EPS) degradation potential, including Saccharimonadales, Saprospiraceae, and Caldilineaceae, whereas the Conv. group showed relatively higher abundance of taxa often associated with proliferation and EPS production (e.g., OLB17, Acinetobacter). Metagenomic functional annotation suggested higher representation of genes and pathways related to carbohydrate processing and energy metabolism in the SA group. As these omics results primarily reflect functional potential rather than confirmed in situ activity, we present a conceptual mechanism in which surplus aeration improves DO distribution and substrate utilization in the field system, thereby favoring EPS breakdown and energy-use efficiency-consistent with the observed reduction in sludge yield.},
}

@article {pmid42061404,
year = {2026},
author = {Su, Q and Chen, S and Lau, LH and Lui, RN and Wang, Y and Xu, Z and Cheung, CP and Ching, JYL and Shen, X and Peng, Y and Tun, HM and Ianiro, G and Rubin, D and Chang, EB and Chan, FKL and Ng, SC},
title = {Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation.},
journal = {Cell reports},
volume = {},
number = {},
pages = {117301},
doi = {10.1016/j.celrep.2026.117301},
pmid = {42061404},
issn = {2211-1247},
abstract = {Fecal microbiota transplantation (FMT) has emerged as a promising therapy for gastrointestinal diseases, yet its clinical efficacy remains individually variable. Here, we analyze multi-kingdom and functional profiles in pre- and post-FMT metagenomes from 515 FMTs across 30 cohorts and 12 diseases, in which 94 metagenomes from 44 FMTs are newly collected. We reveal a robust association between clinical efficacy and post-FMT microbiome convergence of recipients toward donors, across diseases. To predict post-FMT microbial convergence, we develop MOZAIC (Microbiome Matching Optimization via Artificial Intelligence), a framework that integrates multi-dimensional donor-recipient microbiota features. MOZAIC achieves an average area under the curve (AUC) of 0.88 and accuracy/recall >0.80 in forecasting microbiome convergence, with 78.7% accuracy in predicting clinical outcomes, and retrospectively simulates a 1.44-fold improvement (from 49.4% to 71.0%) in clinical response rates over baseline. This study establishes microbiome convergence as a key mediator of FMT and provides a scalable tool for precision matching in microbiota-based therapies.},
}

@article {pmid42061651,
year = {2026},
author = {Neuhaus, S and Tausch, SH and Gulich, K and Körber, N and Grützke, J and Hensel, A and Dahouk, SA and Dieckmann, R},
title = {Kitchen sponges as reservoirs of foodborne pathogens: Microbial growth dynamics, surface cross-contamination, and hygiene implications.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100794},
doi = {10.1016/j.jfp.2026.100794},
pmid = {42061651},
issn = {1944-9097},
abstract = {Foodborne pathogens pose a persistent risk to public health, with domestic environments representing a major but often underestimated source of contamination. In this study, we investigated the survival, proliferation, and transfer potential of Salmonella Enteritidis, Escherichia coli, and Staphylococcus aureus in kitchen sponges harboring an established core microbiota. Using culture-based, metagenomic, and fluorescence in situ hybridization approaches in combination with confocal laser scanning microscopy, we examined pathogen persistence, desiccation tolerance, cross-contamination potential, and spatial microbial organization over 14 days. All three pathogens persisted within the sponge matrix for at least 2 weeks, even at very low initial populations (approximately 2,5log10 colony-forming units (CFU) per sponge section). Escherichia coli and Salmonella Enteritidis rapidly established stable populations reaching approximately 9 log CFU per sponge section, whereas Staphylococcus aureus showed limited growth of approximately 4 log CFU per sponge section, indicating species-specific interactions with the resident microbiota. Notably, pathogen populations remained stable after 3 days of desiccation, confirming the role of sponges as long-term microbial reservoirs. Contact between colonized sponges and surfaces under mild pressure resulted in transfer of up to 5 log CFU to contacted surfaces, highlighting realistic domestic transmission pathways. Sensory changes such as odor or discoloration were not correlated with microbial load, indicating that visual assessment is unreliable for sponge replacement decisions. These results underscore the role of kitchen sponges as critical microbial reservoirs in households and emphasize the need for regular sponge replacement or the use of alternative cleaning utensils. The standardized sponge model developed in this study provides a valuable platform for evaluating sanitation strategies and for understanding microbial interactions relevant to domestic hygiene and public health.},
}

@article {pmid42061790,
year = {2026},
author = {Zhang, Y and Zhang, G and Liang, J and Chang, J and Zhang, P and Fang, W and Wang, Q},
title = {Regulation of greenhouse gas emissions and carbon sequestration in wetland by submerged plant mowing time and potential mechanisms.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124621},
doi = {10.1016/j.envres.2026.124621},
pmid = {42061790},
issn = {1096-0953},
abstract = {Mowing is an important submerged plant growth management measure to maintain the balance of inland wetland ecosystems. However, systematic studies on plant mowing time affecting wetland greenhouse gas (GHG) emissions and carbon sequestration remain scarce. In this research a pilot-scale wetland system was established to investigate the effects of submerged plant Ceratophyllum demersum L. mowing time on GHG emissions and carbon sequestration, and metagenomic techniques were employed to explore the functional microorganisms and genes for carbon and nitrogen cycling in wetland. The results showed that C. demersum L. mowing resulted in CO2 flux reduction of 55.76%-79.34%, CH4 flux reduction of 83.54%-99.48%, and N2O flux reduction of 75.80%-82.88%. The optimal plant mowing time was July, achieving a better trade-off between carbon sequestration and carbon emissions. The C. demersum L. biomass showed obvious temporal dynamics, with the highest biomass for mowing in July, increasing by 12.12% compared with that of control. However, plant mowing slightly reduced the water purification capacity. Microbial analysis revealed that plant mowing downregulated the expression of key functional genes (mcrA, pmoA, norB, nosZ) and decreased the abundance of methanogens and denitrifying bacteria, explaining the reduction in CH4 and N2O fluxes. These findings provide a scientific basis for wetland plant growth management. Future research should explore long-term field validation and effects of environmental variables.},
}

@article {pmid42062403,
year = {2026},
author = {Radwan, HM and El Menofy, NG and Tharwat, EK and Mysara, M and Radwan, SMR},
title = {Metagenomic profiling of microbial communities and the resistome within Egyptian hospital wastewater and tap water.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42062403},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; Egypt ; *Metagenomics/methods ; Hospitals ; *Drinking Water/microbiology ; Humans ; *Microbiota/genetics ; Water Microbiology ; *Metagenome ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a worldwide health concern that compromises the successful treatment of a growing array of infectious diseases, particularly in low- and middle-income countries. AMR is exaggerated by the spread of antimicrobial resistance genes (ARGs) across humans, animals, and environmental reservoirs like water and soil. Hospital wastewater (HWW) is the main source of antimicrobial resistance in the environment. The current study used high throughput metagenomic nanopore sequencing to investigate the microbial abundance and ARGs associated with both HWW and tap water in five different hospitals in Cairo, Egypt. The bacterial community composition of the HWW microbiome identified 25 taxonomic families. The most abundant genera in HWW were Acinetobacter (6%) and Propioniciclav (5%) out of 101 unique genera while, the most abundant in tap water were Enterococcus (53%), Escherichia (15%), and Francisella (14%) out of 89 unique genera. Alpha diversity analysis revealed significantly greater microbial diversity in the HWW samples than in the tap water samples (P value > 0.05), moreover beta diversity analysis revealed a significant difference in the microbial community composition between the tap water and HWW samples (P value > 0.05) using Chao metric for richness estimation and Shannon metric for richness and evenness estimation. Total ARG analysis revealed absence of ARGs in tap water using the three databases, while comparable levels of ARGs were detected in HWW across the five hospitals. In total, 45, 28, and 28 ARG subtypes were identified in the HWW samples using ResFinder, CARD, and the NCBI AMRFinderPlus databases, respectively. The most abundant AMR mechanisms among the five hospitals were linked to the inhibition of protein synthesis. Using the ResFinder database, streptogramin resistance genes were most prevalent in Hospitals 1 and 5 (15% and 40%, respectively); using CARD, aminoglycoside, lincosamide, and macrolide resistance genes were most predominant (relative abundances 35-60%). Using NCBI AMRFinderPlus, streptomycin, tetracycline, and macrolide resistance genes were most prevalent (relative abundances 30.1-60%). Detection of plasmid replicons in HWW identified 39 different plasmid-associated replication genes via the PlasmidFinder database. The Col440l-1, colRNAI-1 and Col440ll-1 plasmid replicons were the most detected across the five hospitals with relative abundances of 16.6%, 10.9% and 9.6%, respectively. This study revealed different microbial communities among HWW and tap water in addition to the widespread occurrence of ARGs and AMR encoding plasmid replicons in the HWW in the five different hospitals in Cairo, Egypt indicating a significant risk associated with HWW, necessitating the implementation of preventative measures to avert their environmental diffusion. To our knowledge, this is one of the first Egyptian studies to apply Oxford Nanopore long-read metagenomic sequencing for simultaneous profiling of microbial communities and the resistome in HWW and tap water, using three ARG databases across five hospitals in two seasons.},
}

*Wastewater/microbiology
Egypt
*Metagenomics/methods
Hospitals
*Drinking Water/microbiology
Humans
*Microbiota/genetics
Water Microbiology
*Metagenome
*Bacteria/genetics/classification/drug effects
*Drug Resistance, Bacterial/genetics

@article {pmid42062603,
year = {2026},
author = {Xu, T and Yang, Y and Zhu, R and Lin, W and Li, J and Zheng, Y and Zhang, P and Zhang, G and Zhao, G and Jiao, N},
title = {DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model.},
journal = {Nature computational science},
volume = {},
number = {},
pages = {},
pmid = {42062603},
issn = {2662-8457},
support = {32470098//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92451303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbial-derived secondary metabolites (SMs) hold great therapeutic potential but are predominantly discovered from cultured species, representing only a fraction of microbial biodiversity. Advances in metagenomics have unveiled reservoirs of biosynthetic gene clusters (BGCs), but translating genomic sequences into precise chemical structures remains challenging owing to the structural complexity of cryptic BGCs and the context-dependent substrate tolerance and cross-reactivity of modular biosynthetic domains. Here we present DeepSeMS, a transformer-based large language model that accurately predicts secondary metabolite chemical structures from BGC sequences. By encoding biosynthetic genes as functional domains and leveraging a feature-aligned data augmentation, DeepSeMS outperformed existing methods and successfully generated chemically valid predictions for 96.38% of cryptic BGCs. Applying DeepSeMS to a global ocean metagenome, we characterized over 60,000 secondary metabolites, revealing chemical diversity, ecological specificity and considerable biomedical potential, especially as antibiotics. This study underscores the capability of deep learning-driven approaches in revealing hidden biosynthetic potential of Earth's largest, yet largely unexplored, microbial ecosystem.},
}

@article {pmid41857781,
year = {2026},
author = {Alexander, JE and Appleton, C and Beatty, SSK and Brown, DC and Carvell-Miller, L and McKee, TS and Morrison, J and Patterson-Kane, JC and Reynolds, R and Wadulack, S and , },
title = {Cohort profile of the first 2,000 canine enrolees in the Mars Petcare Biobank: demographic, hematologic and serum biochemistry results from March 2022 to December 2024.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {41857781},
issn = {1746-6148},
abstract = {BACKGROUND: The MARS PETCARE BIOBANK™ (MPB) is a study recruiting pets visiting Mars Veterinary Health hospitals in the USA over a ten-year period, with the aim of analysing longitudinal data from thousands of otherwise healthy dogs and cats at their first presentation to identify novel and actionable pet health insights . The present study summarises the baseline demographic, haematologic, and serum biochemistry data recorded for the first 2000 dogs enroled in the MPB study between March 2022 and December 2024 and considers how representative they are of the general population in the United States.

RESULTS: The median enrolment age was 3.0 years (0.5–10.0 yrs). The population was 52% male and 48% female with approximately 84% of the population having undergone neutering by their initial study visit. The median enrolment body weight was 20.0 kg (2.5 – 71.5 kg) and the median body condition score was 5/9 (range 3–7). One hundred and twenty eight breeds were represented and 47% of the population were described as mixed breed. The median values for all serum biochemistry and complete blood count parameters were within the applicable reference interval. For certain analytes including serum glucose, amylase, cholesterol, phosphorus, creatine phosphokinase, precision pancreatic lipase, platelet count, haematocrit, and haemoglobin more than 5% of dogs had results outside the reference intervals. On review only 0.25% of dogs were subsequently excluded from continuing the MPB study because the results were considered of clinical significance.

CONCLUSIONS: The MPB aims to enable research to deliver insights applicable to the general dog population accessing primary veterinary care in the USA, and recruits accordingly. These data suggest that the first 2,000 dogs recruited in the MPB are comparable in demographics to other studies of the US population. The number of blood test results falling outside of reference intervals (up to 17% depending on analyte), for dogs deemed by veterinarians to be healthy in the context of the clinical history and examination, raises questions around the definition of health and how reference intervals are used. Data gathered during the study is expected to provide valuable information to studies pertaining to genetic, metagenomic, metabolic, dietary, and environmental risk factors associated with early signals of transition to various common diseases.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-026-05419-6.},
}

@article {pmid41959053,
year = {2026},
author = {Midani, FS and Lee, DH and Moon, Y and Seale, M and Horvath, TD and Ardis, AK and Cantú, J and Coles, E and Pizzini, JD and Zhu, D and Dooling, SW and Ahern, GJ and Ardis, CK and Beckford, A and Ruggiero, NM and Shin, J and Joos, R and Stanton, C and Ross, RP and Dai, DLY and Mandhane, PJ and Petersen, C and Turvey, SE and Kiely, ME and Murray, DM and Costa-Mattioli, M and Tolias, KF and Britton, RA and Danhof, HA},
title = {Infant gut microbiomes contribute to metabolic states that impact brain function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41959053},
issn = {2692-8205},
abstract = {Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.},
}

@article {pmid42043697,
year = {2026},
author = {Lomelí-Álvarez, MF and Escamilla-Montes, R and Diarte-Plata, G and Guo, X and Fierro-Coronado, JA and Rubio-Luque, AM and Vega-Carranza, AS and González, AL},
title = {Dietary and water probiotics enhance immunity, modulate microbiota, and increase survival of Penaeus vannamei challenged with V. parahaemolyticus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42043697},
issn = {1678-4405},
abstract = {This study evaluated the effects of Bacillus licheniformis and Pediococcus pentosaceus administered in both culture water and feed to Penaeus vannamei over a 47-day experiment. Treatments in triplicate were as follows: (I) Commercial Feed (CF); (II) CF + P. pentosaceus in the water (3 × 10[6] CFU/L); (III) CF + B. licheniformis in the water (3 × 10[6] CFU/L); (IV) P. pentosaceus in fermented feed (51 × 10[5] CFU/g); (V) B. licheniformis in fermented feed (147 × 10[6] CFU/g); (VI) Mix of P. pentosaceus (140 × 10[5] CFU/g) + B. licheniformis (180 × 10[5] CFU/g) in fermented feed + Mix of P. pentosaceus + B. licheniformis (3 × 10[6] CFU/L) in the water. Growth, immune effectors (phenoloxidase and superoxide anion), and gut bacterial profiles via 16S metagenomic sequencing were assessed. Survival was determined after a challenge with Vibrio parahaemolyticus. Probiotics did not affect growth. Only B. licheniformis in water and fermented feed elicited a significant immunostimulatory response, increasing superoxide anion production and phenoloxidase activity, respectively. Probiotic administration also modulated the gut microbiota, significantly increasing the relative abundance of beneficial genera like Ruegeria and Haloferula. Measures of both alpha and beta diversity indicated a significant restructuring of the microbial community in response to probiotics. Most major bacterial groups showed predominantly positive intra-group interactions, while Psychromonadaceae solely exhibited negative interactions with other families. Shrimp survival was significantly higher in shrimp treated with probiotics, excluding treatment II. These results demonstrate that probiotics strengthen innate immunity and improves disease resistance in shrimp by enhancing immunocompetence and enriching beneficial gut microbes, offering a viable strategy for sustainable aquaculture health management.},
}

@article {pmid42050656,
year = {2026},
author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K},
title = {Correction: Bacteriophages in gut metagenomes: from analysis to application.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42050656},
issn = {1743-422X},
}

@article {pmid42050727,
year = {2026},
author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S},
title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00577-2},
pmid = {42050727},
issn = {2524-4671},
}

@article {pmid42050730,
year = {2026},
author = {Seppey, M and Benavides, A and Berkeley, MR and Manni, M and Zdobnov, EM},
title = {LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-04089-9},
pmid = {42050730},
issn = {1474-760X},
support = {ESKAS No. 2022.0531//Federal Commission for Scholarships for Foreign Students for the Swiss Government Excellence Scholarship/ ; 310030_189062//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challenging, and novel tools face visibility issues. Here, we present LEMMIv2, an updated platform for continuous benchmarking of metagenomic profilers, providing developers with impartial benchmarks and offering users a catalogue of evaluated tools. New features include support for alternative taxonomies and long-read applications, and a standalone pipeline for local benchmarking. We also extend the approach to 16S amplicon profiling with LEMMI16S, which evaluates methods across several reference databases.},
}

@article {pmid42051014,
year = {2026},
author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L},
title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70280},
pmid = {42051014},
issn = {1744-7917},
support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; },
abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.},
}

@article {pmid42051699,
year = {2026},
author = {Du, Y and Guo, Z and Yao, D and Wang, Y},
title = {Hemophagocytic lymphohistiocytosis secondary to Pneumocystis jirovecii pneumonia: a rare case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1795567},
pmid = {42051699},
issn = {2296-858X},
abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Pneumocystis jirovecii pneumonia (PJP) is extremely rare in children. We present the case of a 10-year-old girl with a history of idiopathic thrombocytopenic purpura (ITP) on long-term oral prednisone, who was admitted for progressive fever, cough, and dyspnea. Metagenomic next-generation sequencing of blood and bronchoalveolar lavage fluid confirmed PJP. Despite targeted antifungal therapy and respiratory support, she developed persistent high-grade fever, pancytopenia, hyperferritinemia, hypofibrinogenemia, and hemophagocytosis on bone marrow aspirate by day 10, meeting diagnostic criteria for HLH. Genetic testing was declined by the parents. Management included dexamethasone, continuous renal replacement therapy, and plasmapheresis. Unfortunately, her condition deteriorated, and she was discharged upon parental request on day 22, succumbing on the same day. To our knowledge, this is the first reported pediatric case of HLH secondary to PJP in China. This case highlights that in children with PJP-especially those on immunosuppressive therapy-the development of persistent fever and cytopenia should prompt immediate evaluation for secondary HLH to enable timely intervention.},
}

@article {pmid42052210,
year = {2026},
author = {Qu, HL and Li, JN and Gao, Y and Xu, XM and Zhang, XB and Yang, SD},
title = {From microscopy to antimicrobial decisions: a clinically grounded roadmap for critical care infectious diseases.},
journal = {Frontiers in artificial intelligence},
volume = {9},
number = {},
pages = {1807400},
pmid = {42052210},
issn = {2624-8212},
abstract = {In the intensive care unit (ICU), antibiotics often begin under extreme uncertainty. Fever, leukocytosis, hypotension, and organ dysfunction may signal bacterial infection, but the same findings are common with aspiration, post-operative inflammation, drug reactions, or sterile systemic inflammation. Cultures take time and their yield falls after antibiotics. Rapid molecular tests and metagenomics can add actionable information, but they also raise the burden of interpreting complex results. Microscopy is one of the few inputs that can shift management within minutes to hours: Gram-stain patterns from positive blood-culture bottles, respiratory specimens, cerebrospinal fluid, and wound material can reshape initial coverage and support early de-escalation when negative. Tissue and cytology help distinguish invasion from key mimics. The gap is consistency-reads vary across observers, workflows differ, and results do not always translate into reliable bedside actions. This review focuses on infectious-disease artificial intelligence (AI) as ICU bedside decision support, rather than as a survey of models. Using ICU sepsis as the primary use case-and neurocritical care as a challenging setting where sedation, brain injury, and noninfectious inflammation often mimic infection-we separate evidence into pathogen signals and host-response signals. We then map both streams to six decisions over the first 72 hours: start now versus pause, choose initial spectrum, reassess and narrow, escalate diagnostics and source control, act on high-risk resistance or invasive pathogens, and stop safely. We summarize where AI is most credible today (Gram-stain assistance, culture-plate triage, urine-culture screening, infection-focused digital pathology, host-response classifiers, and selected metagenomics) and what makes outputs actionable: calibrated probabilities, explicit confidence with safe deferral when uncertain, validation across hospitals and instruments, and endpoints tied to stewardship and safety (time to appropriate therapy, antibiotic days, de-escalation within 72 hours, missed bacteremia). Evidence was updated through February 28, 2026.},
}

@article {pmid42052392,
year = {2026},
author = {Suenaga, H and Fujihara, H},
title = {Molecular basis for adaptive evolution of aromatic degradation enzymes in bacteria revealed by metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1795400},
pmid = {42052392},
issn = {1664-302X},
abstract = {Aromatic hydrocarbons, including persistent polycyclic aromatic hydrocarbons (PAHs), impose strong selective pressures that drive the adaptive evolution of bacterial degradation systems. Metagenomic studies have revealed extensive diversification of key catabolic enzymes, such as ring-hydroxylating and ring-cleavage dioxygenases, through the accumulation of single-nucleotide polymorphisms (SNPs) and structural modifications that increase substrate range and enhance catalytic efficiency in polluted environments. These findings demonstrate that gene mutations that change enzyme properties collectively shape the evolution of aromatic-degrading bacteria. Metagenomics is powerful tools for elucidating these evolutionary processes and advancing applications in bioremediation and industrial biocatalysis.},
}

@article {pmid42052398,
year = {2026},
author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ},
title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794875},
pmid = {42052398},
issn = {1664-302X},
abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.},
}

@article {pmid42052556,
year = {2026},
author = {Chu, T and Liu, J and Zhang, Y and Yang, K and Li, S and Yan, Q and Li, Y},
title = {Metagenome-based virome analysis identifies the oral viral signatures for periodontitis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2662091},
pmid = {42052556},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis (PD) is a chronic infectious disease driven by bacterial biofilms, yet the oral virome's role in pathogenesis remains poorly understood.

OBJECTIVE: This cross-cohort meta-analysis aims to define PD-associated viral signatures, characterize predicted virus-host interactions, and evaluate the diagnostic potential of viral biomarkers.

METHODS: We integrated 89 saliva (44 PD, 45 healthy) and 86 subgingival plaque (48 PD, 38 healthy) metagenomes from six public cohorts for a unified virome analysis.

RESULTS: We identified 156 viral operational taxonomic units (vOTUs) significantly associated with PD (105 in saliva, 66 in subgingival plaque and 15 shared). PD-enriched vOTUs were predicted to target periodontal pathogens including Porphyromonas gingivalis, whereas Streptococcus-targeting phages were decreased. PD-associated vOTUs harbored diverse bacterial defense and anti-defense systems, with those enriched in PD overrepresenting lysozyme and replication-associated genes. Diagnostic models based on key viral markers achieved robust performance, with AUCs of 0.95 (saliva) and 0.92 (subgingival plaque) for classifying PD.

CONCLUSION: This study delineates a distinct oral virome profile in PD, highlights predicted virus-host interactions, and underscores the potential of viral biomarkers for PD diagnosis,providing a basis for future investigations into viral ecology and phage-based interventions.},
}

@article {pmid42052831,
year = {2026},
author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S},
title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {48982},
doi = {10.31083/FBL48982},
pmid = {42052831},
issn = {2768-6698},
support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.

METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.

RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 ± 0.12, suggesting promising discriminatory potential that warrants further validation.

CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Glomerulonephritis, Membranous/microbiology
*Metagenomics/methods
Male
Female
Middle Aged
Feces/microbiology
Adult
*Bacteria/genetics/classification
Case-Control Studies

@article {pmid42053312,
year = {2026},
author = {Chung, B and Wang, S and Hao, Z and Allison, SD and Malik, AA},
title = {Plant litter chemistry and associated changes in microbial decomposition under drought.},
journal = {mBio},
volume = {},
number = {},
pages = {e0043826},
doi = {10.1128/mbio.00438-26},
pmid = {42053312},
issn = {2150-7511},
abstract = {UNLABELLED: Drought has consequences for microbial decomposition rates, including indirect effects through changes in plant litter chemistry. Here, we studied the impact of a decade-long drought on plant litter chemistry and microbial decomposition traits in a semi-arid ecosystem during an 18-month litter bag experiment. We investigated litter sourced from four conditions: grass and shrub vegetation under ambient and reduced precipitation. We hypothesized that litter chemistry drives microbial decomposition capabilities and enzyme activity due to vegetation differences and drought effects on litter chemistry. We found that carbohydrate-rich grass litter had a higher abundance of decomposition genes detected using metagenomics and enzyme activity than more recalcitrant shrub litter, which was richer in lignin and lipids; these patterns were related to substrate supply. Drought decreased some carbohydrate fractions in grass litter but did not change the lignin fraction in grass and shrub litter, suggesting that drought does not make litter more recalcitrant. Most decomposition genes and enzyme activities were not significantly affected by drought, thereby maintaining decomposition rates. Microbial community succession patterns-decreasing fungal abundance and increasing bacterial abundance with time-corresponded with decreasing chitin gene abundance and increasing peptidoglycan gene abundance over time, indicating microbial necromass recycling. We demonstrate minimal litter chemistry-mediated effects of drought but show significant changes in community composition and their decomposition capabilities over time, highlighting that complex microbial-chemical interactions under climate change can influence ecosystem-scale processes.

IMPORTANCE: Climate change is causing more severe and frequent droughts in semi-arid ecosystems, affecting soil microbes breaking down plant litter. Our research focuses on understanding the less studied pathway of drought impact on microbes via changes in plant litter chemistry. Drought can alter the plant litter chemistry by changing the composition and physiology of plants, which can alter microbial decomposition and ecosystem-level carbon cycling. We investigated litter decomposition traits of microbial communities in grass and shrub litter under long-term drought. There were significant changes in litter chemistry under drought but no increase in lignin fraction. Despite this, microbial communities maintained their decomposition capabilities under drought, highlighting the ability of microbes to adapt and continue functioning. We also demonstrate unique microbial community succession patterns and dead biomass recycling, which can have implications for carbon cycling rates in the ecosystem. This study sheds light on the complex microbial interactions that affect ecosystem functioning under climate change.},
}

@article {pmid42053608,
year = {2026},
author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N},
title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02779-2},
pmid = {42053608},
issn = {1432-184X},
support = {Project number: 116O328//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
}

@article {pmid42053852,
year = {2026},
author = {Peng, Q and Lin, Y},
title = {A case report of infective endocarditis caused by Mycoplasma pneumoniae in a child.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42053852},
issn = {1435-4373},
abstract = {OBJECTIVE: This study aimed to investigate the clinical features and management strategies for infective endocarditis(IE) caused by Mycoplasma pneumoniae(M. pneumoniae) in children, in order to enhance understanding of this rare extrapulmonary complication of M. pneumoniae infection and provide clinical insights for its diagnosis and treatment.

METHODS: We retrospectively analyzed the clinical data and management process of a pediatric patient diagnosed with IE who was admitted to our hospital in September 2025.

RESULTS: A 9-year-old male patient was admitted with initial symptoms of fever and cough and was diagnosed with M. pneumoniae pneumonia. Subsequently, prompted by the detection of a faint blowing murmur on auscultation, transthoracic echocardiography was performed, which revealed a vegetation in the right ventricle. Empirical antibiotic treatment with doxycycline combined with vancomycin and ceftriaxone was initiated. M. pneumoniae was detected in two blood specimens using metagenomic next-generation sequencing (mNGS), while all three conventional blood cultures remained negative. Treatment was subsequently adjusted to doxycycline monotherapy. On hospital day 11, follow-up echocardiography examination showed resolution of the vegetative, with no evidence of thromboembolic events. After discharge, the patient continued oral doxycycline for a total treatment duration of 4 weeks. Follow-up revealed good recovery.

CONCLUSIONS: M. pneumoniae pneumonia in children may be complicated by IE. Antimicrobial agents should be guided by regional antimicrobial resistance patterns and resistance gene testing. The addition of anti-inflammatory and anticoagulant therapies should be considered when clinically indicated. mNGS is a valuable diagnostic tool for identifying pathogens in cases of blood culture-negative IE.},
}

@article {pmid42053938,
year = {2024},
author = {Jang, YJ and Moon, JS and Kim, JE and Kim, D and Choi, HS and Oh, I},
title = {Blending Three Probiotics Alleviates Loperamide-Induced Constipation in Sprague-Dawley (SD)-Rats.},
journal = {Food science of animal resources},
volume = {44},
number = {1},
pages = {119-131},
doi = {10.5851/kosfa.2023.e61},
pmid = {42053938},
issn = {2636-0780},
abstract = {BIOVITA 3 bacterial species (BIOVITA 3), a probiotic blend powder containing Clostridium butyricum IDCC 1301, Weizmannia coagulans IDCC 1201 and Bacillus subtilis IDCC 1101, has been used as a food ingredient for gut health. However, its efficacy in improving constipation has not been reported. Therefore, we aimed to investigate the functional effects of oral administration of BIOVITA 3 as well as its component strains alone (at 1.0×10[9] CFU/day) in Sprague-Dawley (SD) rats with loperamide-induced constipation. The study included fecal analysis, gastrointestinal transit ratio, histopathological analysis, short chain fatty acids (SCFAs), and metagenome analysis. As results, the BIOVITA 3 group showed significant improvements in fecal number, water content, gastrointestinal transit ratio, and thickening of the mucosal layer. In the SCFAs analysis, all probiotic-treated groups showed an increase in total SCFAs compared to the loperamide-constipated group. Changes in microbial abundance and the diversity index of three groups (normal, constipated, and BIOVITA 3) were also defined. Of these, the BIOVITA 3 showed a significant improvement in loperamide-constipated SD-rats. This study suggests the possibility that BIOVITA 3 can be applied as an ingredient in functional foods to relieve constipation.},
}

@article {pmid42054100,
year = {2026},
author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE},
title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001705},
pmid = {42054100},
issn = {2057-5858},
mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; },
abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.},
}

Animals
*Metagenomics/methods
*Food Microbiology
Chickens/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
*Meat/microbiology
Cattle
Sheep
Salmon/microbiology
United Kingdom
Microbiota/genetics
Anti-Bacterial Agents/pharmacology
Swine

@article {pmid42054312,
year = {2026},
author = {Revel, J and Leroy, J and Delbecq, S and Constant, O and Marty, F and Naili, C and Barthès, A and Nagy, A and Schmidt-Chanasit, J and Cadar, D and Abd Rahaman, NY and Lajoix, AD and Desmetz, C and Simonin, Y},
title = {Differential Properties of NS1 Glycoproteins in West Nile and Usutu Viruses.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2667565},
doi = {10.1080/22221751.2026.2667565},
pmid = {42054312},
issn = {2222-1751},
abstract = {AbstractWest Nile virus (WNV) and Usutu virus (USUV) are neurotropic orthoflaviviruses of the Flaviviridae family, transmitted primarily by Culex mosquitoes and maintained in enzootic cycles involving birds. While WNV is a well-established human pathogen causing hundreds of neuroinvasive cases annually in Europe, USUV has emerged more recently, with fewer documented human infections but increasing evidence of neurovirulence. The viral nonstructural protein 1 (NS1) plays a central role in orthoflavivirus pathogenesis by modulating host immune responses, disrupting endothelial barrier integrity, and facilitating viral dissemination. However, the functional and biochemical properties of NS1 from WNV and USUV remain poorly characterized. We combined in vitro, in vivo, and clinical approaches to compare NS1 secretion, stability, and its impact on blood-brain barrier. Our results show that WNV NS1 is secreted at significantly higher levels, exhibits greater thermal stability, and disrupts brain endothelial barrier integrity in vitro. In contrast, USUV NS1 is secreted less efficiently, is slightly less stable, and does not compromise blood-brain barrier integrity, despite inducing distinct transcriptional responses in brain endothelial cells. In mice, WNV infection led to higher serum NS1 levels and stronger systemic inflammation than USUV. Clinically, WNV NS1 was detected mainly in patients with neurological symptoms, whereas USUV NS1 remained undetectable in all cases. Altogether, these findings reveal differential NS1 properties between these closely related viruses, with key implications for orthoflavivirus diagnosis and neurovirulence mechanisms.},
}

@article {pmid42054365,
year = {2026},
author = {Santos-Júnior, CD and Escobar, MC and Huber, P and Niño-Garcia, JP and Cardona, GI and Costa-Pereira, R and Sarmento, H},
title = {Resource availability structures microbial competition through genomic niche partitioning.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {18},
pages = {e2526391123},
doi = {10.1073/pnas.2526391123},
pmid = {42054365},
issn = {1091-6490},
support = {862923//EC | Horizon 2020 Framework Programme (H2020)/ ; 304655/2025-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/15842-6//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 23/02850-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 20/11953-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2025hsqd014//Hubei Hongshan Laboratory/ ; },
mesh = {Humans ; Ecosystem ; Metagenome ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Biodiversity ; Bacteria/genetics/classification ; Metagenomics/methods ; Soil Microbiology ; Genomics ; Microbiota/genetics ; *Microbial Interactions ; },
abstract = {Microbial competition for scarce resources shapes biodiversity patterns and ecosystem function across global biomes, yet quantifying this process from genomic data has remained elusive. Here, we introduce CaCo, a scalable metric that transforms metagenomic carbohydrate-active enzyme profiles into precise measures of niche overlap and competition potential (Resource Partitioning Score, RPS). Analyzing 14,691 high-quality metagenome-assembled genomes spanning Ocean, freshwater, soil, and human gut microbiomes, we reveal a striking macroecological pattern: Niche overlap increases from partitioned specialists in oligotrophic oceans to overlapping generalists in carbon-rich environments, including the human gut. This gradient aligns with classic niche theory, as phylogenetic signals indicate that closely related taxa may compete most intensely. Multitiered validation, spanning BIOLOG phenotypes, synthetic cocultures, and interaction gradients, confirms CaCo's predictive power and captures competitive exclusion. CaCo bridges genomic potential and ecological reality, providing niche-breadth metrics and enabling testable predictions of how resource availability shapes microbial competition and community structure.},
}

Humans
Ecosystem
Metagenome
Phylogeny
*Gastrointestinal Microbiome/genetics
Biodiversity
Bacteria/genetics/classification
Metagenomics/methods
Soil Microbiology
Genomics
Microbiota/genetics
*Microbial Interactions

@article {pmid42054706,
year = {2026},
author = {Vilaseca, A and Toledano, M and Flanagan, EP},
title = {Complexities in evaluation and management of infectious myelopathies.},
journal = {Current opinion in infectious diseases},
volume = {39},
number = {3},
pages = {227-239},
doi = {10.1097/QCO.0000000000001204},
pmid = {42054706},
issn = {1473-6527},
mesh = {Humans ; *COVID-19/complications ; *Spinal Cord Diseases/diagnosis/virology/therapy/etiology ; SARS-CoV-2 ; *Myelitis/diagnosis/virology ; Magnetic Resonance Imaging ; },
abstract = {PURPOSE OF REVIEW: To review recent advances in infectious myelopathies and integrate them into a practical, syndrome-based approach that supports early recognition, guides testing, and avoids pitfalls.

RECENT FINDINGS: Advances in MRI pattern recognition and pathogen-specific diagnostics have refined the evaluation of infectious myelopathies, with strategies tailored to geographic epidemiology, host susceptibility, and distinction from immune-mediated causes. During the COVID-19 pandemic, SARS-CoV-2-associated myelopathy emerged as a rare para- or postinfectious cause of myelitis. The pandemic coincided with a decline in enterovirus outbreaks and acute flaccid myelitis, which are now re-emerging, underscoring the importance of epidemiologic surveillance. Metagenomic next-generation sequencing is useful in suspected infectious myelopathy because it can identify unexpected pathogens from cerebrospinal fluid, but its imperfect sensitivity and contamination risk mean it should complement rather than replace conventional testing. Growing recognition of compartmentalized central nervous system inflammation and cerebrospinal fluid viral escape in HIV myelopathy has shifted management toward antiretroviral resistance patterns and treatment optimization. Therapeutic advances remain limited and largely pathogen-specific, although targeted approaches such as mogamulizumab for HTLV-1-associated myelopathy are promising.

SUMMARY: Recent progress in infectious myelopathies has been driven by improved pathogen detection and more tailored diagnostic strategies, although treatment advances are beginning to emerge.},
}

Humans
*COVID-19/complications
*Spinal Cord Diseases/diagnosis/virology/therapy/etiology
SARS-CoV-2
*Myelitis/diagnosis/virology
Magnetic Resonance Imaging

@article {pmid42055201,
year = {2026},
author = {Lu, L and Pan, C and Fu, L and Zhao, L and Wang, HY and Yao, W and Yang, M},
title = {Subchronic exposure to environmental levels of fluoxetine disturbs gut microbiota-mediated intestinal barrier homeostasis and triggers delayed feeding response in zebrafish (Danio rerio).},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110551},
doi = {10.1016/j.cbpc.2026.110551},
pmid = {42055201},
issn = {1532-0456},
abstract = {Fluoxetine (FLX), a selective serotonin reuptake inhibitor, is frequently detected in aquatic environments because of its widespread use and inefficient removal by sewage treatment. Long-term FLX residues may induce chronic effects in non-target aquatic organisms. The intestine is a key metabolic and immune organ in fish, and may be affected by prolonged FLX exposure. However, studies on FLX-induced intestinal toxicity and its underlying molecular mechanisms are scarce. In the present study, adult female zebrafish were exposed to environmentally relevant FLX concentrations for 28 days, and subchronic toxic effects were assessed using an integrated approach combining physio-biochemical, behavioral, pathological, and multi-omics analyses. The results showed that the 28-day FLX exposure reduced the adult fish condition factor and altered feeding behavior. Notably, maternal FLX increased F1 offspring mortality and decreased the hatching rate, body length, and heart rate. In FLX-exposed adult intestines, goblet cell villus height was reduced and oxidative stress was induced, and transcriptome analysis revealed differentially expressed genes enriched in metabolism, neurodegenerative disease, and circadian rhythm pathways. Additionally, 16S rRNA and metagenomic sequencing showed FLX decreased gut microbiota α-diversity, altered community composition and assembly process, and enhanced antibiotic resistance genes. These findings highlight the dual threats of pharmaceutical pollution to ecological and public health, and provide support for the formulation of environmental and health protection measures.},
}

@article {pmid42055262,
year = {2026},
author = {Trinh, HP and Lee, SH and Park, HD},
title = {Mitigating nitrite stress and restoring functional redundancy in anammox reactor via acetate-driven DNRA-anammox coupling.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134732},
doi = {10.1016/j.biortech.2026.134732},
pmid = {42055262},
issn = {1873-2976},
abstract = {Frequent fluctuations in nitrite concentrations and unstable control of partial nitritation often lead to excessive NO2[-] accumulation, resulting in performance deterioration in anammox-based systems. To address this challenge, an anammox reactor was operated for 180 days to investigate the inhibitory effects of elevated NO2[-]/NH4[+]ratios on anammox activity and to evaluate the effectiveness of external carbon supplementation in promoting dissimilatory nitrate reduction to ammonium (DNRA)-related pathways that contribute to NO2[-] reduction. Increasing NO2[-]/NH4[+]ratio from 1.3 to 3.0 decreased the nitrogen removal efficiency from 96.7% to 26.6%, reduced the relative abundance of anammox bacteria (Ca. Kuenenia and Ca. Jettenia) from 41.5% to 7.0% and promoted Nitrospira to 7.7%. In contrast, acetate supplementation at a C/N ratio of 0.2 suppressed Nitrospira to 0.2% and enhanced the abundance of anammox and DNRA-performing bacteria (e.g., Fimbriimonadaceae, Mycobacterium, Anaerolineales, Caldilineaceae, and Ignavibacteriaceae) to 31.2% and 15.7%, respectively. Metagenome-assembled genome analysis confirmed the enrichment of functional genes associated with anammox (hzsABC and hdh) and DNRA metabolism (nirBD and nrfAH), corresponding to the recovery of nitrogen removal efficiency to 82.3%. Quantitative microbial network analysis further revealed that functional redundancy index declined from 0.56 to 0.42 under nitrite stress but recovered to 0.53 following acetate supplementation, indicating the restoration of a functionally buffered microbial community. Overall, these results demonstrate that low-level acetate supplementation, (C/N = 0.2) effectively stimulated DNRA-mediated NO2[-] reduction to NH4[+] by both DNRA-performing bacteria, thereby supporting anammox activity and providing an energy-efficient strategy to mitigate NO2[-] accumulation and stabilize nitrogen removal in anammox-based systems.},
}

@article {pmid42055314,
year = {2026},
author = {Zhang, Y and Xia, J and Qiu, Z and Tian, S and Wang, J and Ren, X and Chen, M},
title = {Successful Treatment of Balamuthia Mandrillaris Amebic Encephalitis Diagnosed by MetaCAP in China: A Case Report and Review of 25 Survival Cases.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108745},
doi = {10.1016/j.ijid.2026.108745},
pmid = {42055314},
issn = {1878-3511},
abstract = {Balamuthia mandrillaris, a free-living amoeba, can cause Balamuthia amebic encephalitis (BAE), a rare and often fatal cerebral infection. The reported mortality rate is >90%, largely attributable to the absence of specific clinical manifestations, sensitive diagnostic methods and effective therapeutic interventions. We herein describe a middle-aged, male patient diagnosed with BAE using Metagenomic Capture sequencing (MetaCAP) who achieved full recovery following early medical therapy without neurosurgical treatment. Our findings indicate that MetaCAP serves as a rapid and sensitive diagnostic approach, and sulfasalazine may confer a potential anti-inflammatory benefit in the management of BAE. In addition, we reviewed 25 survival cases of BAE reported in the PubMed database up to now.},
}

@article {pmid42055803,
year = {2026},
author = {Auwal, AM and Matthews, R and Cook, C and Sargent, B and Easton, A and Ray, STJ and Ellul, MA and Michael, BD},
title = {Suspected encephalitis in adults.},
journal = {Practical neurology},
volume = {},
number = {},
pages = {},
doi = {10.1136/pn-2024-004299},
pmid = {42055803},
issn = {1474-7766},
abstract = {'Query encephalitis' is one of the most common reasons for inpatient neurology referral in the context of an acutely confused patient. Growing evidence suggests that time to treatment is a key determinant of outcome in both infectious and autoimmune encephalitis; hence, these two causes should be considered simultaneously at presentation. However, under-recognition and the existence of several mimics make a rapid diagnosis of encephalitis challenging. Appreciation of clinical syndromes can guide aetiological investigation and consequent treatment. In this article, we discuss clinical phenotypes associated with both infectious and autoimmune encephalitis, as well as a systematic approach to their investigation and up-to-date treatment strategies. We also highlight ongoing areas of research, such as metagenomics and therapeutic trials.},
}

@article {pmid42056322,
year = {2026},
author = {Thakkar, S and Rathour, R and Rana, SS and Samant, S and Kikani, BA and Madamwar, D and Desai, C},
title = {Biochar-augmented microaerophilic fixed-film bioreactor integrated with an aerobic membrane bioreactor effectively reduces persistent, mobile chemicals in the CETP effluent treatment.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42056322},
issn = {1573-0972},
support = {File No. GSBTM/JD(R&D)/662/2022-23/00292469//Gujarat State Biotechnology Mission (GSBTM), Department of Science and Technology, Government of Gujarat/ ; },
mesh = {*Bioreactors/microbiology ; *Charcoal/chemistry ; Aerobiosis ; *Water Pollutants, Chemical/metabolism ; *Waste Disposal, Fluid/methods ; Bacteria/genetics/classification/metabolism/isolation & purification ; Membranes, Artificial ; *Water Purification/methods ; Biodegradation, Environmental ; Wastewater/chemistry/microbiology ; Biological Oxygen Demand Analysis ; },
abstract = {Different classes of chemical compounds including persistent, mobile chemicals (PMCs) often bypass the conventional treatment processes of common effluent treatment plants (CETPs), resulting in their unmonitored release into aquatic environments. In this study, an integrated treatment system comprising a microaerophilic fixed-film bioreactor (MFB) and an aerobic membrane bioreactor (Ae-MBR) was engineered to treat secondary CETP effluent. Two types of packing materials in the engineered MFBs were evaluated: one with wood charcoal (C-MFB) and another with 30% (w/w) biochar-augmented charcoal (BAC-MFB). The BAC-MFB showed better treatment efficiency, achieving 69.17% colour (Pt-Co units) removal and 93.01% COD removal at an optimal 3d hydraulic retention time (HRT). Integration with Ae-MBR further enhanced the treatment, achieving > 95% COD and > 94% colour removal, with an overall > 85% reduction in total number of parent chemical compounds and a specific > 83% reduction in PMCs from CETP effluent. At 3d HRT, bacterial community analysis revealed dominance of Campylobacterota and Bacillota in BAC-MFB under microaerophilic conditions, whereas Bacillota dominated in the Ae-MBR under aerobic conditions. The predicted metagenome analysis revealed significant enrichment of benzoate and aminobenzoate degradation pathways in the integrated system. While the BAC-MFB treatment alone achieved sufficient COD removal, its integration with Ae-MBR markedly enhanced the reduction in overall chemical complexity including PMCs from the CETP effluent. This study demonstrates that the engineered hybrid BAC-MFB-Ae-MBR system is a sustainable solution for the treatment of industrial CETP effluents.},
}

*Bioreactors/microbiology
*Charcoal/chemistry
Aerobiosis
*Water Pollutants, Chemical/metabolism
*Waste Disposal, Fluid/methods
Bacteria/genetics/classification/metabolism/isolation & purification
Membranes, Artificial
*Water Purification/methods
Biodegradation, Environmental
Wastewater/chemistry/microbiology
Biological Oxygen Demand Analysis

@article {pmid42056687,
year = {2026},
author = {Wedell, E and Shen, C and Warnow, T},
title = {Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2981},
number = {},
pages = {37-52},
pmid = {42056687},
issn = {1940-6029},
mesh = {*Phylogeny ; *Software ; *Metagenomics/methods ; Algorithms ; Likelihood Functions ; *Computational Biology/methods ; },
abstract = {Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.},
}

*Phylogeny
*Software
*Metagenomics/methods
Algorithms
Likelihood Functions
*Computational Biology/methods

@article {pmid42056742,
year = {2026},
author = {Zhang, X and Li, Q and Yang, H and Li, H and Hu, C},
title = {Active responses of cyanobacterial crusts directly exposed to the extreme stratospheric environment.},
journal = {Life sciences in space research},
volume = {50},
number = {},
pages = {133-145},
doi = {10.1016/j.lssr.2026.01.001},
pmid = {42056742},
issn = {2214-5532},
abstract = {The stratosphere's highly hostile environment offers a unique and relatively accessible setting to evaluate extremophilic adaptation for extraterrestrial colonization. The accelerating pace of the Martian project has underscored the need for a better understanding of the synergistic responses of microbial communities in Mars-like habitats. Here, we loaded the cyanobacterial crust, a model system with multiple trophic levels, onto a balloon-borne astrobiology platform for a direct-exposure experiment in the stratosphere, aligned with the ground-control and indoor-simulated groups. After short-term in-situ exposure, we performed multi-omics analyses to delineate alterations in community composition and the community-level metabolic response. We observed a significant shift in the community composition of active members, with the relative abundance of photoautotrophs (except Scytonema) declining while that of chemotrophs increased. However, we demonstrated the unique thriving of the cyanobacterial genus Scytonema, attributed to its synthesis of the anti-ultraviolet compound scytonemin, its diverse material, and its energy acquisition. Meanwhile, the distinct metabolic profiles exhibited by various species and their interspecies metabolic interactions synergistically facilitated the retention of organic carbon and nitrogen, ultimately sustaining the stability of the biocrust community. Our study underscores the adaptive resilience of cyanobacterial crusts under stratospheric stresses. Notably, the robustness of Scytonema, particularly its unique survival capabilities, highlights its potential for extraterrestrial applications.},
}

@article {pmid42056812,
year = {2026},
author = {Fu, Y and Zhuang, H and Shi, J},
title = {Reshaping of the electron transport chain and carbon metabolism by low-loading Fe3O4@PU for enhanced phenolic compounds degradation in an algal-bacterial biofilm system.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142207},
doi = {10.1016/j.jhazmat.2026.142207},
pmid = {42056812},
issn = {1873-3336},
abstract = {While previous algal-bacterial biofilm systems without magnetite have shown limited resilience to high concentration phenolic compounds, this study demonstrates that introducing low loading (5%) nano-Fe3O4 substantially enhances degradation stability by optimizing electron transfer pathways. Four algal-bacterial reactors with varying Fe3O4 loadings (5-50%) were constructed using polyurethane carriers to treat phenolic wastewater under increasing total phenol (TPh) concentrations (50-300 mg/L). The 5% loading reactor (R1) demonstrated outstanding performance, achieving > 80% TPh removal and approximately 76% COD removal even at the highest loading. Compared to without magnetite systems, R1 achieved 13-15% higher TPh degradation at 300 mg/L. R1 also exhibited the highest electron transfer system activity (0.487 μg O2·gVSS[-1]·h[-1]) and cytochrome c content (72.12 mg/g VSS), indicating that Fe3O4 serves as an electron shuttle, compensating for endogenous electron carrier limitations. Metagenomic analysis revealed that the enhanced performance stemmed from robust carbohydrate metabolism, particularly the upregulation of key glycolytic enzymes (pfkA) and glycogen degrading enzymes (GH13), ensuring efficient NADH/ATP production. This metabolic advantage supplied reducing power to the Fe3O4 optimized electron transport chain, synchronizing electron generation with respiratory utilization. These findings demonstrate that low-dose Fe3O4 optimizes natural electron transfer pathways by coupling metabolic flux with respiratory chain activity, offering a cost effective strategy for treating high strength industrial wastewater.},
}

@article {pmid42046358,
year = {2026},
author = {Chen, K and Huang, L},
title = {[Metagenomic next - generation sequencing for diagnosis of infection of unknown origin in intensive care units: a bibliometric analysis].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {38},
number = {1},
pages = {79-83},
doi = {10.16250/j.32.1915.2026077},
pmid = {42046358},
issn = {1005-6661},
mesh = {*Bibliometrics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Intensive Care Units ; *Metagenomics/methods ; },
abstract = {OBJECTIVE: To investigate the scientific outputs of metagenomic next-generation sequencing (mNGS) for diagnosis of infection of unknown origin in intensive care units (ICUs), and to decipher the latest advances, frontier trends and spatiotemporal evolution of research hotpots in mNGS for diagnosis of infection of unknown origin in ICUs.

METHODS: Publications pertaining to the application of mNGS in diagnosis of infection of unknown origin in ICUs were retrieved from Web of Science Core Collection (WOSCC) from January 1, 2015 to December 31, 2024. The software Scimago Graphica 1.0.30 was employed to generate the network maps of collaboration relationships between countries, international collaborative relationships, author collaborations, institutional collaborative relationships, and a heatmap of journals, and the software VOSviewer 1.6.18 was used to create a heatmap of keywords, and maps of keyword co-occurrence clustering and keyword clustering timelines. In addition, the keyword burst map was created using the software CiteSpace 6.3.R3.

RESULTS: A total of 1 707 publications were included in the final analysis, and the number of publications appeared an overall tendency towards a rise from 2015 to 2024, with the largest number of publications seen in 2024 (545 publications). The largest number of publications was recorded in China (1 390 publications), followed by in USA (190 publications) and United Kingdom (31 publications), and China led the global research in this field, with 81% of global related researches linked with China. Frontiers in Cellular and Infection and Microbiology published the largest number of articles (212 publications, 12.42%), and Joseph Derisi was the most productive author (33 publications). Author collaborations occurred within groups; however, there was a lack of close inter-group collaborations, with University of California, San Francisco and Chan Zuckerberg Biohub-based group seen as the largest collaborative group. High-frequency co-occurrence keywords included mNGS, infection, diagnosis, case report, community-acquired pneumonia and bronchoalveolar lavage fluid, and the 100 most common high-frequency co-occurrence keywords were assigned into four clusters. Keyword clustering timeline analysis revealed that the research hotspots in this field shifted from virus sequencing and sequence alignment to severe pulmonary infections, and keyword burst analysis showed identification, mNGS and virus as top three keywords with the highest burst intensity.

CONCLUSIONS: mNGS was mainly used for identification of viruses among patients with infections of unknown origins in ICUs from 2015 to 2024, and future research priority shifted to pathogen detection for severe pulmonary infections.},
}

*Bibliometrics
*High-Throughput Nucleotide Sequencing/methods
Humans
*Intensive Care Units
*Metagenomics/methods

@article {pmid42046871,
year = {2026},
author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q},
title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.},
journal = {Journal of Zhejiang University. Science. B},
volume = {27},
number = {4},
pages = {375-389},
doi = {10.1631/jzus.B2400495},
pmid = {42046871},
issn = {1862-1783},
support = {2021YFA0805904//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mice ; Germ-Free Life ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Metagenomics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Mice, Inbred C57BL ; Female ; },
abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.},
}

Animals
*Gastrointestinal Microbiome/genetics
Humans
Mice
Germ-Free Life
*Fecal Microbiota Transplantation/methods
Feces/microbiology
*Metagenomics
Reproducibility of Results
High-Throughput Nucleotide Sequencing
Male
*Metagenome
Mice, Inbred C57BL
Female

@article {pmid42047611,
year = {2026},
author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C},
title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.},
journal = {Pediatric dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pde.70219},
pmid = {42047611},
issn = {1525-1470},
support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson & Johnson Consumer Inc./ ; },
abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.

METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.

RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.

CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.},
}

@article {pmid42047812,
year = {2026},
author = {Zhu, R and Zhang, J and Shen, HL},
title = {Hip joint infection by Prevotella denticola in rheumatoid arthritis : A case diagnosed with metagenomic sequencing.},
journal = {Wiener klinische Wochenschrift},
volume = {},
number = {},
pages = {},
pmid = {42047812},
issn = {1613-7671},
abstract = {BACKGROUND: Infection, as a complication of rheumatoid arthritis (RA), has attracted increasing attention from rheumatologists. Here, we present the first case of RA with hip joint infection, which was driven by infection with Prevotella denticola. Anaerobic bacterial infection was identified by metagenomic next-generation sequencing (mNGS).

METHODS: We describe the case of a 56-year-old woman with a history of RA who was admitted for intense hip joint pain and intermittent fever following long-term oral glucocorticoid (GC) treatment.

RESULTS: Although blood and hip joint effusion cultures for aerobic and anaerobic organisms were negative, we considered the possibility of a clinical diagnosis of hip joint infection; therefore, empirical antibiotic treatment was initiated but it was ineffective in this case. Prevotella denticola was identified by mNGS from the hip joint effusion obtained via ultrasound-guided puncture and the organism was resistant to the initial antimicrobial treatment. Finally, the adjustment of antimicrobial treatment led to successful treatment.

CONCLUSION: Patients with RA have a significantly greater risk of infections than the general population; however, Prevotella denticola infection of the hip joint has not been previously reported. The combination of ultrasound-guided puncture and mNGS to accurately recognize and treat joint infection in patients with RA in a timely manner is necessary to prevent the development of complications, a strategy worthy of further clinical application.},
}

@article {pmid42048337,
year = {2026},
author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM},
title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347959},
doi = {10.1371/journal.pone.0347959},
pmid = {42048337},
issn = {1932-6203},
mesh = {Colombia ; *Mangifera/microbiology ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Air Pollutants/metabolism ; Microbiota/genetics ; *Metagenome ; Phylogeny ; Cities ; },
abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.},
}

Colombia
*Mangifera/microbiology
*Bacteria/genetics/classification/drug effects
Metagenomics
RNA, Ribosomal, 16S/genetics
*Air Pollutants/metabolism
Microbiota/genetics
*Metagenome
Phylogeny
Cities

@article {pmid42048878,
year = {2026},
author = {Shi, W and Qin, Y and Li, W and Xu, J and Xu, H and Liu, Y},
title = {The dual role of phosphorus regeneration in controlling arsenic speciation: Iron-reducing bacteria in a seasonally ice-covered lake.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142206},
doi = {10.1016/j.jhazmat.2026.142206},
pmid = {42048878},
issn = {1873-3336},
abstract = {While the reductive dissolution of iron (hydro)oxides by dissimilatory iron‑reducing bacteria (DFeRB) can mobilize sediment bound arsenic (As), the role of concomitant phosphorus (P) regeneration in actively governing As speciation transformation, rather than mere release, remains mechanistically unclear, especially under seasonally contrasting redox regimes of ice-covered lakes. This study demonstrated that DFeRB mediated P regeneration exerts a dual, season‑dependent control over As speciation in lacustrine sediments. Through microcosm experiments simulating ice‑bound and summer periods, combined with sequential extraction, X‑ray diffraction, metagenomics, and structural equation modeling (SEM), and partial least-squares path modeling (PLS-PM), resolved that regenerated P not only promote As desorption via competitive adsorption but also redirect a substantial speciation of released As into a stable, pyrite‑coprecipitated pool (As‑S7). This sequestration pathway was particularly pronounced under ice‑bound anoxia, where DFeRB sustained a low‑rate, long‑duration reduction mode, as evidenced by persistent iron‑reduction gene (K02650, K17230) abundance and delayed As(III) peak release. SEM/PLS-PM quantified the seasonal shift in dominant mechanisms: summer release was driven by intensive P competition (including organic phosphorus), whereas ice‑bound conditions favored Fe‑S‑As co‑precipitation, effectively coupling prolonged microbial iron reduction to long‑term As immobilization. These findings establish P regeneration as a decisive switch between As mobility and stability in anaerobic sediments and define the seasonal microbial‑mineral feedbacks that modulate this switch. This work provides a predictive basis for assessing As fate in seasonally stratified water bodies under changing climatic conditions and a process-based basis for risk assessment and eutrophication management.},
}

@article {pmid42049031,
year = {2026},
author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q},
title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102780},
doi = {10.1016/j.xcrm.2026.102780},
pmid = {42049031},
issn = {2666-3791},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.},
}

@article {pmid42049067,
year = {2026},
author = {Khandelwal, S and Mishra, A and Pandey, SK},
title = {Integrating microbial bioremediation, multi-omics, and emerging technologies for polycyclic aromatic hydrocarbon (PAHs) detoxification.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107519},
doi = {10.1016/j.mimet.2026.107519},
pmid = {42049067},
issn = {1872-8359},
abstract = {Environmental organic pollutants, identified as Polycyclic Aromatic Hydrocarbons (PAHs), are widespread and toxic. These hydrocarbons are commonly produced by industrial activities, burning fossil fuels, and crude oil discharges. Their high hydrophobicity, tendency to bioaccumulate, and mutagenic, carcinogenic, teratogenic, and genotoxic properties lead to significant environmental and human health risks. Additionally, their low bioavailability and chemical stability complicate PAHs remediation. In recent years, various methods have been explored to reduce their impact, including conventional physical and chemical treatments; however, these often face issues such as inadequate removal, high costs, lengthy processes, and environmental concerns. Bioremediation has emerged as a promising, environmentally friendly solution. This approach involves microorganisms such as bacteria, fungi, algae, and archaea utilizing specific enzymatic pathways-like dioxygenases, monooxygenases, peroxidases, and laccases-to transform PAHs into less toxic substances. Advances in genomics and metagenomics have identified key catabolic genes (e.g., nah, Phn, nid, pah) and regulatory mechanisms that enhance microbial resistance in PAH-contaminated environments. Since PAHs' low bioavailability and solubility often limit bioremediation alone, integrated strategies are gaining prominence. In-situ and ex-situ methods-including bioaugmentation, bio-stimulation, composting, and phytoremediation-boost microbial degradation of PAHs. Furthermore, advanced technologies such as multi-omics platforms, CRISPR-based genetic engineering, and artificial intelligence (AI) are transforming the field by enabling the development of targeted microbial strains, improving bioremediation efficiency, and creating predictive models. This review offers a recent, comprehensive outline by unifying PAHs toxicity, microbial degradation, traditional remediation, and advanced biotechnological tools into a single framework. A comprehensive and recent update of microbial and biotechnological approaches for sustainable PAHs bioremediation is offered by this review.},
}

@article {pmid42049248,
year = {2026},
author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM},
title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70161},
doi = {10.1002/cph4.70161},
pmid = {42049248},
issn = {2040-4603},
support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; },
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Lactobacillus/physiology ; Prospective Studies ; Middle Aged ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Adult ; Aged ; *Hypertension, Pulmonary/microbiology ; Ventricular Dysfunction, Right ; },
abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.

METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.

RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.

CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.},
}

Humans
Male
Female
*Gastrointestinal Microbiome/physiology
*Lactobacillus/physiology
Prospective Studies
Middle Aged
*Pulmonary Arterial Hypertension/microbiology/physiopathology
Adult
Aged
*Hypertension, Pulmonary/microbiology
Ventricular Dysfunction, Right

@article {pmid42049488,
year = {2026},
author = {Lan, K and Bai, D and Yuan, L and Luo, H and Jin, J and Li, SC and Wu, LF and Sun, XS and Liu, SL and Chen, QY and Mai, HQ and Liu, YX and Tang, LQ},
title = {Metagenomic identification of gut microbiome signatures for accurate diagnosis and prognostic prediction of Epstein-Barr virus-associated nasopharyngeal carcinoma.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338223},
pmid = {42049488},
issn = {1468-3288},
abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. The gut microbiome can influence outcomes of viral infections but the potential links among the gut microbiome, EBV infection and NPC remain unclear.

OBJECTIVE: To characterise gut microbiome alterations in EBV-associated NPC, evaluate microbiome-based diagnostic performance (alone and in combination with EBV markers), and explore associations between microbial features, EBV DNA burden, prognosis and the tumour microenvironment.

DESIGN: We conducted a large-scale shotgun metagenomic study including 516 patients with EBV-associated NPC and 263 healthy controls. Microbiome dysbiosis, functional pathways and associations with plasma EBV DNA were assessed. Species-level markers were used to build a random forest classifier for NPC diagnosis, and performance was evaluated alone and in combination with EBV-specific markers. Survival analyses were performed to identify microbial features associated with NPC-related mortality and relationships with an immune-suppressive tumour microenvironment were explored.

RESULTS: NPC was characterised by gut microbiome dysbiosis, including depletion of short-chain fatty acid-producing species and reduced butanoate metabolism, which were significantly associated with plasma EBV DNA. A random forest classifier based on species-level markers distinguished NPC from controls with an area under the curve (AUC) of 0.917; performance improved to an AUC of 0.984 when combined with EBV-specific markers. Specific microbial species were associated with NPC-related mortality and prognostic microbial features were linked to an immune-suppressive tumour microenvironment.

CONCLUSION: EBV-associated NPC is associated with distinct gut microbiome and functional alterations that correlate with plasma EBV DNA. Microbial markers show strong diagnostic potential, particularly when integrated with EBV-specific markers, and prognostic microbial features may be linked to an immune-suppressive tumour microenvironment, supporting a potential role of the gut microbiome in NPC tumourigenesis.},
}

@article {pmid42049592,
year = {2026},
author = {Pailhoriès, H and Velo-Suarez, L and Moalic, Y and Alcoforado-Diniz, J and Gouriou, S and Bessou, A and Cambau, E and Burgel, PR and Herrmann, JL and Héry-Arnaud, G and , },
title = {A disrupted microbial network and an ecological shift towards anaerobes in NTM-infected cystic fibrosis patients.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.04.005},
pmid = {42049592},
issn = {1873-5010},
abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens in people with cystic fibrosis (pwCF), but the ecological factors shaping their presence remain poorly understood. This study characterized the airway microbiota associated with NTM-positive culture using 16S rRNA gene sequencing of sputum from 108 pwCF (36 NTM-positive and 72 NTM-negative), matched by age, sex at birth, and CFTR genotype. Analyses integrated diversity metrics, differential-abundance modeling, multivariate regression, and microbial network inference, while accounting for Pseudomonas aeruginosa colonization. NTM-positive individuals exhibited slightly higher α-diversity and enrichment in strictly anaerobic taxa such as Alloprevotella tannerae, Stomatobaculum spp., and Prevotella nanceiensis, alongside reduced network connectivity. P. aeruginosa remained the dominant ecological driver, strongly reducing community diversity and structure. Partial Least Squares regression revealed that CFTR modulators (lumacaftor/ivacaftor) use and lung function (FEV1%) were associated with distinct, commensal-enriched communities. In contrast, NTM status was associated with a distinct axis, indicating an independent ecological niche. Overall, NTM-positive cultures were associated with an anaerobe-enriched but less structured microbiota, likely reflecting localized hypoxia and biofilm-associated microenvironments rather than a direct effect of disease severity or modulator therapy. These findings highlight the role of airway microecology in NTM presence and provide a framework for understanding host-microbe interactions in chronic CF airway infections.},
}

@article {pmid42049781,
year = {2026},
author = {Manohar, CS and Ghose, M and Parab, AS},
title = {Integrated metagenomic analysis of bacteriomes associated with beach-cast seaweeds reveals metabolic potential for biotechnological and environmental applications.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46393-1},
pmid = {42049781},
issn = {2045-2322},
support = {MLP2019//Council of Scientific and Industrial Research, India/ ; },
}

@article {pmid42050358,
year = {2026},
author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y},
title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70567},
pmid = {42050358},
issn = {1365-3040},
support = {2024CXPT072//Key R&D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.},
}

@article {pmid41436515,
year = {2025},
author = {Algarni, AD and Abd El-Samie, FE and Soliman, NF and Emara, HM and Algarni, F and Abd-Alhalem, SM and Marie, HS},
title = {Exploiting fuzzy weights in CNN model-based taxonomic classification of 500-bp sequence bacterial dataset.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44733},
pmid = {41436515},
issn = {2045-2322},
mesh = {Datasets as Topic ; *Fuzzy Logic ; *Convolutional Neural Networks ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics ; Deep Learning ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; },
abstract = {Taxonomic classification plays a crucial role in understanding the diversity and evolutionary relationships among bacteria. Accurately classifying bacterial DNA sequences based on a limited 500-bp segment remains challenging. This paper presents an improved Fuzzy-weighted Convolutional Neural Network (F-CNN) for taxonomic classification of bacterial DNA sequences, specifically focusing on the 500-bp segments. The proposed model aims to overcome the limitations of traditional classification methods by leveraging the power of deep learning and fuzzy logic processing. The improved fuzzy deep learning model is proposed to handle the problem of classifying samples with similar probabilities in the classification layer. It incorporates a feature selection stage using various techniques and a fuzzy weighting system to handle the uncertainty associated with similar classes in the classification layer and optimize parameters using fuzzy weights. The experimental results on the Ribosomal Database Project Release 11 (RDP 11) sequences dataset show the superiority of the proposed model, especially at the 500-bp region. Experimental results on the RDP 11 dataset, which includes over 1.4 million bacterial gene sequences, demonstrate the superior performance of the proposed model, achieving a classification accuracy up to 84.03% at the genus level for 500-bp segments and demonstrating high generalization when applied to longer sequences. This paper has significant implications for various fields, including microbiology, epidemiology, and environmental science, where accurate classification of bacteria is crucial for understanding their roles in different ecosystems and disease outbreaks.},
}

Datasets as Topic
*Fuzzy Logic
*Convolutional Neural Networks
DNA, Bacterial/genetics
*Bacteria/classification/genetics
Deep Learning
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Computational Biology/methods

@article {pmid42036837,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70359},
doi = {10.1111/1751-7915.70359},
pmid = {42036837},
issn = {1751-7915},
support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; },
mesh = {*Microbiota ; *Chitin/metabolism ; Soil Microbiology ; *Bacteria/enzymology/genetics/classification ; Phenotype ; Chitinases/genetics/metabolism ; Genetic Association Studies ; },
abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.},
}

*Microbiota
*Chitin/metabolism
Soil Microbiology
*Bacteria/enzymology/genetics/classification
Phenotype
Chitinases/genetics/metabolism
Genetic Association Studies

@article {pmid42037322,
year = {2026},
author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP},
title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {9},
pages = {e71828},
doi = {10.1096/fj.202600054R},
pmid = {42037322},
issn = {1530-6860},
support = {APIDOM-BACTERIOB//CHU de La Réunion/ ; //Institut National de la Santé et de la Recherche Médicale (Inserm)/ ; //University of La Réunion/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Periodontitis/microbiology/metabolism/complications/pathology ; Male ; Female ; *Intra-Abdominal Fat/metabolism/pathology ; Middle Aged ; Adult ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/metabolism/microbiology/pathology ; *Metabolic Diseases/microbiology/metabolism ; Dysbiosis/microbiology ; Porphyromonas gingivalis ; *Mouth/microbiology ; },
abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Periodontitis/microbiology/metabolism/complications/pathology
Male
Female
*Intra-Abdominal Fat/metabolism/pathology
Middle Aged
Adult
*Obesity, Morbid/microbiology/complications/metabolism
*Inflammation/metabolism/microbiology/pathology
*Metabolic Diseases/microbiology/metabolism
Dysbiosis/microbiology
Porphyromonas gingivalis
*Mouth/microbiology

@article {pmid42037351,
year = {2026},
author = {Chakraborty, S and Mukherjee, D and Sar, P},
title = {Genome-resolved insights into arsenic-impacted paddy soil and microcosm-derived microbiomes from West Bengal, India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0005926},
doi = {10.1128/mra.00059-26},
pmid = {42037351},
issn = {2576-098X},
abstract = {This study reports 32 metagenome-assembled genomes (MAGs) reconstructed from arsenic (As)-impacted paddy soils of West Bengal, India, and microcosms from these soil samples. These MAGs, represented by 10 bacterial and 2 archaeal phyla, provided critical insights into the metabolic and biogeochemical potential of microbiomes in a highly As-impacted agroecosystem.},
}

@article {pmid42037384,
year = {2026},
author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ},
title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0358725},
doi = {10.1128/spectrum.03587-25},
pmid = {42037384},
issn = {2165-0497},
abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.},
}

@article {pmid42037401,
year = {2026},
author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q},
title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0248125},
doi = {10.1128/aem.02481-25},
pmid = {42037401},
issn = {1098-5336},
abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.},
}

@article {pmid42037579,
year = {2026},
author = {Virtuoso, FAS and Boekhorst, J and van Ravenstein, S and Schouten, D and Juanpere-Borràs, M and Broekhuis, F and Vissia, S and Mazebedi, R and Araldi, A and van Langevelde, F},
title = {DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70144},
doi = {10.1111/1755-0998.70144},
pmid = {42037579},
issn = {1755-0998},
support = {//Wageningen University and Research/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Feces/chemistry ; *Diet ; *Carnivora/physiology/classification ; Workflow ; *Metagenomics/methods ; },
abstract = {Metabarcoding of faecal samples is a powerful, non-invasive approach for investigating the feeding ecology of carnivores, revealing prey diversity and unexpected dietary components with greater resolution than traditional methods. However, the approach remains technically demanding, as challenges and potential biases arise at every stage, from scat collection and DNA extraction to primer selection, sequencing, and data interpretation. Methodological details for these steps are often scattered across studies, limiting reproducibility and accessibility for ecologists. Here, we present a comprehensive field-to-sequencer workflow for dietary metabarcoding of terrestrial carnivores using Oxford Nanopore Technologies (ONT), covering all stages from sample collection to ecological interpretation. Drawing on field-collected scats of brown (Parahyaena brunnea) and spotted hyenas (Crocuta crocuta) across arid and semi-arid savannas in Botswana, we illustrate practical decisions, technical considerations, and common pitfalls encountered throughout the process. By integrating field, laboratory, and bioinformatic components into a single, accessible framework, this paper provides a pragmatic reference for ecologists aiming to design robust, transparent, and comparable studies of carnivore diet composition.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Feces/chemistry
*Diet
*Carnivora/physiology/classification
Workflow
*Metagenomics/methods

@article {pmid42038227,
year = {2026},
author = {Fu, L and Zhang, Y and Wang, L and Li, X},
title = {Primary amoebic meningoencephalitis caused by Naegleria fowleri in a 6-year-old girl: case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1801355},
pmid = {42038227},
issn = {2296-2360},
abstract = {BACKGROUND: Primary amoebic meningoencephalitis (PAM) is caused by Naegleria fowleri, a rare but highly fatal central nervous system infection with a mortality rate exceeding 95%. Early diagnosis is challenging due to the close similarity of its clinical manifestations and cerebrospinal fluid (CSF) findings to those of acute bacterial meningitis. Metagenomic next-generation sequencing (mNGS) has become a vital tool for identifying rare or unexpected pathogens.

CASE PRESENTATION: A previously healthy 6-year-old girl was admitted with fever, vomiting, and headache of 1 day's duration. Six days before symptom onset, she had played in natural freshwater bodies. After admission, she developed persistent high fever and rapidly progressive altered mental status, followed by two episodes of generalized tonic-clonic seizures, hemoptysis, acute respiratory failure, and circulatory shock. Initial cranial magnetic resonance imaging showed no abnormalities. CSF analysis revealed marked inflammatory changes: a white blood cell count of 3,072 × 10[6]/L, markedly elevated protein (3,667.6 mg/L), and significantly decreased glucose (0.08 mmol/L). Despite administration of broad-spectrum antibiotics, glucocorticoids, osmotherapy, and comprehensive intensive care unit management, the patient died approximately 11 h after admission following three cardiac arrests. Two days postmortem, CSF mNGS confirmed infection with Naegleria fowleri (copy number 3 × 10[5] copies/mL), establishing the diagnosis of PAM.

CONCLUSIONS: This pediatric case serves as a warning that PAM should be considered in children with a history of freshwater exposure and rapidly progressive meningoencephalitis, even when early imaging is normal and CSF findings resemble bacterial meningitis. Early lumbar puncture, rapid molecular diagnostics, and heightened clinician vigilance are critical for the timely initiation of targeted therapy.},
}

@article {pmid42038247,
year = {2026},
author = {Li, X and Jiang, Y and Dai, R and Yang, Y and Wang, W},
title = {Rickettsia felis meningoencephalitis in a child: a case report and literature review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1763281},
pmid = {42038247},
issn = {2296-2360},
abstract = {Rickettsia felis (R. felis) infection occasionally invades the central nervous system, causing encephalitis or meningoencephalitis. Although the disease typically presents as mild to moderate illness, delayed diagnosis and treatment may increase the risk of adverse prognosis in pediatric patients. This article reports a case of R. felis meningoencephalitis in a child diagnosed by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid. mNGS analysis detected high-confidence R. felis-specific sequences, and potential background microbial contamination was effectively excluded through a bioinformatics pipeline, thereby providing critical evidence for etiological confirmation. Due to insufficient clinical awareness, limited pathogen detection methods, and the self-limiting nature of the disease, R. felis infection is prone to missed diagnosis and misdiagnosis in febrile children. The clinical manifestations are nonspecific; even with central nervous system involvement, routine laboratory tests are unlikely to suggest the microbial etiology, contributing to the underrecognition and underreporting of pediatric R. felis meningoencephalitis. Therefore, enhancing diagnostic awareness and achieving early precise diagnosis and treatment may help shorten the disease course and improve patient outcomes.},
}

@article {pmid42038299,
year = {2026},
author = {Liu, HJ and Wang, LF and Li, XY and Li, L},
title = {Toxicity-guided dose modification for disseminated Nocardia farcinica brain abscess in a patient with pneumoconiosis: a brief research report.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1805920},
pmid = {42038299},
issn = {1663-9812},
abstract = {BACKGROUND: Optimal antimicrobial strategies for disseminated nocardiosis with central nervous system (CNS) involvement remain poorly defined, particularly regarding trimethoprim-sulfamethoxazole (TMP-SMX) dosing in immunocompromised patients with severe drug intolerance.

METHODS: This observational case study analyzed the clinical course and pharmacological management of a 55-year-old male gold miner with pneumoconiosis and chronic corticosteroid use who developed Nocardia farcinica brain abscess. Diagnosis was established via metagenomic next-generation sequencing (mNGS) and phenotypic culture. An individualized antimicrobial regimen was designed based on toxicity monitoring.

RESULTS: Diagnosis of N. farcinica was confirmed by mNGS within 48 h. The patient initially failed empirical meropenem but responded to combination therapy with imipenem, amikacin, and TMP-SMX. Due to grade III gastrointestinal toxicity (CTCAE v5.0), TMP-SMX was de-escalated from 15 mg·kg[-1]·d[-1]-11.25 mg·kg[-1]·d[-1], with maintenance at 7.5 mg·kg[-1]·d[-1]. Clinical improvement was observed at Day 120, though durable cure remains unconfirmed.

CONCLUSION: In extreme circumstances of severe dose-limiting toxicity, temporary TMP-SMX dose reduction with intensive monitoring may be feasible as a bridge to complete guideline-concordant therapy, though this approach falls below current recommendations and requires robust therapeutic drug monitoring. Species-directed antimicrobial selection and early molecular diagnosis facilitated initial clinical resolution in this high-risk immunocompromised host.},
}

@article {pmid42038409,
year = {2026},
author = {Nousias, O and Duffy, FG and Duffy, IJ and McCauley, M and Whilde, J and Duffy, DJ},
title = {Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {2},
pages = {lqag040},
pmid = {42038409},
issn = {2631-9268},
mesh = {Animals ; *Rivers/microbiology ; *Biodiversity ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; *Nanopore Sequencing/methods ; DNA, Environmental/genetics ; Environmental Health ; Animals, Wild/genetics ; Metagenome ; },
abstract = {As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.},
}

Animals
*Rivers/microbiology
*Biodiversity
*Metagenomics/methods
*Environmental Monitoring/methods
Humans
*Nanopore Sequencing/methods
DNA, Environmental/genetics
Environmental Health
Animals, Wild/genetics
Metagenome

@article {pmid42038418,
year = {2026},
author = {Vlasovets, O and Schaipp, F and Simpson, L and Bolyen, E and Caporaso, JG and Mueller, CL},
title = {Sparse regression, classification, and microbial network estimation in QIIME2 with q2-classo and q2-gglasso.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {42038418},
issn = {2331-8422},
abstract = {MOTIVATION: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce.

RESULTS: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors.

AVAILABILITY: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.},
}

@article {pmid42038553,
year = {2026},
author = {Rodríguez-Rodríguez, Y and Disla, AMM and Ortega, MER and Gandini, G and Tejada-Tejada, P and Guevara, MÁ and Franco, EF and Dantas, CWD and Ramos, RT and Jáuregui-Haza, UJ},
title = {Microbial Profiling and Biosafety Assessment of a Sargassum-Based Liquid Biofertilizer Using 16S rRNA Metagenomics.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {3219583},
pmid = {42038553},
issn = {1687-918X},
abstract = {Sargassum seaweed is increasingly abundant in the Caribbean, creating ecological disruption but also providing biomass for agricultural inputs. This study compares the microbial diversity and safety of a Sargassum-based liquid biofertilizer (SBLB-INTEC) with those of a conventional product (LB-BANELINO) using 16S rRNA amplicon sequencing, rather than culture-dependent methods. Both formulations contained key nutrients (K, Ca, and Mg) and low levels of heavy metals. They harbored dense but relatively simple bacterial communities dominated by Firmicutes, particularly Bacilli, with Proteobacteria and other phyla at lower abundances. Staphylococcus (Staphylococcaceae) was highly abundant in both products, while SBLB-INTEC showed a somewhat more balanced community, including Delftia and other Comamonadaceae. Shannon diversity tended to be higher in SBLB-INTEC, but differences in alpha- and beta-diversity between formulations were not statistically significant. Because 16S data cannot distinguish viable from nonviable cells or resolve strain-level pathogenicity, these results do not prove the absence of pathogens; instead, they provide a genus-level baseline to guide targeted culture, qPCR, and functional assays. Overall, the combination of a favorable chemical profile and microbial groups commonly associated with nutrient cycling and plant-associated functions suggests that SBLB-INTEC could become a valuable component of integrated nutrient management in tropical agriculture, offering hope for a more sustainable future pending confirmatory plant-response and biosafety studies. We recommend integrating these microbial data into a national biofertilizer monitoring framework, combining metagenomic surveys with targeted qPCR and resistance gene screening.},
}

@article {pmid42038636,
year = {2026},
author = {Ryder, JH and Turbett, SE},
title = {Mindful diagnostics: a central nervous system infection case study.},
journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE},
volume = {6},
number = {1},
pages = {e96},
pmid = {42038636},
issn = {2732-494X},
abstract = {A clinical case is presented to discuss a framework for use of advanced diagnostics for central nervous system infections. Advantages, limitations, and diagnostic stewardship strategies are discussed for each modality: multiplex molecular meningitis/encephalitis panel, plasma microbial cell-free DNA sequencing, and cerebrospinal fluid metagenomic next generation sequencing.},
}

@article {pmid42039195,
year = {2026},
author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H},
title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1749584},
pmid = {42039195},
issn = {1664-3224},
mesh = {Female ; Humans ; *Virome ; *Mycobiome ; *Vaginosis, Bacterial/microbiology/virology ; *Microbiota ; Papillomavirus Infections/microbiology/virology ; Vagina/microbiology/virology ; *Reproductive Health ; *Genitalia, Female/microbiology/virology ; Bacteriophages ; },
abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.

METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.

RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.

CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.},
}

Female
Humans
*Virome
*Mycobiome
*Vaginosis, Bacterial/microbiology/virology
*Microbiota
Papillomavirus Infections/microbiology/virology
Vagina/microbiology/virology
*Reproductive Health
*Genitalia, Female/microbiology/virology
Bacteriophages

@article {pmid42039480,
year = {2026},
author = {Liu, J and De Paolis Kaluza, MC and Bromberg, Y},
title = {16S rRNA k-mer composition encodes microbial functional potential.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.718937},
pmid = {42039480},
issn = {2692-8205},
abstract = {16S rRNA amplicon sequencing is widely used to profile microbiome taxonomic composition and functional potential. Most 16S rRNA-based analysis methods depend on comparing sequenced reads against reference marker genes from previously characterized organisms. Thus, method accuracy declines in environments dominated by uncharacterized microbes. We uncovered a direct link between 16S rRNA and genome-encoded functions. Using fully sequenced bacterial genomes, we show that (i) whole-genome k-mer composition is predictive of functions encoded in the genome and (ii) 16S rRNA k-mer profiles reflect their source genome k-mer compositions. Leveraging these relationships, we developed embeRNA, a neural network-based framework that predicts functions directly from 16S rRNA k-mer embeddings, without taxonomy assignment or phylogenetic placement. Furthermore, by producing per-function probability scores rather than categorical assignments, embeRNA allows users to adapt decision thresholds to match study goals and sample characteristics, e.g. balancing precision vs. recall or accounting for community novelty. We trained embeRNA on a large collection of bacterial function-omes and evaluated it using a stringent "novel microbes" benchmark, where all test 16S rRNA sequences were dissimilar to those seen in training (all <97% identical). On this test set of phylogenetically novel organisms, embeRNA outperformed reference-based methods overall and achieved significantly better performance for the "hard to label" set of functions. In testing on soil metagenomes with paired 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data, embeRNA recovered most WMS-inferred functions and yielded abundance profiles strongly correlated with WMS results. Together, our results indicate that 16S rRNA k-mer composition carries substantial functional signal and that 16S amplicon data can be used to complement WMS-based inference to broaden functional characterization of microbiomes, particularly in understudied environments.},
}

@article {pmid42039609,
year = {2026},
author = {Maldonado Pereira, L and Mutawi, TMA and Singh, A and Sanderson, B and Rekowski, MJ and Barnaba, C and Medina Meza, IG},
title = {Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.12.717948},
pmid = {42039609},
issn = {2692-8205},
abstract = {Dietary oxysterols are biologically active cholesterol oxidation products ubiquitous in Western diets, yet their systemic effects on host metabolism and the gut microbiome remain largely unexplored. Here, we employed an integrated multi-omics approach - shotgun metagenomics, quantitative proteomics, untargeted metabolomics, and bulk RNA-seq - to characterize the impact of DOxS exposure on the gut-liver axis in rats fed a Western diet (WD vs. WD-DOxS). Hepatic proteomics revealed near-complete suppression of the mevalonate/cholesterol biosynthesis pathway, particularly in males, while de novo lipogenesis enzymes (Scd1, Fasn, Plin2) were paradoxically upregulated, consistent with dual oxysterol signaling through SREBP inhibition and LXR activation. Bile acid synthesis was concurrently suppressed, confirmed by metabolomics. Strikingly, RNA-seq across liver, heart, and brain detected virtually no differentially expressed genes, establishing that DOxS act predominantly through post-transcriptional mechanisms. In the gut, DOxS increased microbial α-diversity while depleting Limosilactobacillus reuteri, with concomitant loss of the barrier-protective metabolite 3-indoleacrylic acid. Tissue-specific responses were widespread, with liver and colon frequently mounting opposing metabolic and immune responses to the same dietary challenge. Cross-omics integration revealed convergent microbiome-metabolite axes connecting microbial remodeling to both hepatic lipid reprogramming and colonic barrier disruption. These findings reposition dietary oxysterols from food-quality markers to active modulators of the gut-liver axis, with implications for metabolic disease and intestinal barrier integrity.},
}

@article {pmid42039751,
year = {2026},
author = {Chen, XG and Zhou, L and Duan, K and Shi, SY and Subi, A and Sun, HW and Lu, YM and Hu, L and Yang, ZT},
title = {Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1786413},
pmid = {42039751},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Male ; Virulence Factors/genetics ; Female ; Middle Aged ; Virulence/genetics ; Aged ; Intensive Care Units ; *Bacteria/genetics/drug effects/pathogenicity/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/microbiology/diagnosis ; *Host-Pathogen Interactions ; Anti-Bacterial Agents/pharmacology ; Adult ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection. However, its integrative value in simultaneously revealing resistance, virulence, and host-response interplay in Intensive Care Unit(ICU)-infected patients remains underexplored.

METHODS: In this retrospective cohort study of 156 ICU-infected patients, we compared the diagnostic performance of mNGS against conventional microbiological testing (CMT). We analyzed mNGS-derived antibiotic resistance genes (ARGs) and virulence factors (VFs) and correlated them with host immune-inflammatory markers and clinical outcomes.

RESULTS: mNGS demonstrated a significantly higher positive detection rate (89.7% vs. 67.3%, P < 0.001) and clinical concordance (75.6% vs. 35.9%, P < 0.001) than CMT. It revealed a high mixed-infection rate (72.1%). ARGs were detected in 49.0% of bacterial infections, predominantly β-lactamase genes, showing 72.0% concordance with phenotypic susceptibility. Key VFs (e.g., rmpA in K. pneumoniae) were identified. Based on mNGS results, 47.4% of patients had their antimicrobial therapy adjusted.

CONCLUSION: mNGS provides a comprehensive diagnostic tool by integrating pathogen identification, resistance and virulence profiling, and host-response context, enabling more precise and timely management of ICU-infected patients.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Male
Virulence Factors/genetics
Female
Middle Aged
Virulence/genetics
Aged
Intensive Care Units
*Bacteria/genetics/drug effects/pathogenicity/isolation & purification/classification
*Drug Resistance, Bacterial/genetics
*Bacterial Infections/microbiology/diagnosis
*Host-Pathogen Interactions
Anti-Bacterial Agents/pharmacology
Adult

@article {pmid42039753,
year = {2026},
author = {Li, X and Fang, J and Li, D and Cai, B and Yin, J and Zheng, Y and Yin, G},
title = {Performance evaluation of mNGS in pathogen diagnosis of skin and soft tissue infections and its optimization effect on antibiotic decision-making.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1771148},
pmid = {42039753},
issn = {2235-2988},
mesh = {Humans ; *Soft Tissue Infections/diagnosis/microbiology/drug therapy ; Retrospective Studies ; Male ; Female ; *Anti-Bacterial Agents/therapeutic use ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Antimicrobial Stewardship ; Aged ; *Metagenomics/methods ; *Bacteria/genetics/isolation & purification/classification/drug effects ; *Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy ; Young Adult ; Coinfection/diagnosis/microbiology/drug therapy ; Adolescent ; Clinical Decision-Making ; },
abstract = {BACKGROUND: Skin and soft tissue infections (SSTIs), often caused by polymicrobial pathogens, pose diagnostic challenges due to the limitations of conventional methods, including low sensitivity and prolonged turnaround time. This diagnostic gap has perpetuated empirical antibiotic use in clinical practice. Metagenomic next-generation sequencing (mNGS), with its unbiased pathogen detection capability, offers a transformative approach for rapid and precise microbial identification in SSTIs.

OBJECTIVE: To evaluate the clinical utility of mNGS compared to conventional microbiological testing in guiding antibiotic stewardship for complex SSTIs.

METHODS: A retrospective cohort study was conducted at the First Affiliated Hospital of Zhengzhou University from April 2023 to May 2025, enrolling 69 patients with clinically diagnosed complex SSTIs. All patients underwent concurrent mNGS testing, conventional bacterial culture, and pathological examination. The diagnostic performance of mNGS was systematically compared with culture methods, with emphasis on culture-negative cases and polymicrobial infections. The impact of mNGS-guided antibiotic adjustments was assessed.

RESULTS: mNGS demonstrated significantly higher pathogen detection rates than conventional culture (P < 0.001), with a concordance of 37.5% between the two methods. Among 24 culture-negative patients, mNGS identified pathogens in 20 cases (83.3% detection rate). For polymicrobial infections (n = 20), culture detected pathogens in only 2 cases, whereas mNGS successfully identified multiple pathogens in the majority. Antibiotic therapy was adjusted based on mNGS results in 11.9% (8/69) of patients.

CONCLUSION: mNGS substantially improves pathogen detection in complex SSTIs compared to conventional methods. Beyond diagnostic accuracy, its clinical value lies in enabling targeted antibiotic therapy, thereby optimizing antimicrobial stewardship and potentially reducing healthcare costs.},
}

Humans
*Soft Tissue Infections/diagnosis/microbiology/drug therapy
Retrospective Studies
Male
Female
*Anti-Bacterial Agents/therapeutic use
Middle Aged
Adult
*High-Throughput Nucleotide Sequencing/methods
Antimicrobial Stewardship
Aged
*Metagenomics/methods
*Bacteria/genetics/isolation & purification/classification/drug effects
*Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy
Young Adult
Coinfection/diagnosis/microbiology/drug therapy
Adolescent
Clinical Decision-Making

@article {pmid42039757,
year = {2026},
author = {Wu, Y and Zhang, J and Su, W and Zhang, Z},
title = {Global epidemiology of tick-borne Alpharhabdovirinae: a meta-analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1791903},
pmid = {42039757},
issn = {2235-2988},
mesh = {Animals ; Phylogeny ; *Ticks/virology ; Humans ; *Tick-Borne Diseases/epidemiology/virology ; Genome, Viral ; },
abstract = {INTRODUCTION: The Alpharhabdovirinae subfamily of the family Rhabdoviridae encompasses a diverse and expanding group of tick-borne viruses, some of which pose potential risks as emerging human pathogens. Despite increasing detection through metagenomic surveillance, the global diversity, phylogenetic relationships, and taxonomic framework of tick-borne Alpharhabdovirinae (TBA) remain poorly characterized.

METHODS: This study conducted a comprehensive meta-analysis of all publicly available TBA sequences based on phylogenetic analysis of five structural proteins (N, P, M, G, L), combined with host associations and geographic distributions.

RESULTS: 345 TBA strains were classified into 12 distinct phylogenetic clusters, each exhibiting unique evolutionary and ecological characteristics. These clusters include: (1) seven species-level lineages within the genus Alpharicinrhavirus, predominantly associated with Hyalomma and Haemaphysalis ticks across Eurasia; (2) a cluster related to Manly virus, widely distributed in Amblyomma, Haemaphysalis, and Rhipicephalus ticks acrossAustralia and China, exhibiting additional protein-coding genes of unknown function; (3) the genus Ledantevirus (21 species), characterized by broad host tropism including bats, rodents, and humans, with some members displaying phosphoprotein phylogenetic anomalies suggestive of recombination; (4) the genus Lostrhavirus, together with Tongliao Rhabd tick virus 1, forming a cluster associated with Hyalomma and Amblyomma ticks; (5) a Mononegavirus cluster comprising Alpharicinrhavirus heilongjiang, Alpharicinrhavirus skanevik (Norway mononegavirus 1), and Mononegavirales sp. specifically associated with Ixodesticks in Eurasia; and (6) one clusters with incomplete protein repertoires and uncertain taxonomic positions, including Tahe rhabdovirus 3 and Yanbian Rhabd tick virus 1 which lacks phosphoprotein entirely. This study provide a refined phylogenetic framework for TBA viruses, clarify their evolutionary relationships, and highlight critical knowledge gaps, including numerous uncharacterized hypothetical proteins and incomplete genomes that warrant further investigation.

DISCUSSION: This study underscores the importance of enhanced global surveillance and genomic characterization to assess the emergence potential and public health threat posed by this diverse group of tick-borne viruses.},
}

Animals
Phylogeny
*Ticks/virology
Humans
*Tick-Borne Diseases/epidemiology/virology
Genome, Viral

@article {pmid42039802,
year = {2026},
author = {Adhikary, K and Selim, S and Sarkar, R and Ganguly, K and Das, J and Almuhayawi, MS and Alruhaili, MH and Gattan, HS and Karak, P},
title = {Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780132},
pmid = {42039802},
issn = {1664-302X},
abstract = {Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres to enhance plant resilience under environmental stress. This review places particular emphasis on multi-kingdom microbial interactions including bacteria, fungi, protists, and archaea and their potential for tailored, stress-specific applications within engineered rhizosphere systems. By integrating knowledge from microbial ecology, genomics, and systems biology, researchers have begun to unravel the complex interactions between plants and their associated microbial communities. Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations. Moreover, the manipulation of root exudation patterns and soil physicochemical properties can be harnessed to recruit beneficial microbes and suppress harmful ones. The review also examines the role of synthetic biology tools, such as CRISPR-based genome editing and metabolic pathway engineering, in optimizing microbial traits for enhanced plant support. However, knowledge gaps remain in understanding multi-kingdom dynamics, optimizing SynComs for specific environmental contexts, and translating laboratory successes to reliable, field-scale applications. Additionally, advances in high-throughput screening, machine learning, and metagenomic profiling are accelerating the identification of key microbial taxa and functions relevant to plant health. Despite these promising developments, challenges remain in scaling these approaches for field applications and ensuring their ecological safety and consistency. This review explores the need for interdisciplinary efforts to translate laboratory insights into field-ready technologies, ultimately contributing to the development of climate-resilient and sustainable agricultural systems.},
}

@article {pmid42039826,
year = {2026},
author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C},
title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797687},
pmid = {42039826},
issn = {1664-302X},
abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.

METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.

RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 × 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.

CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.},
}

@article {pmid42039832,
year = {2026},
author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M},
title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761627},
pmid = {42039832},
issn = {1664-302X},
abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.

METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.

RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.

CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.},
}

@article {pmid42040306,
year = {2026},
author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q},
title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1782544},
pmid = {42040306},
issn = {1664-462X},
abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.

METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.

RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.

DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.},
}

@article {pmid42040505,
year = {2026},
author = {Collado, C and Romero-Tena, P and Wegener, G and Elvert, M and Menapace, W and Laso-Pérez, R},
title = {Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag072},
pmid = {42040505},
issn = {2730-6151},
abstract = {Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest [13]C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly [13]C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (Desulfobacterota) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.},
}