@article {pmid41627460,
year = {2026},
author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT},
title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {167},
pmid = {41627460},
issn = {1432-072X},
support = {DTDLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; Infant ; Vietnam ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification/virology ; *Bacteriophages/genetics/isolation & purification/classification ; Child, Preschool ; Male ; Female ; Metagenome ; Diarrhea/microbiology ; Southeast Asian People ; },
abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.},
}

Humans
Infant
Vietnam
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/classification/genetics/isolation & purification/virology
*Bacteriophages/genetics/isolation & purification/classification
Child, Preschool
Male
Female
Metagenome
Diarrhea/microbiology
Southeast Asian People

@article {pmid41627458,
year = {2026},
author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T},
title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {53},
pmid = {41627458},
issn = {1432-0614},
support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Forests ; DNA, Bacterial/genetics ; Endangered Species ; Conservation of Natural Resources ; Time Factors ; Sequence Analysis, DNA ; },
abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.},
}

Animals
*Deer/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Metagenomics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Forests
DNA, Bacterial/genetics
Endangered Species
Conservation of Natural Resources
Time Factors
Sequence Analysis, DNA

@article {pmid41625985,
year = {2026},
author = {Taboada, S and Riesgo, A and Busch, K and Erpenbeck, D and Hentschel, U and Galià, C and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {15},
pmid = {41625985},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.},
}

@article {pmid41624426,
year = {2026},
author = {Santi, I and Pavloudi, C and Abagnale, M and Azua, I and Baña, Z and Bastianini, M and Belser, C and Berg, K and Bilbao, J and Bird, K and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Cunliffe, M and Daguin, C and Deneudt, K and Díaz de Cerio, O and Exter, K and Fauvelot, C and Fontana, Y and Frada, MJ and Galand, PE and Gallia, R and Garczarek, L and González Fernández, J and Guillou, L and Heynderickx, H and Koplovitz, G and Labrune, C and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhães, C and Margiotta, F and Moal, H and Moussy, A and Not, F and Percopo, I and Paredes Rosendo, E and Péru, E and Poulain, J and Praebel, K and Rigaut-Jalabert, F and Romac, S and Rzeznik-Orignac, J and Sarno, D and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Tramontano, F and Trano, AC and Wincker, P and Pade, N},
title = {Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e178484},
pmid = {41624426},
issn = {1314-2828},
abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.},
}

@article {pmid41527012,
year = {2026},
author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P},
title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.},
journal = {Alzheimer's research & therapy},
volume = {18},
number = {1},
pages = {23},
pmid = {41527012},
issn = {1758-9193},
mesh = {Humans ; *Alzheimer Disease/microbiology ; Male ; Female ; Aged ; *Microbiota ; *Dysbiosis/microbiology ; *Mouth/microbiology ; Aged, 80 and over ; Middle Aged ; Saliva/microbiology ; },
abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.

METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.

RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.

CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.

TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.},
}

Humans
*Alzheimer Disease/microbiology
Male
Female
Aged
*Microbiota
*Dysbiosis/microbiology
*Mouth/microbiology
Aged, 80 and over
Middle Aged
Saliva/microbiology

@article {pmid41484966,
year = {2026},
author = {Fu, R and Liang, XJ and Yang, WM and Li, R and Shi, YR and Guo, L and Yu, H and Chen, YH and Wang, HN},
title = {Gut microbial signatures in schizophrenia: exploring archaea, fungi, and bacteria.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {113},
pmid = {41484966},
issn = {1471-244X},
support = {LHJJ24YF06//Interdisciplinary Integration Project of Xijing hospital/ ; 82201679//National Natural Science Foundation of China/ ; 82330043//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *Schizophrenia/microbiology ; *Archaea/genetics/isolation & purification ; *Bacteria/genetics/isolation & purification/classification ; *Fungi/genetics/isolation & purification ; *Dysbiosis/microbiology ; Feces/microbiology ; Middle Aged ; Case-Control Studies ; },
abstract = {BACKGROUND: Gut microbial, mainly bacterial dysbiosis, has been demonstrated in patients with schizophrenia (SCH). However, the signatures and differences of minority gut microbiota in SCH, such as archaea and fungi, have been poorly addressed.

METHODS: We obtained stool samples from 61 SCH patients and 69 healthy controls (HC), and analyzed the compositional and functional alterations of gut archaea, fungi, and bacteria using metagenomic shotgun sequencing (MSS). Additionally, we developed potential biomarkers to distinguish SCH from HC.

RESULTS: SCH patients showed significantly lower archaeal α-diversity compared with that of HC. Whereas there were significant differences between SCH and HC in β-diversity at the species level of archaea, fungi and bacteria. Meanwhile, the functional differences between the two groups were concentrated in glucose, lipid and amino acid metabolic pathways. Furthermore, we established potential diagnostic archaeal (9 species, AUC = 0.73), fungal (8 species, AUC = 0.69), and bacterial (22 species, AUC = 0.74) microbiomes for differentiating SCH patients from HC.

CONCLUSIONS: This study describes a more comprehensive understanding of abnormal gut microbiome in SCH and might provide candidate targets for the development of a microbe-based diagnosis for SCH.

TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2000032118, registration date: 2020/04/20.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Adult
*Schizophrenia/microbiology
*Archaea/genetics/isolation & purification
*Bacteria/genetics/isolation & purification/classification
*Fungi/genetics/isolation & purification
*Dysbiosis/microbiology
Feces/microbiology
Middle Aged
Case-Control Studies

@article {pmid41457176,
year = {2025},
author = {Paul, D and Talukdar, D and Kapuganti, RS and Gupta, V and Narendrakumar, L and Jana, P and Kumar, P and Singh, J and Kumari, S and Basak, C and Kamboj, K and Bakshi, S and Lal, S and Tanwar, S and Kumar, R and Babele, P and Bajpai, M and Kumar, Y and Mutreja, A and Mandal, S and Wadhwa, N and Banerjee, SK and Das, B},
title = {Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1274},
pmid = {41457176},
issn = {2041-1723},
support = {RAD/22017/19/2022-KGD-DBT//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; GCI-13012/2/2025-GCl//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; },
mesh = {*Sewage/microbiology ; India ; *Anti-Bacterial Agents/pharmacology/analysis ; *Microbiota/genetics/drug effects ; *Bacteria/genetics/drug effects/isolation & purification/classification ; Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Humans ; Interspersed Repetitive Sequences/genetics ; Cities ; Microbial Sensitivity Tests ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in microbially dense environments. In this study, we use sewage samples (n = 381) collected from six Indian states between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. We find antibiotics from seven drug classes and detect over 2000 bacterial amplicon sequence variants (ASVs). Metagenomic (n = 220) and isolated genome sequences (n = 305) of aerobic and anaerobic bacterial species identify 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs are predominantly present in multidrug-resistant (MDR) bacterial pathogens. Comparative core genome analysis of MDR bacterial isolates (n = 7166) shows strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur and facilitate the evolution and spread of AMR pathogens in both community and healthcare settings. Additionally, the dipstick-based assay developed for ARGs detection can be used for sewage surveillance in low-resource settings for better understanding of resistance prevalence.},
}

*Sewage/microbiology
India
*Anti-Bacterial Agents/pharmacology/analysis
*Microbiota/genetics/drug effects
*Bacteria/genetics/drug effects/isolation & purification/classification
Drug Resistance, Multiple, Bacterial/genetics
*Drug Resistance, Bacterial/genetics
Metagenomics
Humans
Interspersed Repetitive Sequences/genetics
Cities
Microbial Sensitivity Tests

@article {pmid41457077,
year = {2025},
author = {Peng, L and Chen, JW and Chen, YZ and Di, XP and Lin, LD and Li, BY and Zhang, C and Wang, W and Gao, XS and Ma, YC and Shen, SH and Li, HR and Xu, XF and Zeng, X and Shen, H and Sun, Q and Jin, T and Luo, DY},
title = {Multi-omics analysis identifies a microbiota-bile acid-TLR signaling axis driving bladder injury in interstitial cystitis.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1299},
pmid = {41457077},
issn = {2041-1723},
support = {82422015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82270720//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400904//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82500827//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M752250//China Postdoctoral Science Foundation/ ; 2025T180613//China Postdoctoral Science Foundation/ ; },
mesh = {*Cystitis, Interstitial/microbiology/metabolism/pathology ; Animals ; *Toll-Like Receptor 3/metabolism/genetics ; *Urinary Bladder/pathology/metabolism/microbiology/injuries ; Signal Transduction ; Humans ; Mice ; *Bile Acids and Salts/metabolism ; Female ; Urothelium/metabolism/pathology ; Metabolomics/methods ; *Microbiota ; Single-Cell Analysis ; Mice, Inbred C57BL ; Male ; Multiomics ; },
abstract = {Hunner-type interstitial cystitis/bladder pain syndrome (HIC) is a debilitating condition defined by bladder pain and urinary urgency, yet its upstream drivers remain poorly understood. To identify upstream mechanisms that exacerbate urothelial injury, here we apply an integrative multi-omics framework combining metagenomic sequencing, targeted metabolomics of urine and serum, and single-cell RNA sequencing. This approach reveals a microbial signature enriched in Enterococcus avium and a marked alteration in bile acid metabolism, including increased taurochenodeoxycholic acid (TCDCA). Single-cell analysis indicates that these changes converge on Toll-like receptor 3 (TLR3) activation in urothelial cells. Further validations show that a microbiota-bile acid-TLR3 axis disrupts epithelial barrier integrity and triggers inflammatory responses in experimental models. Transplantation and metabolite administration confirm the causal role of E. avium and TCDCA, while TLR3 inhibition ameliorates injury. These findings uncover an upstream pathway linking gut-derived metabolites to bladder pathology and suggest opportunities for biomarker development and targeted therapies for HIC.},
}

*Cystitis, Interstitial/microbiology/metabolism/pathology
Animals
*Toll-Like Receptor 3/metabolism/genetics
*Urinary Bladder/pathology/metabolism/microbiology/injuries
Signal Transduction
Humans
Mice
*Bile Acids and Salts/metabolism
Female
Urothelium/metabolism/pathology
Metabolomics/methods
*Microbiota
Single-Cell Analysis
Mice, Inbred C57BL
Male
Multiomics

@article {pmid41354462,
year = {2026},
author = {Wang, X and Liu, Y and Sun, Z and Li, J and Lu, Z and Huang, J and Hu, S and Cao, P and Cao, X and Li, S and Ruan, J and Liu, J and Xie, J and Sun, H and Chen, T and Li, S and Zhu, Z and Wen, Z and Tuan, RS and Hunter, DJ and Li, ZA and Shi, D and Ding, C},
title = {Multi-Omics Reveal the Dysregulated Gut-Joint Axis in Knee Synovitis: Data from Two Osteoarthritis Studies in China.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {7},
pages = {e12020},
pmid = {41354462},
issn = {2198-3844},
support = {2023YFE0209700//National Key Research and Development Program of China/ ; GZC20231059//Postdoctoral Fellowship Program of CPSF/ ; 2024M761326//China Postdoctoral Science Foundation/ ; 2023A1515110748//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011794//Guangdong Basic and Applied Basic Research Foundation/ ; 82373653//National Science Foundation of China/ ; 82572825//National Science Foundation of China/ ; 2024A04J5169//Science and Technology Projects in Guangzhou/ ; A2401031//Shenzhen Medical Research Funds/ ; 1194737//Arthritis Australia and an NHMRC Investigator Grant Leadership 2/ ; 82325035//National Natural Science Foundation of China for Distinguished Young Scholars/ ; 82530083//Key Project of the National Science Foundation of China/ ; },
mesh = {Humans ; China ; *Synovitis/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Female ; *Osteoarthritis, Knee/metabolism/microbiology ; Middle Aged ; Proteomics/methods ; *Knee Joint/metabolism/pathology ; Aged ; Metabolomics/methods ; Dysbiosis/metabolism ; Synovial Fluid/metabolism ; Multiomics ; },
abstract = {Gut microbiota dysbiosis and associated host immuno-metabolic disorders may play a role in knee synovitis. Herein, integrated multi-omics analyses of stool and blood samples from subjects from Pearl River Osteoarthritis Cohort (PROC, N = 207) are conducted to explore the potential gut-joint axis. Specifically, gut metagenomics, serum metabolomics and plasma proteomics are carried out. Knee synovitis is identified by magnetic resonance imaging. A total of 87 synovitis cases are identified in PROC, which are characterized by increased Firmicutes/Bacteroidetes (F/B) ratio. Alterations in microbial functions of both leucine and geraniol degradation are closely associated with increased serum 3-hydroxyisovaleric acid and decreased geranic acid. These perturbations are significantly correlated with F/B ratio and down-regulated plasma TWEAK. Building upon these, the potential synovial targets are explored using a synovial single-cell dataset and the Nanjing Osteoarthritis Cohort (NOC, N = 22). Synovial fluid proteomics, histological analysis, and in vitro experiments with human fibroblast-like synoviocytes (FLS) are conducted for NOC subjects with different synovitis grades. An upregulated TWEAK receptor is found in higher grade of synovitis. In vitro, higher TWEAK induced down-regulated TWEAK receptor in FLS. The study for the first time revealed the gut-joint axis in knee synovitis, providing new insight into potential targets for synovitis treatment.},
}

Humans
China
*Synovitis/metabolism/microbiology
*Gastrointestinal Microbiome/physiology/genetics
Male
Female
*Osteoarthritis, Knee/metabolism/microbiology
Middle Aged
Proteomics/methods
*Knee Joint/metabolism/pathology
Aged
Metabolomics/methods
Dysbiosis/metabolism
Synovial Fluid/metabolism
Multiomics

@article {pmid41620752,
year = {2026},
author = {Sharma, A and Küsel, K and Wegner, CE and Pérez-Carrascal, OM and Taubert, M},
title = {Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02325-1},
pmid = {41620752},
issn = {2049-2618},
support = {218627073//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; },
abstract = {BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.

RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (> 90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.

CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.},
}

@article {pmid41620643,
year = {2026},
author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R},
title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2623356},
doi = {10.1080/19490976.2026.2623356},
pmid = {41620643},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Socioeconomic Factors ; Bacteria/classification/genetics/isolation & purification ; *Social Class ; },
abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.},
}

*Gastrointestinal Microbiome
Humans
*Socioeconomic Factors
Bacteria/classification/genetics/isolation & purification
*Social Class

@article {pmid41564978,
year = {2026},
author = {Yuan, C and Jin, P and He, Z and Guo, J and Xiong, M and Sun, J and Wang, L and Wang, Z and Han, N and Feng, W and Hou, Y and Qi, H and Jia, Z},
title = {Maxing Shigan decoction serves as a key component of Lianhua Qingwen in alleviating lung and gut injury by restoring gut microbiota homeostasis and inhibiting inflammation via TLR4/NF-κB and JAK2/STAT3 dual regulation.},
journal = {Microbial pathogenesis},
volume = {212},
number = {},
pages = {108285},
doi = {10.1016/j.micpath.2026.108285},
pmid = {41564978},
issn = {1096-1208},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Toll-Like Receptor 4/metabolism ; *Drugs, Chinese Herbal/pharmacology ; NF-kappa B/metabolism ; STAT3 Transcription Factor/metabolism ; Mice ; *Acute Lung Injury/drug therapy ; Janus Kinase 2/metabolism ; Inflammation/drug therapy ; Lung/drug effects/pathology ; Male ; Lipopolysaccharides ; Colitis, Ulcerative/drug therapy/chemically induced ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Cytokines/metabolism ; },
abstract = {Lianhua Qingwen (LHQW), a clinically validated herbal medicine containing Maxing Shigan Decoction (MXSGT) and others, shows broad efficacy in various respiratory disease. However, its regulatory role on the gut-lung axis, particularly the contribution of its MXSGT components, remains unexplored. This study employed a formula-disassembled approach to decipher this mechanism. Three preparations, including the complete LHQW prescription, LHQW excluding MXSGT components (LHQW-MXSGT), and MXSGT along, were administered to LPS-induced acute lung injury and DSS-induced ulcerative colitis to evaluate their therapeutic effects via the gut-lung axis. Pathological changes, mucosal barrier integrity, inflammatory cell infiltration and pro-inflammatory cytokine levels were evaluated by H&E staining, histochemical staining, immunofluorescence, ELISA, RT-qPCR and Western blot. Metagenomic analysis (16S rDNA sequencing) was conducted to examine their regulatory role of gut microbiota. Network pharmacology analysis and cellular validation was employed to explore their underlying mechanisms. Our analyses demonstrated that LHQW and MXSGT, but not LHQW-MXSGT, significantly attenuated lung/intestinal pathology damage, reduced pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and restored gut barrier proteins (ZO-1, Occludin, MUC2). LHQW/MXSGT suppressed pathogenic bacteria (Escherichia coli, Salmonella, Klebsiella pneumoniae) while enriching Akkermansia muciniphila, correlating with decreased systemic LPS. Network pharmacology and subsequent validation identified dual inhibition of TLR4/NF-κB and JAK2/STAT3 pathways as key mechanism of MXSGT. In conclusion, MXSGT serves a pivotal pharmacologically active component of LHQW for its gut-lung axis regulation, acting through gut microbiota homeostasis restoration, intestinal barrier integrity maintenance, and anti-inflammatory signaling pathways, providing compelling scientific evidence supporting LHQW's potential therapeutic application in managing diseases characterized by comorbid gut and lung inflammation.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Toll-Like Receptor 4/metabolism
*Drugs, Chinese Herbal/pharmacology
NF-kappa B/metabolism
STAT3 Transcription Factor/metabolism
Mice
*Acute Lung Injury/drug therapy
Janus Kinase 2/metabolism
Inflammation/drug therapy
Lung/drug effects/pathology
Male
Lipopolysaccharides
Colitis, Ulcerative/drug therapy/chemically induced
Homeostasis/drug effects
Signal Transduction/drug effects
Mice, Inbred C57BL
Disease Models, Animal
Cytokines/metabolism

@article {pmid41494246,
year = {2026},
author = {Ding, J and Guo, T and Xia, H and Huang, K and Li, M and Li, F},
title = {Earthworm mediated microbial quorum sensing accelerates organic matter transformation during vermicomposting of dewatered sludge.},
journal = {Waste management (New York, N.Y.)},
volume = {212},
number = {},
pages = {115332},
doi = {10.1016/j.wasman.2026.115332},
pmid = {41494246},
issn = {1879-2456},
mesh = {*Oligochaeta/physiology ; *Quorum Sensing ; Animals ; *Composting/methods ; *Sewage/microbiology ; Biodegradation, Environmental ; Humic Substances ; Microbiota ; Bacteria/metabolism ; Acyl-Butyrolactones/metabolism ; },
abstract = {Vermicomposting (VC) relies on the synergistic interaction between earthworms and microorganisms to drive the degradation of organic matter (OM). Quorum sensing (QS), which governs earthworm-microorganism interactions, may influence dissolved organic matter (DOM) transformation during VC. However, the presence of QS and the functional roles of signaling molecules during VC remain unclear. This study investigated earthworm mediated microbial QS in driving microbial community succession and accelerating DOM transformation during VC, by contrasting the process without earthworms. The results showed that VC exhibited a distinct decomposition pathway, achieving significantly faster DOM degradation and mineralization (P < 0.01), compared to the control. Additionally, earthworms markedly facilitated the transformation of protein-like compounds into humic-like substances over a shorter period. Their presence also modified acyl-homoserine lactone (AHL) synthesis patterns and suppressed AHLs hydrolysis, resulting in a 96.14 % increase (P < 0.01) in short-chain AHLs. Metagenomic analysis revealed that earthworm in VC significantly altered the bacterial diversity (P < 0.05), enriching modularity coefficient and deterministic processes by 18.75 % and 87.03 %, respectively. Finally, AHL-responsive microorganisms significantly influencing physicochemical and DOM transformation during the VC. This study suggests that earthworms enhance AHL-type QS regulation in microbial communities, improving their metabolic functions and accelerating DOM transformation.},
}

*Oligochaeta/physiology
*Quorum Sensing
Animals
*Composting/methods
*Sewage/microbiology
Biodegradation, Environmental
Humic Substances
Microbiota
Bacteria/metabolism
Acyl-Butyrolactones/metabolism

@article {pmid41482085,
year = {2026},
author = {Yang, B and Xia, Q and Ji, X and Su, K and Yu, T and Xiao, Z and Shi, C and Luo, Z and Wang, X and Xu, W and Gao, Y and Hua, H and Shan, J},
title = {Ganjie Decoction protects against respiratory syncytial virus infection by activating PI3K/AKT-apoptosis axis and regulating gut microbiota metabolism.},
journal = {Journal of ethnopharmacology},
volume = {360},
number = {},
pages = {121142},
doi = {10.1016/j.jep.2025.121142},
pmid = {41482085},
issn = {1872-7573},
mesh = {Animals ; *Respiratory Syncytial Virus Infections/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Phosphatidylinositol 3-Kinases/metabolism ; Mice, Inbred BALB C ; Apoptosis/drug effects ; Signal Transduction/drug effects ; Humans ; *Antiviral Agents/pharmacology ; Lung/drug effects/pathology/virology ; Molecular Docking Simulation ; Female ; Male ; },
abstract = {Ganjie Decoction (GJD), a traditional Chinese medicine (TCM) formula commonly used for respiratory diseases, has shown therapeutic potential against RSV pneumonia. However, its pharmacological mechanisms against respiratory syncytial virus (RSV) pneumonia are not fully understood.

AIM OF STUDY: This study aimd to characterize the active components of GJD and systematically investigate its therapeutic effects and underlying mechanisms in RSV-induced pneumonia.

MATERIALS AND METHODS: To evaluate the therapeutic efficacy of GJD in RSV-infected mice, we monitored body weight, performed qPCR, and conducted histopathological examination of lung tissues. The chemical constituents of GJD were characterized using UPLC-MS. Key bioactive compounds and their potential targets were predicted using network pharmacology and molecular docking. The underlying mechanisms were further elucidated using immunohistochemistry and western blotting. The interactions between GJD and the gut microbiota were explored using antibiotic depletion, fecal microbiota transplantation (FMT), metagenomic sequencing, and in vitro co-culture assays. Untargeted metabolomics was employed to assess GJD-induced metabolic alterations. Finally, the role of the key metabolite 4-hydroxyphenylacetic acid (4-HPA) was investigated in vivo and in vitro through qPCR, immunohistochemistry, ELISA, Western blot, cell viability assays and immunofluorescence.

RESULTS: GJD significantly mitigated weight loss, attenuated pulmonary viral load, and suppressed inflammation in RSV-infected mice. Network pharmacology and molecular docking revealed that specific compounds in GJD target the PI3K/AKT signaling pathway. This finding was validated by western blotting and immunohistochemistry, which demonstrated that GJD suppresses PI3K/AKT pathway activation, thereby attenuating apoptosis and ameliorating RSV-induced pneumonia. Notably, these protective effects were markedly attenuated in mice with depleted gut microbiota, while therapeutic effects of GJD against RSV pneumonia were transferable via gut microbiota transplantation. GJD restored RSV-induced dysbiosis of the gut microbiota, with Lactobacillus reuteri emerging as one of the most enriched microbes following treatment. Metabolomics analysis identified 4-HPA as a microbiota-dependent metabolite significantly upregulated by GJD. Remarkably, administration of 4-HPA reproduced GJD's therapeutic effects in RSV-infected mice and activated the KEAP1/NRF2 antioxidant pathway, suggesting that 4-HPA functions as a key mediator of GJD's anti-RSV activity.

CONCLUSIONS: These findings suggest that GJD alleviates RSV pneumonia through a synergistic mechanism that modulates the PI3K/AKT-apoptosis pathway, restores gut microbial balance, and normalizes metabolic disturbances. This study systematically elucidates the mechanistic basis underlying the therapeutic effects of GJD against RSV pneumonia.},
}

Animals
*Respiratory Syncytial Virus Infections/drug therapy
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Proto-Oncogene Proteins c-akt/metabolism
Mice
Phosphatidylinositol 3-Kinases/metabolism
Mice, Inbred BALB C
Apoptosis/drug effects
Signal Transduction/drug effects
Humans
*Antiviral Agents/pharmacology
Lung/drug effects/pathology/virology
Molecular Docking Simulation
Female
Male

@article {pmid41201733,
year = {2026},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {54},
number = {1},
pages = {111-126},
pmid = {41201733},
issn = {1439-0973},
mesh = {*Biofilms/growth & development ; Humans ; *Coinfection/microbiology/diagnosis ; *Microbiota ; *Precision Medicine/methods ; },
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

*Biofilms/growth & development
Humans
*Coinfection/microbiology/diagnosis
*Microbiota
*Precision Medicine/methods

@article {pmid41193697,
year = {2026},
author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA},
title = {Gut virome dynamics: from commensal to critical player in health and disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {23},
number = {2},
pages = {126-144},
pmid = {41193697},
issn = {1759-5053},
mesh = {Humans ; *Virome/physiology ; *Gastrointestinal Microbiome/physiology ; Bacteriophages ; },
abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.},
}

Humans
*Virome/physiology
*Gastrointestinal Microbiome/physiology
Bacteriophages

@article {pmid41143690,
year = {2026},
author = {Kim, KJ and Garcia, MM and Romero, AS and Jin, Y and Chi, J and Campen, MJ and Gu, H and Richardson, JR and Castillo, EF and Cui, JY},
title = {In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {209},
number = {1},
pages = {},
doi = {10.1093/toxsci/kfaf145},
pmid = {41143690},
issn = {1096-0929},
support = {R01 ES032037/ES/NIEHS NIH HHS/United States ; T32ES007032//UW Environmental Pathology/Toxicology Training/ ; //Environmental Health and Microbiome Research Center (EHMBRACE)/ ; //Sheldon Murphy Endowment/ ; 5P30ES007033-27//UW EDGE Center/ ; 1U01AG088557/GF/NIH HHS/United States ; 1R01AG070776/GF/NIH HHS/United States ; //Dianne Isakson Distinguished Professorship/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Mice, Inbred C57BL ; *Microplastics/toxicity ; *Metabolome/drug effects ; Feces/microbiology ; Mice ; Metabolomics ; },
abstract = {Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. MPs, defined as plastic particles less than 5 mm in diameter, are formed through the degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, and food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested MPs. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57BL/6 mice were orally gavaged with mixed plastic (5 µm) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly(lactic-co-glycolic acid), twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. A total of 1,162 bacterial species and 1,437 metabolites were evaluated for downstream analysis. MPs' exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition, along with substantial regulation of predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways, such as amino acid metabolism, sugar metabolism, and inflammation. Additionally, short-chain fatty acid (SCFA)-targeted metabolomics showed significant changes in neuroprotective SCFA levels in both sexes. Our study demonstrates that MPs dysregulate the gut microbiome and serum metabolome, highlighting potential human disease risks.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Male
Female
Mice, Inbred C57BL
*Microplastics/toxicity
*Metabolome/drug effects
Feces/microbiology
Mice
Metabolomics

@article {pmid40905099,
year = {2026},
author = {Gem, H and Ebadi, M and Sebastian, G and Abasaeed, R and Lloid, M and Minot, SS and Dean, DR and Rashidi, A},
title = {Dental plaque microbiota following allogeneic hematopoietic cell transplantation and risk of chronic graft-versus-host disease.},
journal = {Haematologica},
volume = {111},
number = {2},
pages = {620-631},
doi = {10.3324/haematol.2025.288279},
pmid = {40905099},
issn = {1592-8721},
mesh = {Humans ; *Graft vs Host Disease/etiology/diagnosis/microbiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Female ; Male ; Middle Aged ; Adult ; *Dental Plaque/microbiology ; *Microbiota ; Transplantation, Homologous ; Chronic Disease ; Aged ; Young Adult ; },
abstract = {Microbiota disruptions have been associated with short-term complications after allogeneic hematopoietic cell transplantation (alloHCT). However, only a few studies have examined the relationship between dysbiosis and chronic graft-versus-host disease (cGvHD), the main long-term immunologic toxicity of alloHCT. Considering the role of oral microbiota in systemic inflammatory diseases, we evaluated whether oral microbiota at day 28 post HCT corresponding to clinical recovery from the acute events after transplantation is associated with subsequent cGvHD. Shotgun metagenomic sequencing of 207 saliva and supragingival plaque samples collected longitudinally at baseline (pre-conditioning), day +28, and day +84 from 37 patients (11 with subsequent moderate/severe cGvHD) revealed a significant association between day +28 plaque microbiota composition and cGvHD. Two orthogonal statistical approaches demonstrated Streptococcus sanguinis and Prevotella loescheii in day +28 plaque to be associated with cGvHD. Metagenome-based functional analysis identified 4 microbial metabolic pathways associated with future cGvHD, 2 of which were highly attributed to S. sanguinis. These pathways - ethanolamine utilization and glycerol metabolism - increase bacterial fitness by providing an alternative carbon/nitrogen source and improving survival in inflamed tissues. Our findings propose a novel mechanism by which the early post-transplant dental biofilm may contribute to cGvHD months later, offering a potential target for early prophylactic intervention.},
}

Humans
*Graft vs Host Disease/etiology/diagnosis/microbiology
*Hematopoietic Stem Cell Transplantation/adverse effects
Female
Male
Middle Aged
Adult
*Dental Plaque/microbiology
*Microbiota
Transplantation, Homologous
Chronic Disease
Aged
Young Adult

@article {pmid41619244,
year = {2025},
author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS},
title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {42},
number = {4},
pages = {435-445},
doi = {10.47665/tb.42.4.010},
pmid = {41619244},
issn = {2521-9855},
mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/classification ; Animals ; *Microbiota ; Male ; *Lice Infestations/epidemiology/parasitology ; Female ; Child ; Child, Preschool ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Vulnerable Populations ; Infant ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.},
}

Humans
Malaysia/epidemiology
*Pediculus/genetics/classification
Animals
*Microbiota
Male
*Lice Infestations/epidemiology/parasitology
Female
Child
Child, Preschool
*Genetic Variation
RNA, Ribosomal, 16S/genetics
Vulnerable Populations
Infant
Bacteria/classification/genetics/isolation & purification

@article {pmid41618383,
year = {2026},
author = {Pérez-Pérez, L and Arguello, H and Cobo-Díaz, JF and Galisteo, C and Puente, H and Gómez-Martínez, S and Carvajal, A},
title = {From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {25},
pmid = {41618383},
issn = {1297-9716},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; EDU-1868-2022//Junta de Castilla y León/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; *Swine Diseases/microbiology ; *Gram-Negative Bacterial Infections/veterinary/microbiology ; *Brachyspira hyodysenteriae/physiology ; Feces/microbiology ; Disease Susceptibility/veterinary/microbiology ; },
abstract = {Restrictions on antibiotics use have increased interest in the gut microbiota relationship to host health, particularly in enteric infections. The present field study, performed on two farms with endemic swine dysentery (SD) infection, characterises the faecal microbiota in 102 faecal samples from 13 diseased and 13 non-diseased pigs by shotgun metagenomic sequencing. The samples were collected during four samplings, which allowed us to monitor the animals before, during and after the clinical disease to investigate the role of the gut microbiota in disease outcome, assess the impact of infection on microbial composition and evaluate the microbiota evolution following recovery. Samples collected before disease demonstrated that SD susceptible pigs had lower microbial diversity, with significantly lower abundance of Treponema rectale, Prevotella spp. or Ruminiclostridium E compared with SD resistant pigs, which remained healthy. Marked alterations in microbial species composition and their functional profiles were evident during clinical disease. Brachyspira hyodysenteriae, Dysosmobacter sp. BX15, Acetivibrio ethanolgignens and Mucispirillum sp. 910586745 were significantly increased in abundance, which was associated with an increase of functions such as Bacteroides capsular polysaccharide transcription antitermination proteins or pterin carbinolamine dehydratase. No changes in the microbiota were observed after the disease when compared with non-diseased pigs, thus evidencing a restoration of the microbiota composition after therapeutic treatment and recovery. The study demonstrates that the microbiota may play a relevant role in SD disease outcome and evidences the changes that occur during clinical disease do not persist over time after pig therapeutic treatment.},
}

Animals
Swine
*Gastrointestinal Microbiome
*Swine Diseases/microbiology
*Gram-Negative Bacterial Infections/veterinary/microbiology
*Brachyspira hyodysenteriae/physiology
Feces/microbiology
Disease Susceptibility/veterinary/microbiology

@article {pmid41617723,
year = {2026},
author = {Pratama, AA and Pérez-Carrascal, O and Sullivan, MB and Küsel, K},
title = {Diversity and ecological roles of hidden viral players in groundwater microbiomes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68914-2},
pmid = {41617723},
issn = {2041-1723},
support = {EXC 2051, Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-SC0023307//U.S. Department of Energy (DOE)/ ; },
abstract = {Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.24 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) (≥ 5 kb), with 99% novel at order, family and genus levels against global ocean, freshwater and/or other publicly available datasets. In silico host predictions suggest that vOTUs primarily targeted Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea, which reflects abundant and active groundwater microbial members. Patterns of virus-host abundance ratios, CRISPR-spacers, and prophage screening suggest the potential for multi-layer interactions involving CPR/DPANN lineages, their hosts, and viruses. Additionally, we identified 289 KEGG metabolic modules, 31.1% of which were targeted by 3378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling. These findings provide a baseline for exploring how viruses influence microbial community dynamics, metabolic reprogramming and nutrient cycling in groundwater.},
}

@article {pmid41616624,
year = {2026},
author = {Sun, Y and Zhang, M and Teng, Y and Yin, Y and Ran, J and Su, H and Li, H and Huang, X and Long, Z and Sun, X and Pan, H and Wang, X and Li, M},
title = {Human activities and horizontal gene transfer shape the resistome landscapes of non-human primates.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141276},
doi = {10.1016/j.jhazmat.2026.141276},
pmid = {41616624},
issn = {1873-3336},
abstract = {Antibiotic resistance represents a growing threat to human, animal, and ecosystem health, yet its dynamics in wildlife remain poorly understood. We conducted a systematic analysis of the gut resistomes in non-human primates (NHPs) and environmental soils in Guizhou Province, China, a biodiversity hotspot. Metagenomic analyses reveal that human activities and horizontal gene transfer (HGT) influence primate resistome landscapes and enhance their dissemination potential. A total of 1927 antibiotic resistance ontologies (AROs) distributed across 1477 species-level genome bins (SGBs), providing a comprehensive genomic catalog of the NHPs resistome. Bacterial genera such as Pseudomonas, Stenotrophomonas, and Comamonas drive ARG mobilization, with a core subset of ARGs that reliably predict overall resistance burdens. Notably, widely distributed primate species, with large habitat ranges and frequent interspecies interactions exhibit the most potential for ARG dissemination. Ecological modeling identifies current and future hotspot regions requiring prioritized monitoring amid ongoing human disturbance and climate change. These findings provide a molecular-indicator-based framework for environmental antibiotic resistance (AR) monitoring and conservation strategies for endangered species. Despite limitations in temporal and spatial coverage, our study highlights the need to integrate wildlife, particularly NHPs, as sentinel species into "One Health" AR surveillance and policy. This approach will strengthen our understanding of ARG transmission dynamics and their long-term impacts on host adaptation, ecosystem stability, and public health.},
}

@article {pmid41609167,
year = {2026},
author = {Koo, WLY and Thng, KX and Tiew, PY and Chotirmall, SH},
title = {The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {87},
number = {1},
pages = {50163},
doi = {10.31083/BJHM50163},
pmid = {41609167},
issn = {1750-8460},
support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000955//Singapore Ministry of Health's National Medical Research Council/ ; RT1/22//Singapore Ministry of Education/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy ; *Microbiota ; Dysbiosis/microbiology ; *Lung/microbiology ; Disease Progression ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating respiratory condition marked by chronic symptoms and frequent exacerbations, contributing to significant morbidity and mortality. The advent of molecular microbiology and next-generation sequencing (NGS) has expanded our understanding of the lung microbiome, and integration of microbiome datasets with other omics reveals important microbial-metabolic-immuno-inflammatory interactions that influence COPD pathogenesis. Recent studies have highlighted dysbiosis of the airway microbiome, with shifts in bacterial, viral, and fungal communities playing a crucial role in disease progression, exacerbations and clinical outcomes. Moreover, microbiome changes are observed in COPD associated overlap syndromes, complicating diagnosis and treatment. This review synthesizes current microbiome research in COPD, focusing on its clinical relevance, including its potential as a diagnostic and prognostic tool. We additionally discuss the challenges of integrating microbiome data into clinical practice, emphasizing the need for personalized, precision medicine approaches to optimize COPD management and improve patient outcomes.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/therapy
*Microbiota
Dysbiosis/microbiology
*Lung/microbiology
Disease Progression

@article {pmid41606855,
year = {2025},
author = {Yang, J and He, Y and Huang, J and Li, M and Wu, X and Pei, X and Yang, X},
title = {Decoding resistome profiles and horizontal transfer of antibiotic resistance genes across the pork production chain under One Health sectors.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117259},
doi = {10.1016/j.foodres.2025.117259},
pmid = {41606855},
issn = {1873-7145},
mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *One Health ; *Drug Resistance, Bacterial/genetics ; *Pork Meat/microbiology ; Food Microbiology ; Abattoirs ; Metagenome ; Microbiota/genetics ; Metagenomics ; Bacteria/genetics ; },
abstract = {The emergence of antimicrobial resistance has become a global threat to public health. Intensive antibiotic use in swine farming has accelerated the proliferation of antibiotic resistance genes (ARGs) in animal-derived foods, making the production chain a potential ARG transmission route to humans. However, shared resistome profiles and horizontal gene transfer (HGT) mechanisms along this chain remain unclear. Here, we systematically investigated the resistome profile, ARGs' host, and potential HGT of ARGs across interconnected swine farm, slaughterhouse, and retail market by metagenomic assembly and binning. From 42 metagenomes, 1354 ARG subtypes were identified, with 303 shared across all interfaces. Both microbiome and mobile genetic elements (MGEs) contributed to the variation in ARG profiles. Pseudomonadota were the dominant drivers that shape the resistome through plasmid-mediated HGT. Among the 133 reconstructed ARG-carrying genomes (ACGs), 38 of them carried multiple ARGs, indicating the potential mobility of ARGs. Notably, 3 ACGs taxonomically assigned to Pseudomonas_E alcaligenes, Serratia_J grimesii, and Escherichia coli carrying 9, 13, and 41 ARGs, respectively. Furthermore, MetaCHIP analysis uncovered 445 potential HGT events, and ARGs including CpxR, macB, fusA, and vanR were annotated as potentially transferred subtypes. This study decodes the resistome profiles and tracks horizontal ARG transfer at the community level across the entire pork supply chain - from swine farms to retail outlets. To our knowledge, few studies have explored ARG transmission subtypes and directional flows among humans, pigs, and environmental compartments in the pork production chain using metagenomic approaches. These findings highlight the important role of the pork production chain as a critical transmission vector for ARGs under One Health framework.},
}

*Gene Transfer, Horizontal
Animals
Swine
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*One Health
*Drug Resistance, Bacterial/genetics
*Pork Meat/microbiology
Food Microbiology
Abattoirs
Metagenome
Microbiota/genetics
Metagenomics
Bacteria/genetics

@article {pmid41529347,
year = {2026},
author = {Singh, S and Bajaj, A and Manickam, N},
title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181331},
doi = {10.1016/j.scitotenv.2025.181331},
pmid = {41529347},
issn = {1879-1026},
mesh = {*Microbiota ; Biodegradation, Environmental ; Rivers/microbiology ; *Soil Microbiology ; Bacteria/classification ; *Plastics/metabolism ; India ; *Soil Pollutants/metabolism/analysis ; Waste Disposal Facilities ; Water Pollutants, Chemical/analysis ; Biodiversity ; },
abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).},
}

*Microbiota
Biodegradation, Environmental
Rivers/microbiology
*Soil Microbiology
Bacteria/classification
*Plastics/metabolism
India
*Soil Pollutants/metabolism/analysis
Waste Disposal Facilities
Water Pollutants, Chemical/analysis
Biodiversity

@article {pmid41491699,
year = {2026},
author = {Wang, R and Zhang, W and He, Z and Zhou, Y and Chen, C and Song, K and Shang, Q and Wu, Y and Gu, P and Shu, D and Zhao, L},
title = {Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {13},
pmid = {41491699},
issn = {1474-760X},
support = {2023BCF01026//Key Research and Development Program of Ningxia/ ; 2025NC-YBXM-068//Key Research and Development Projects of Shaanxi Province/ ; 32372501//National Natural Science Foundation of China/ ; },
mesh = {*Vitis/microbiology/genetics ; *Disease Resistance/genetics ; *Microbiota ; *Plant Diseases/microbiology/genetics ; *Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; Fusarium/pathogenicity ; Metagenomics ; Bacteria/genetics ; },
abstract = {BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear.

RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance.

CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.},
}

*Vitis/microbiology/genetics
*Disease Resistance/genetics
*Microbiota
*Plant Diseases/microbiology/genetics
*Plant Roots/microbiology
Rhizosphere
Soil Microbiology
Fusarium/pathogenicity
Metagenomics
Bacteria/genetics

@article {pmid41457274,
year = {2025},
author = {Catry, A and Abrouk, D and Fierling, N and Mendoza, AIS and Rey, M and Vesga, P and Heiman, CM and Garrido-Sanz, D and Bouffaud, ML and Buscot, F and Giongo, A and Smalla, K and Comte, G and Keel, C and Muller, D and Moënne-Loccoz, Y},
title = {Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {16},
pmid = {41457274},
issn = {1474-760X},
support = {BiodivERsA3 ERA-Net SuppressSOIL//Biodiversa+/ ; grant SuppressSOIL no. ANR19-EBI3-0007//Agence Nationale de la Recherche/ ; grant SuppressSOIL no. 31BD30_186540//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; grant no. 51NF40_180575//NCCR Microbiomes/ ; BU 941/30-1//Deutsche Forschungsgemeinschaft/ ; project DiControl 031A560A-F//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Nicotiana/microbiology ; *Soil Microbiology ; Rhizosphere ; *Plant Diseases/microbiology ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; },
abstract = {BACKGROUND: In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant-microbe interactions and soil suppressiveness remain poorly understood. Here, we use Swiss and Savoie soils suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco, to test the hypothesis that plant-microbe interactions and suppressiveness are influenced by both the geological origin and geographic positioning of soils. Soils are compared based on tobacco health, soil physicochemistry and organic matter profiles, taxonomic and functional microbial diversity, and plant physiological responses.

RESULTS: Soil physicochemistry and metabolomic profiling of soil organic matter show differences based on suppressiveness status, soil geology and geography. The taxonomic (metabarcoding of prokaryotes and fungi) and functional (metagenomics) diversity of the tobacco rhizosphere reveals that the microbiota is influenced by geography and geology which, in turn, affects suppressiveness. Additionally, shoot metabolomics shows that tobacco responses are impacted by soil geography and geology, particularly in Savoie soils regarding two nicotinic derivatives.

CONCLUSIONS: Overall, suppressiveness is influenced by both the geological origin and geographic positioning of the soils, with distinct patterns in the two regions. In Swiss soils, suppressiveness is primarily associated with major differences in rhizosphere microbiota composition and functions between suppressive and conducive soils. In contrast, in Savoie soils, suppressiveness is linked to distinct plant physiological responses (pointing to induced systemic resistance) rather than strong microbial shifts. This study highlights the importance of considering the biogeographic features shaping disease-suppressive soils and their microbiota-plant interactions.},
}

*Nicotiana/microbiology
*Soil Microbiology
Rhizosphere
*Plant Diseases/microbiology
Plant Roots/microbiology
Soil/chemistry
Microbiota

@article {pmid41429195,
year = {2026},
author = {Ji, J and Guo, J and Huang, Y and Chen, K and Xu, Y and Liang, W and Lin, Z and Xiong, C and Han, X and Liu, J and Hei, Z and Chen, S and Yao, W and Chen, C},
title = {Electroconvulsive therapy modulates brain plasticity in male depression: Links to gut microbial metabolites and diet-derived regulation of Wnt/BDNF signaling.},
journal = {The Journal of nutritional biochemistry},
volume = {150},
number = {},
pages = {110240},
doi = {10.1016/j.jnutbio.2025.110240},
pmid = {41429195},
issn = {1873-4847},
mesh = {Animals ; Male ; *Gastrointestinal Microbiome/physiology ; *Brain-Derived Neurotrophic Factor/metabolism ; *Neuronal Plasticity ; Mice ; *Electroconvulsive Therapy ; *Depression/therapy/metabolism ; *Wnt Signaling Pathway ; Mice, Inbred C57BL ; Fatty Acids, Volatile/metabolism ; Diet ; Probiotics ; Brain/metabolism ; },
abstract = {Electroconvulsive therapy (ECT) stands as the most effective intervention for treatment-resistant depression; however, its interaction with dietary regulation of the gut-brain axis has not been thoroughly explored. This study aimed to elucidate the mechanistic link between ECT, gut microbiota remodeling, short-chain fatty acid (SCFA) production, and neural plasticity. In this study, mice were subjected to chronic restraint stress (6 h/d for 28 consecutive days) to establish a depression-like model. Utilizing a translational approach that incorporated behavioral assessments, multimodal neuroimaging techniques such as PET-CT and laser speckle contrast imaging, along with multiomics analyses including metagenomics, metabolomics, and transcriptomics in rodent models, we demonstrated that ECT induced significant gut microbiota remodeling, characterized by an enrichment of SCFA-producing genera like Lactobacillus and Bifidobacterium. This remodeling was associated with restored intestinal barrier integrity and elevated plasma SCFA levels. Mechanistically, these microbial metabolites activated hippocampal Wnt/β-catenin signaling pathways, enhancing synaptic plasticity restoration, while concurrent probiotic supplementation further amplified brain-derived neurotrophic factor (BDNF) expression via SCFA-dependent epigenetic mechanisms. Neuroimaging corroborated the normalization of cerebral glucose metabolism and hemodynamic function post-ECT. In conclusion, our findings unveil a novel gut-brain communication pathway by which ECT exerts its antidepressant effects, positioning SCFAs as vital mediators connecting microbial metabolic alterations to neural plasticity. This research not only redefines the role of nutritional biochemistry in neuromodulation but also suggests the potential of microbial metabolite monitoring to tailor antidepressant therapies for enhanced efficacy.},
}

Animals
Male
*Gastrointestinal Microbiome/physiology
*Brain-Derived Neurotrophic Factor/metabolism
*Neuronal Plasticity
Mice
*Electroconvulsive Therapy
*Depression/therapy/metabolism
*Wnt Signaling Pathway
Mice, Inbred C57BL
Fatty Acids, Volatile/metabolism
Diet
Probiotics
Brain/metabolism

@article {pmid41428487,
year = {2026},
author = {Deng, C and Hu, J and Chen, Q and Zhou, S and Ni, J},
title = {Expanded global groundwater microbial diversity reveals bioprospecting potential.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116760},
doi = {10.1016/j.celrep.2025.116760},
pmid = {41428487},
issn = {2211-1247},
mesh = {*Groundwater/microbiology ; Phylogeny ; *Bacteria/genetics/classification ; *Microbiota/genetics ; *Bioprospecting ; Archaea/genetics/classification ; Genome, Bacterial/genetics ; Genome, Archaeal/genetics ; Biodiversity ; Metagenomics ; Metagenome ; },
abstract = {Although the terrestrial subsurface harbors a substantial fraction of Earth's microbial biomass, the genomic diversity of groundwater microbiomes and their potential for bioprospecting remain poorly characterized. Here, we recovered 44,320 bacterial and archaeal genomes from in-house and publicly available metagenomic datasets, establishing a large-scale groundwater microbiota catalog (GWMC) spanning 167 phyla, including four candidate phyla and over 12,000 previously uncharacterized species. This unprecedented phylogenetic diversity was accompanied by a bimodal genome size distribution (0.3-12.8 Mbp), revealing divergent strategies of genomic allocation. By mining extensive genomic resources, we found that small genomes prioritized molecular defense and redox regulation, whereas large genomes frequently harbored greater biosynthetic potential. Notably, we establish the largest selenoprotein catalog to date and highlight groundwater as an overlooked hotspot of microbial selenium metabolism. Overall, this work advances our understanding of microbial diversity in aquifers and uncovers underexplored genomic resources with potential for biotechnology and biomedicine.},
}

*Groundwater/microbiology
Phylogeny
*Bacteria/genetics/classification
*Microbiota/genetics
*Bioprospecting
Archaea/genetics/classification
Genome, Bacterial/genetics
Genome, Archaeal/genetics
Biodiversity
Metagenomics
Metagenome

@article {pmid41423811,
year = {2026},
author = {Gordon, ES and Goc, J and Grier, A and Thomas, C and , and Lentine, J and Sockolow, RE and Sonnenberg, GF},
title = {Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia.},
journal = {Inflammatory bowel diseases},
volume = {32},
number = {2},
pages = {303-313},
doi = {10.1093/ibd/izaf295},
pmid = {41423811},
issn = {1536-4844},
support = {//Weill Cornell Medicine Department of Pediatrics/ ; R01AI143842/NH/NIH HHS/United States ; R01AI123368/NH/NIH HHS/United States ; R01AI145989/NH/NIH HHS/United States ; U01AI095608/NH/NIH HHS/United States ; R01AI162936/NH/NIH HHS/United States ; R01CA274534/NH/NIH HHS/United States ; R37AI174468/NH/NIH HHS/United States ; //Pathogenesis of Infectious Disease/ ; //Burroughs Welcome Fund/ ; //Meyer Cancer Center Collaborative Research Initiative/ ; //Dalton Family Foundation/ ; //Rosanne H. Silbermann Foundation/ ; //Weill Cornell Medicine Division of Pediatric Gastroenterology and Nutrition/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Child ; *Anemia, Iron-Deficiency/microbiology/etiology ; Cross-Sectional Studies ; Adolescent ; Case-Control Studies ; Feces/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Iron deficiency anemia (IDA) is the most common extra-intestinal complication in inflammatory bowel disease (IBD). The persistence of iron deficiency in patients living with quiescent IBD remains poorly understood. Given the extensive body of research linking IBD pathogenesis to microbiome disruptions, it is hypothesized that alterations in the microbiota or immune responses may drive the persistence of IDA in quiescent Crohn's disease. This study aimed to determine whether changes in the gut microbiota or immune phenotypes contribute to IDA, while uncovering potential mechanisms driving IDA in quiescent disease.

METHODS: This cross-sectional, descriptive, and analytical study utilized 141 samples from pediatric Crohn's disease patients with and without iron deficiency as well as healthy controls for initial 16S microbiome analysis and a smaller subset for Shotgun Metagenomics and immunologic analyses. Fecal and peripheral blood samples were obtained from the Jill Roberts Institute Live Cell Bank.

RESULTS: While no major differences were observed in the overall gut microbiome composition between pediatric patients with quiescent Crohn's disease, with or without IDA, notable shifts in specific microbial strains were identified. Specifically, levels of Anaerobutyricum soehngenii and Alistipes shahii were significantly altered. Metagenomic analysis revealed an enrichment of pathways related to short-chain fatty acid metabolism and ascorbate degradation, indicative of functional change in these microbes.

CONCLUSIONS: This is the first comprehensive microbiome analysis of quiescent pediatric Crohn's disease with concomitant IDA. The findings indicate modest but significant microbial strain-level differences and associated functional pathways, potentially implicating microbiota-mediated mechanisms in the persistence of IDA.},
}

Humans
*Crohn Disease/microbiology/complications
*Gastrointestinal Microbiome
Male
Female
Child
*Anemia, Iron-Deficiency/microbiology/etiology
Cross-Sectional Studies
Adolescent
Case-Control Studies
Feces/microbiology
Metagenomics
RNA, Ribosomal, 16S/genetics

@article {pmid41420859,
year = {2026},
author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA},
title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116724},
doi = {10.1016/j.celrep.2025.116724},
pmid = {41420859},
issn = {2211-1247},
mesh = {Humans ; Honduras ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Rural Population ; Male ; Female ; COVID-19/virology/microbiology ; Adult ; Metagenomics ; Middle Aged ; SARS-CoV-2 ; Metagenome ; },
abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.},
}

Humans
Honduras
*Gastrointestinal Microbiome/genetics
*Genetic Variation
Rural Population
Male
Female
COVID-19/virology/microbiology
Adult
Metagenomics
Middle Aged
SARS-CoV-2
Metagenome

@article {pmid41419779,
year = {2025},
author = {Liu, Y and Chen, S and Li, H and Mahtab, N and Sun, Y and Li, Y and Song, J and Sun, D and Liang, M and Chen, J and Sun, J and Gong, B and Jing, J and Bu, R},
title = {Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {125},
pmid = {41419779},
issn = {2052-4463},
support = {2024GXNSFBA010371//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069226//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069232//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; },
mesh = {China ; *Geologic Sediments/microbiology ; Wetlands ; Archaea/genetics ; *Genome, Bacterial ; *Genome, Microbial ; *Genome, Archaeal ; Bacteria/genetics/classification ; Metagenome ; Microbiota ; },
abstract = {Mangrove sediments, being organic-rich and anoxic, host diverse and functionally important microorganisms that play crucial roles in global biogeochemical cycling. In order to characterize this diversity at the genome-resolved level, we collected 38 sediment samples encompassing both surface (0-5 cm) and core (up to 90 cm) depths from six representative mangrove sites across Guangxi Province, China. Using a standardized pipeline for assembly, binning, and dereplication, we reconstructed 2,965 non-redundant metagenome-assembled genomes (MAGs), comprising 2,383 bacterial and 582 archaeal genomes spanning 78 microbial phyla. This dataset captures the high microbial diversity and functional potential within mangrove sediments under variable environmental conditions. It provides a valuable genomic resource for investigating the structure, metabolism, and ecological roles of sediment microbial communities in intertidal, nutrient-rich ecosystems, supporting future studies on microbial adaptation and biogeochemical cycling in global blue carbon environments.},
}

China
*Geologic Sediments/microbiology
Wetlands
Archaea/genetics
*Genome, Bacterial
*Genome, Microbial
*Genome, Archaeal
Bacteria/genetics/classification
Metagenome
Microbiota

@article {pmid41408023,
year = {2026},
author = {Wang, H and Zhang, M and Hua, B and He, J and Yang, Y and Wu, W and Zhang, Y and Wei, F and Cai, Y and Wang, Q},
title = {Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens.},
journal = {Clinical rheumatology},
volume = {45},
number = {2},
pages = {857-873},
pmid = {41408023},
issn = {1434-9949},
support = {C2301008，C2404002//Shenzhen Medical Research Fund/ ; 2023B1515230002//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515010294//Guangdong Basic and Applied Basic Research Foundation/ ; 0102018-2019-YBXM-1499-01-0414//Treatment and Prevention Integration Project of Shenzhen Municipal Health Commission/ ; SZSM202311030//Sanming Project of Medicine in Shenzhen/ ; No. NSFC 82302037//The National Natural Science Foundation of China/ ; KYQD2024355//Shenzhen High-level Hospital Construction Fund and Peking University Shenzhen Hospital Scientific Research Fund/ ; },
mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Clostridium/genetics ; Female ; Adult ; Male ; Middle Aged ; Metagenomics ; Metabolomics ; Case-Control Studies ; Metabolome ; Dysbiosis/microbiology ; Eubacteriales ; },
abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear pathogenesis. Emerging evidence indicates that the gut microbiome may play a critical role in immune regulation. This study aimed to investigate gut microbiome and metabolome alterations in SLE patients, with a focus on the pro-inflammatory bacterium Clostridium scindens (C. scindens), and explore its potential contribution to disease pathogenesis.

METHOD: We performed metagenomic sequencing to analyze gut microbial composition in SLE patients and healthy controls, alongside untargeted metabolomic profiling of peripheral blood to assess systemic metabolic changes. We examined species diversity, taxonomic differences at both phylum and species levels, and metabolic alterations. Statistical analyses identified significant associations and potential diagnostic markers.

RESULTS: SLE patients did not show a consistent reduction in species diversity, but exhibited significant microbial compositional differences compared to healthy controls. These patterns suggest potential diagnostic utility. Metabolomic analysis revealed systemic metabolic disturbances linked to gut dysbiosis. Ruminococcus gnavus was associated with altered amino acid, lactose, and sphingolipid metabolism, potentially affecting host immunity. Notably, C. scindens appeared to contribute to immune dysregulation via bile acid metabolism.

CONCLUSIONS: This study reveals distinct microbial and metabolic profiles in SLE, identifying C. scindens as a potential driver of immune imbalance. The findings suggest that targeting the gut microbiome could offer novel strategies for diagnosis and therapeutic intervention in SLE. Key Points • Gut microbial composition is significantly altered in SLE patients compared to healthy controls. • Metabolomic profiling reveals systemic disturbances linked to gut dysbiosis. • Clostridium scindens is associated with bile acid metabolism and immune dysregulation in SLE. • The gut microbiome may serve as a potential target for diagnosis and treatment in SLE.},
}

Humans
*Lupus Erythematosus, Systemic/microbiology/metabolism
*Gastrointestinal Microbiome
*Clostridium/genetics
Female
Adult
Male
Middle Aged
Metagenomics
Metabolomics
Case-Control Studies
Metabolome
Dysbiosis/microbiology
Eubacteriales

@article {pmid41250628,
year = {2026},
author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL},
title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {37},
number = {1},
pages = {9-24},
pmid = {41250628},
issn = {2191-0286},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/physiology ; Probiotics/therapeutic use/administration & dosage ; *Urinary Tract Infections/microbiology ; Dysbiosis/microbiology ; Prebiotics/administration & dosage ; Animals ; *Urinary Tract/microbiology ; Female ; },
abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/complications
*Microbiota/physiology
Probiotics/therapeutic use/administration & dosage
*Urinary Tract Infections/microbiology
Dysbiosis/microbiology
Prebiotics/administration & dosage
Animals
*Urinary Tract/microbiology
Female

@article {pmid41205408,
year = {2026},
author = {Bao, C and Ma, Y and Li, M and Li, Y and Zhang, C and Liu, X and Fan, R and Cui, W and Fan, X and Zheng, F and Duan, F and Liu, J},
title = {Assessment of glymphatic dysfunction in ulcerative colitis using DKI-ALPS: An innovative imaging biomarker.},
journal = {Journal of neuroradiology = Journal de neuroradiologie},
volume = {53},
number = {1},
pages = {101402},
doi = {10.1016/j.neurad.2025.101402},
pmid = {41205408},
issn = {0150-9861},
mesh = {Humans ; *Colitis, Ulcerative/diagnostic imaging/physiopathology/microbiology/complications ; Male ; Female ; Adult ; Middle Aged ; *Glymphatic System/diagnostic imaging/physiopathology ; Biomarkers ; Gastrointestinal Microbiome ; *Diffusion Magnetic Resonance Imaging/methods ; Case-Control Studies ; *Diffusion Tensor Imaging/methods ; },
abstract = {PURPOSE: Ulcerative colitis (UC) is associated with higher anxiety, depression, and cognitive disorders linked to brain glymphatic dysfunction. In this study, we used along-the-perivascular-space (ALPS) index (based on DTI and DKI) to determine if UC relates to glymphatic dysfunction and explore how microbiota dysbiosis and inflammation affect brain glymphatic function.

MATERIALS AND METHODS: In this study, 63 patients with UC and 68 healthy controls underwent 3-Tesla MRI scans to evaluate DTI-ALPS and DKI-ALPS index. The protocol included diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) sequences to calculate the ALPS index, which quantifies glymphatic system function. All participants completed cognitive (MMSE) and depression (SAS/SDS) assessments (SAS/SDS). Patients with UC also underwent assessment for inflammation and gut microbiota (based on metagenomic analysis). Data analysis was performed using correlation analysis and linear regression.

RESULTS: Patients with UC showed lower DTI-ALPS index (1.25) and DKI-ALPS index (1.40) compared to controls (1.40 vs. 1.69; P < 0.001). In multi-adjusted linear regression models, UC was associated with lower DTI-ALPS index and DKI-ALPS index (β =-0.142 vs.-0.284), with DKI-ALPS showing higher sensitivity. The results remained significant even after stratification by age and sex. The Mayo score correlated negatively with DTI and DKI-ALPS index. The ALPS index correlates with gut microbiota, particularly those involved in butyrate and short-chain fatty acid (SCFA) production. DTI-ALPS index was significantly correlated with ESR (β =-0.003), CRP (β =-0.035), SII (β =-0.062), INFLA (β =-0.010), and SIRI (β =-0.058). We also observed significant correlations between DKI ALPS index and ESR (β =-0.006), CRP (β =-0.051), SII (β =-0.130), INFLA (β =-0.017), SIRI (β =-0.095), IL-6 (β =-0.081) and NLR (β =-0.108).

CONCLUSIONS: UC is associated with brain glymphatic dysfunction, correlating with inflammation level. DKI-ALPS serves as a more sensitive method than DTI-ALPS, offering a new approach for managing ulcerative colitis through glymphatic dysfunction.},
}

Humans
*Colitis, Ulcerative/diagnostic imaging/physiopathology/microbiology/complications
Male
Female
Adult
Middle Aged
*Glymphatic System/diagnostic imaging/physiopathology
Biomarkers
Gastrointestinal Microbiome
*Diffusion Magnetic Resonance Imaging/methods
Case-Control Studies
*Diffusion Tensor Imaging/methods

@article {pmid41166145,
year = {2026},
author = {Ding, W and Zhang, H and Wen, J and Xiong, G and Cheng, M and Liu, J and Zhao, Y and Miao, Q and Deng, H and Xu, Z and Mi, L and Tan, Z and Su, L and Long, Y and Ning, K},
title = {A Multiomics Analysis Reveals a Gut Microbiome: LPC Metabolic Axis Driving Postoperative Inflammation in Cardiopulmonary Bypass Patients.},
journal = {Shock (Augusta, Ga.)},
volume = {65},
number = {2},
pages = {188-200},
doi = {10.1097/SHK.0000000000002722},
pmid = {41166145},
issn = {1540-0514},
support = {2023YFA1800900//the National Key R&D Program of China/ ; 2018YFC0910502//the National Key R&D Program of China/ ; 32071465//the National Natural Science Foundation of China/ ; 31871334//the National Natural Science Foundation of China/ ; 31671374//the National Natural Science Foundation of China/ ; 2022-PUMCH-B-115//National High-Level Hospital Clinical Research Founding/ ; 2022-PUMCH-D-005//National High-Level Hospital Clinical Research Founding/ ; 2023â€I2Mâ€2â€002//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; *Cardiopulmonary Bypass/adverse effects ; Middle Aged ; Aged ; *Inflammation/metabolism/etiology ; *Postoperative Complications/metabolism/microbiology ; *Lysophosphatidylcholines/metabolism ; Metabolomics ; Metabolome ; Multiomics ; },
abstract = {BACKGROUND: Patients undergoing cardiac surgery with cardiopulmonary bypass (CSCPB) are at substantial postoperative risk, which may be influenced by alterations in gut microbiota and metabolites. The roles of these biological changes in postoperative outcomes remain inadequately explored.

METHODS: We collected 54 preoperative samples and 33 postoperative samples from 60 CSCPB patients. Metagenomic and metabolomic sequencing were performed to identify the gut microbiota and serum and fecal metabolites. We examined the dynamic pattern of these microbiota and metabolites, as well as their associations with the postoperative risks. Additionally, we developed a predictive model for postoperative risk based on preoperative microbiome and metabolome data.

RESULTS: We revealed significant alterations of gut microbiota (P = 0.012), serum metabolites (P = 3.50 e-10), and fecal metabolites (P = 0.0081) in patients following CSCPB, among which lysophosphatidylcholines (LPCs) exhibited notable changes. Particularly, we identified a potential regulatory function of the microbiota on LPC metabolism, which further influences the postoperative risk. The predictive model for intensive care unit stay duration achieved a mean absolute error of 1.27 days and an R² of 0.63, suggesting its utility in assessing postoperative risk. Also, our study provides a valuable resource (catalogue GM3C) for further investigation into potential medical targets in CSCPB patients, comprising more than 2,000 metagenome-assembled genomes and 3 million unigenes.

CONCLUSIONS: Our study reveals that the gut microbiome and LPC-centered metabolism form a functional network influencing postoperative risk in CSCPB patients. These findings underscore the role of gut-derived signals in modulating noninfectious inflammatory responses and host imbalance, offering a multiomics framework for decoding systemic complications beyond classical sepsis paradigms.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT04032938). Registered 25 July 2019, https://clinicaltrials.gov/study/NCT04032938#study-record-dates .},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
Male
*Cardiopulmonary Bypass/adverse effects
Middle Aged
Aged
*Inflammation/metabolism/etiology
*Postoperative Complications/metabolism/microbiology
*Lysophosphatidylcholines/metabolism
Metabolomics
Metabolome
Multiomics

@article {pmid41087549,
year = {2026},
author = {Chauhan, M and Maniya, H and Mori, P and Nagpal, R and Tirgar, P and Kumar, V},
title = {Assessment of multi-strain probiotics in regulating diet-induced obesity in Balb/c mice model.},
journal = {International journal of obesity (2005)},
volume = {50},
number = {1},
pages = {202-212},
pmid = {41087549},
issn = {1476-5497},
mesh = {Animals ; *Probiotics/therapeutic use/pharmacology ; *Obesity/prevention & control ; Mice, Inbred BALB C ; Mice ; Male ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND/OBJECTIVES: This study investigated the efficacy of a novel multi-strain probiotic (MSP), composed of Limosilactobacillus fermentum BAB 7912, Bacillus rugosus PIC5CR, and Bacillus rugosus PIB9CR, in preventing and reverting diet-induced obesity in Balb/c male mice.

SUBJECTS/METHODS: This study used 8-week-old Balb/c mice. A total of 40 mice were divided into five groups namely control negative (CN), control with obesity (CO), and three treatment groups: microbial consortium treated (MCT), Healthy control 1 (HC1), and Healthy control 2 (HC2). Obesity was induced using a high-fat diet. MSP formulation developed indigenously as part of previous study, was fed to Balb/c mice at different time intervals to study its preventive and ameliorative potential. Animals were dissected for the collection of blood as well as various organs to study the effect of MSP feeding on obesity status. Results were validated using histopathological and metagenomic data.

RESULTS: The CN and other treatment groups gained significant weight at the end of 6 weeks, while no significant weight gain was observed among HC1 group animals that were fed with HFD and MSP together. This highlights the preventive effect of continuous MSP feeding in the HC1 animal group. Initial liver histopathology in the HC1 group revealed enlarged hepatocytes and fat droplets. By week 9, the MCT group, which received MSP with a basal diet, showed liver recovery towards normal, accompanied by body weight improvement from 28.02 ± 0.7 g to 26.18 ± 0.96 g. Metagenomic analysis revealed that MSP treatment increased the relative abundance of health-promoting bacteria, notably Lactobacillaceae (specifically Lactobacillus).

CONCLUSIONS: Findings indicated that continuous consumption of MSP contributes significantly in prevention of obesity and associated metabolic disorders. Future studies are needed to explore the mechanisms underlying these effects and to evaluate the potential of MSP for human health.},
}

Animals
*Probiotics/therapeutic use/pharmacology
*Obesity/prevention & control
Mice, Inbred BALB C
Mice
Male
Diet, High-Fat/adverse effects
Disease Models, Animal
Gastrointestinal Microbiome

@article {pmid40971415,
year = {2026},
author = {Vermeer, E and Prins, FM and Hidding, IJ and Jagt, JZ and de Jonge, R and Benninga, MA and Gacesa, R and Weersma, RK and de Boer, NKH and de Meij, TGJ},
title = {Metagenomic Sequencing Reveals Distinct Gut Microbiome Profiles in Therapy-Naïve de Novo Pediatric Inflammatory Bowel Disease.},
journal = {Inflammatory bowel diseases},
volume = {32},
number = {2},
pages = {207-219},
doi = {10.1093/ibd/izaf184},
pmid = {40971415},
issn = {1536-4844},
support = {WO 19-25//The Dutch Digestive Foundation (MLDS)/ ; WO 19-25//Right on Time/ ; //The Dutch Digestive Foundation/ ; },
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Child ; Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Adolescent ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Biomarkers/analysis ; Child, Preschool ; },
abstract = {BACKGROUND AND AIMS: Microbiome studies reveal distinct microbial differences in inflammatory bowel disease (IBD), indicating its potential role in pathophysiology and as a noninvasive diagnostic biomarker. This study aims to profile the gut microbiome in children with IBD, compared to both healthy controls (HC) and controls with gastrointestinal symptoms (CGI), and to assess the potential of microbiome profiles as noninvasive diagnostic markers for de novo treatment-naïve pediatric IBD, and as early predictive markers for therapy response.

METHODS: We analyzed baseline fecal samples and clinical data from 103 therapy-naïve children with IBD, 75 CGI, and 356 age and sex matched HC. Metagenomic sequencing was performed, and prediction models assessed diagnostic potential and prediction of induction therapy response at 3 months.

RESULTS: Alpha diversity progressively decreased from HC to CGI (P < .001) and decreased even further in IBD patients (P = .0056). Beta diversity analysis showed significant clustering differences (P < .001, R2 = 0.045). Differential abundance analysis revealed 116 species differing between HC and IBD, and 30 species between CGI and IBD. Prediction models based on microbiome features accurately distinguished IBD from HC (area under the curve [AUC] = 0.96) and from CGI (AUC = 0.71). However, these models were outperformed by clinical features, such as fecal calprotectin. Microbiome-based prediction of response to induction therapy in general showed limited accuracy (AUC = 0.63), as well as for response to nutritional induction therapy (AUC = 0.67).

CONCLUSIONS: We observed profound gut microbiome differences between de novo, therapy-naïve pediatric IBD patients and controls. While microbiome profiles hold promise for improving diagnostic precision, their predictive value for therapy response seems limited.},
}

Humans
Female
Male
*Gastrointestinal Microbiome/genetics
Child
Feces/microbiology
*Metagenomics/methods
Case-Control Studies
Adolescent
*Inflammatory Bowel Diseases/microbiology/diagnosis
Biomarkers/analysis
Child, Preschool

@article {pmid41606854,
year = {2025},
author = {Okoye, CO and Abhadiomhen, SE and Ezenwanne, BC and Chen, X and Jiang, H and Wu, Y and Jiang, J},
title = {Machine learning-based predictive modeling of foodborne pathogens and antimicrobial resistance in food microbiomes using omics techniques: A systematic review.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117255},
doi = {10.1016/j.foodres.2025.117255},
pmid = {41606854},
issn = {1873-7145},
mesh = {*Machine Learning ; *Food Microbiology ; *Foodborne Diseases/microbiology ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; Animals ; Genomics/methods ; Metagenomics ; Salmonella/pathogenicity/genetics ; Food Safety ; Humans ; },
abstract = {The globalization of food systems has heightened the risk of foodborne pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter, exacerbated by rising antimicrobial resistance (AMR). Traditional pathogen identification and AMR risk surveillance methods are often labor-intensive and low-throughput, while single-omics approaches fail to capture microbial complexity. Moreover, reliance on individual machine learning (ML) models limits predictive robustness, posing challenges to food safety and public health. This systematic review evaluates ML-based predictive modeling integrated with omics techniques (genomics, metagenomics, and transcriptomics) for foodborne pathogen and AMR risk surveillance. Following PRISMA guidelines, 1245 articles from PubMed, Scopus, and other databases (2015-2025) were screened, selecting 13 relevant studies. These studies applied ML algorithms, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Support Vector Machines (SVM), to enhance predictive accuracy. The selected studies demonstrated predictive accuracies up to 99 % and AUROC scores above 0.90. Key discoveries include genetic markers for Salmonella virulence, Listeria attribution to fruits and dairy, and 145 mobile antimicrobial resistance genes (ARGs) in poultry. Despite these advancements, limitations such as small sample sizes, inconsistent metadata, overfitting, and computational scalability hinder real-world implementation. This review underscores the potential of ML-driven omics frameworks to revolutionize foodborne pathogen and AMR risk monitoring, paving the way for smarter, more resilient food safety systems. However, methodological inconsistencies necessitate standardized protocols, larger datasets, and explainable AI (XAI) to improve reliability and applicability in global food safety monitoring.},
}

*Machine Learning
*Food Microbiology
*Foodborne Diseases/microbiology
*Microbiota
*Drug Resistance, Bacterial/genetics
Animals
Genomics/methods
Metagenomics
Salmonella/pathogenicity/genetics
Food Safety
Humans

@article {pmid41606218,
year = {2026},
author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N},
title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {65},
pmid = {41606218},
issn = {1573-0972},
mesh = {Humans ; *Multigene Family ; *Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Biosynthetic Pathways/genetics ; Metagenome ; },
abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.},
}

Humans
*Multigene Family
*Microbiota/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
Biosynthetic Pathways/genetics
Metagenome

@article {pmid41604303,
year = {2026},
author = {Guo, Z and Cheng, H and Shi, H and Liu, D and Zhai, X and Li, X and Zhang, X and Liu, L and Zhang, XH and Zhang, Y},
title = {Potential for microbial methanethiol-dependent dimethylsulfide production in different marine sediments.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116891},
doi = {10.1016/j.celrep.2025.116891},
pmid = {41604303},
issn = {2211-1247},
abstract = {Dimethyl sulfide (DMS) plays a pivotal role in sulfur cycling and climate regulation. This study investigates microbial DMS production via the methylation of hydrogen sulfide (H2S) and methanethiol (MeSH) in nearshore, pelagic deep-sea, and cold-seep sediments using culture-dependent and -independent methods. DMS production is detected in all sediments with exogenous MeSH addition. High mdd abundance is found in pelagic deep-sea sediments (24.55%-26.73%) from the Kuroshio-Oyashio Extension region, as well as in the nearshore sediments (25.78%). Metagenomic analyses reveal previously unrecognized Mdd-encoding taxa, such as Polyangia, and eight Bacteroidota and Bacillota isolates may possess unknown Mdd enzymes. Importantly, a widespread alternative pathway that converts H2S to MeSH is identified, representing a significant source of MeSH. These findings reveal a prevalent and diverse microbial pathway for DMS production in marine sediments, underscoring the need for further investigation to discover Mdd[+] microbial contributors.},
}

@article {pmid41564488,
year = {2026},
author = {Huang, Z and Shen, J and Wang, J and Wang, C and Liu, H and Tian, C and Feng, J and Wang, X},
title = {Seasonal dynamics of sedimentary dissolved organic matter in plateau lakes: Driving effects on microbial community and functional genes in elements cycling.},
journal = {Journal of environmental management},
volume = {399},
number = {},
pages = {128688},
doi = {10.1016/j.jenvman.2026.128688},
pmid = {41564488},
issn = {1095-8630},
mesh = {*Lakes/chemistry ; Seasons ; *Geologic Sediments/chemistry ; Microbiota ; Carbon ; },
abstract = {Plateau lakes, as sensitive zones to global climate change and critical hubs for land-water carbon exchange, remain understudied in terms of the seasonal dynamics of their sedimentary dissolved organic matter (DOM) and its interactions with microbial ecological function. This study employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic techniques to unravel the seasonal variations of DOM and their regulatory roles in microbial community and elements cycling. During the dry season, low water temperature (WT), dissolved oxygen (DO), and high electrical conductivity (EC) promoted accumulation of lignin-like and carboxyl-rich aliphatic molecules (CRAMs), with Fuxian Lake exhibiting the strongest sequestration. The subsequent wet period raised microbial biomass carbon (MBC) and easily oxidizable organic carbon (EOC), lowered average mass-to-charge ratios and increased both nominal hydrogen-to-carbon ratios (H/C) and the molecular lability index (MLB%). Labile sugars and peptides enhanced microbial α-diversity, whereas refractory compounds selected for specialist taxa and intensified community differentiation. Random forest identified sugars, peptides, O3S + O5S, biological index (BIX), and WT as core drivers of element cycling genes expression. Functional gene modules diverged along trophic status. The oligotrophic deep lake underwent seasonal turnover, whereas the eutrophic shallow lake preserved stable supermodules integrating multiple metabolic pathways to buffer perturbations. Anthropogenic disturbances elevated sulfur/nitrogen-containing heteroatomic compounds and threatened sediment carbon sinks and element cycling balance. This study advances the understanding of DOM-driven biogeochemical cycles and provides a scientific framework for managing multi-element interactions in climatically sensitive plateau lakes.},
}

*Lakes/chemistry
Seasons
*Geologic Sediments/chemistry
Microbiota
Carbon

@article {pmid41495321,
year = {2026},
author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K},
title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4066},
pmid = {41495321},
issn = {2045-2322},
support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Poecilia/genetics/physiology ; Male ; *Predatory Behavior ; Rivers ; *DNA, Environmental/analysis/genetics ; *Introduced Species ; Japan ; *Pigmentation ; Ecosystem ; DNA Barcoding, Taxonomic ; Color ; },
abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.},
}

Animals
*Poecilia/genetics/physiology
Male
*Predatory Behavior
Rivers
*DNA, Environmental/analysis/genetics
*Introduced Species
Japan
*Pigmentation
Ecosystem
DNA Barcoding, Taxonomic
Color

@article {pmid41495312,
year = {2026},
author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA},
title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {40},
pmid = {41495312},
issn = {1432-184X},
mesh = {*Carbon Dioxide/metabolism ; *Geologic Sediments/microbiology ; *Carbon Cycle ; *Hydrogen/metabolism ; Formates/metabolism ; Autotrophic Processes ; Seawater/microbiology ; Acetic Acid/metabolism ; Lakes/microbiology ; Biodiversity ; Phylogeny ; *Bacteria, Anaerobic/metabolism/genetics/classification/isolation & purification ; *Bacteria/metabolism/classification/genetics ; Metagenome ; Metagenomics ; },
abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.},
}

*Carbon Dioxide/metabolism
*Geologic Sediments/microbiology
*Carbon Cycle
*Hydrogen/metabolism
Formates/metabolism
Autotrophic Processes
Seawater/microbiology
Acetic Acid/metabolism
Lakes/microbiology
Biodiversity
Phylogeny
*Bacteria, Anaerobic/metabolism/genetics/classification/isolation & purification
*Bacteria/metabolism/classification/genetics
Metagenome
Metagenomics

@article {pmid41454222,
year = {2025},
author = {Li, J and Sun, Z and Chai, S and Li, H and Wang, Y and Tian, J},
title = {AR-CDT NET: a deep deformable convolutional network for gut microbiome-based disease classification.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {23},
pmid = {41454222},
issn = {1471-2105},
support = {No.GZY-ZJ-SY-2303//Zhejiang Province Traditional Chinese Medicine Key Laboratory Project/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Deep Learning ; Metagenomics/methods ; Computational Biology/methods ; },
abstract = {Advances in metagenomic sequencing have increasingly implicated gut microbiome dysbiosis in numerous complex diseases, yet its application for precise differential diagnosis remains a major challenge. Existing computational approaches often show limited predictive performance and insufficient robustness when applied to large-scale, imbalanced microbiome datasets, and they typically lack mechanisms to effectively capture microbial community-level or functional guild interactions. To address these limitations, we developed AR-CDT Net, a novel deep learning framework that integrates a Multi-Scale Deformable Convolution (MS-DConv) module with a Channel-wise Dynamic Tanh (CD-Tanh) activation function to achieve more accurate and robust classification of host disease states. Evaluated on a large-scale cohort comprising over 8000 samples spanning eight disease phenotypes, AR-CDT Net demonstrated highly competitive within-cohort performance, outperforming nine representative models across the majority of classification tasks. Importantly, in a stringent cross-dataset generalization test, the model was trained on the highly imbalanced primary multi-disease cohort and validated on relatively balanced independent external cohorts. It achieved a statistically significant AUC of 0.7921 on the highly heterogeneous external T2D cohort, confirming that AR-CDT captures transferable biological signals rather than dataset-specific artifacts. Furthermore, by combining dimensionality reduction with SHAP-based interpretation of our One-vs-Rest (OvR) classifiers, AR-CDT disentangles disease-specific pathogenic signatures from the shared dysbiotic background among clinically distinct yet microbially similar diseases.},
}

*Gastrointestinal Microbiome
Humans
*Deep Learning
Metagenomics/methods
Computational Biology/methods

@article {pmid41345979,
year = {2025},
author = {Sakanaka, A and Furuno, M and Ishikawa, A and Katakami, N and Inoue, M and Mayumi, S and Kurita, D and Nishizawa, H and Omori, K and Taya, N and Isomura, ET and Kudoh, M and Takeuchi, H and Amano, A and Shimomura, I and Fukusaki, E and Kuboniwa, M},
title = {Diabetes alters the supragingival microbiome through plasma-to-saliva migration of glucose and fructose.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {48},
pmid = {41345979},
issn = {2049-2618},
support = {22H03300, 22H00487, 22K10311, 21K18281//Japan Society for the Promotion of Science/ ; JP16gm0710005//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Saliva/metabolism/chemistry/microbiology ; Female ; Male ; Dental Caries/microbiology ; *Microbiota ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood/complications ; *Glucose/metabolism ; Middle Aged ; *Fructose/metabolism/blood ; Adult ; Biofilms/growth & development ; Metabolomics/methods ; Aged ; *Gingiva/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {BACKGROUND: Dental caries, a dysbiotic biofilm disease driven by polymicrobial acidogenesis, often coexists with type 2 diabetes (T2D). Previous studies suggest covarying relationships between circulating and salivary metabolites in patients with T2D. However, the role of hyperglycemia-induced saccharide migration from plasma to saliva in caries pathogenesis remains unclear. Here, we developed a novel method for untargeted metabolomics profiling of trace saliva from sublingual and submandibular glands, comparing this profile with those of plasma and whole saliva in participants with T2D (n = 31) and those with normoglycemia (n = 30). This comparison aimed to determine how circulating saccharide migration into the oral cavity and its subsequent microbial consumption are linked to dental caries. Additionally, shotgun metagenomic sequencing was combined with this analysis to investigate the cariogenic impact of circulating saccharide migration on the composition and function of supragingival biofilm using MetaPhlAn4 and HUMAnN3 pipelines.

RESULTS: The metabolomics profiles of glandular saliva showed intermediate dissimilarity between plasma and whole saliva, reflecting cardiometabolic traits more sensitively than whole saliva. Glucose and fructose showed a decreasing positive correlation with glycemic parameters in the order of plasma, glandular saliva, and whole saliva, suggesting systemic-to-oral migration and subsequent microbial consumption. Saccharide migration was more pronounced in participants with dental caries and plaque accumulation, coinciding with shifts in supragingival microbiota, including depletion of Streptococcus sanguinis, Corynebacterium durum, and Rothia aeria, and enrichment of Streptococcus mutans, Veillonella parvula, and Actinomyces sp. oral taxon 448. Glycolytic potential increased at the community level. Improved glycemic control reduced fructose migration and mitigated dysbiosis, decreasing fructose phosphotransferase abundance and shifting the S. mutans-S. sanguinis balance. Experimental validation demonstrated that fructose promotes S. mutans dominance over S. sanguinis in dual-species biofilms.

CONCLUSIONS: This study establishes saccharide migration as a metabolic driver of supragingival dysbiosis in T2D. The findings highlight the role of both glucose and fructose in caries pathogenesis and suggest that glycemic control could serve as an effective strategy as part of caries control. Video Abstract.},
}

Humans
*Saliva/metabolism/chemistry/microbiology
Female
Male
Dental Caries/microbiology
*Microbiota
*Diabetes Mellitus, Type 2/microbiology/metabolism/blood/complications
*Glucose/metabolism
Middle Aged
*Fructose/metabolism/blood
Adult
Biofilms/growth & development
Metabolomics/methods
Aged
*Gingiva/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40965138,
year = {2025},
author = {Barker, HA and Bhimani, S and Tirado, D and Canas, JJ and Lemos, LN and Roesch, LFW and Ferraro, MJ},
title = {Deficiency of cannabinoid receptors enhances host susceptibility to bacterial infection.},
journal = {mBio},
volume = {16},
number = {10},
pages = {e0208825},
pmid = {40965138},
issn = {2150-7511},
support = {//Consortium for Medical Marijuana Clinical Outcomes Research/ ; R01 AI158749/AI/NIAID NIH HHS/United States ; 5T32AI007110-38//National Institute of Allergy and Infectious Diseases/ ; T32 AI007110/AI/NIAID NIH HHS/United States ; AI158749-04//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Animals ; Mice ; *Disease Susceptibility/microbiology ; Salmonella typhimurium ; *Salmonella Infections/genetics ; Mice, Knockout ; Host-Pathogen Interactions ; *Receptor, Cannabinoid, CB2/genetics ; *Receptor, Cannabinoid, CB1/genetics ; Disease Models, Animal ; Inflammation ; Immunity, Mucosal ; Homeostasis ; Gastrointestinal Microbiome ; Macrophages/microbiology ; Mice, Inbred C57BL ; Male ; Female ; Dysbiosis ; },
abstract = {Host resilience to bacterial infection depends on tightly regulated immune responses, which can be shaped by metabolic cues, including the contribution from bioactive lipids. The endocannabinoid system (ECS), a lipid signaling network known for its neuromodulatory roles, also influences immunity; however, the receptor-specific contributions of cannabinoid receptor 1 (CB1R) and cannabinoid receptor 2 (CB2R) in host-pathogen interactions remain incompletely defined in this context. Using receptor-deficient mouse models, we investigated how CB1R and CB2R modify immune responses to Salmonella Typhimurium. CB1R-deficient (CB1R-KO) mice exhibited heightened systemic inflammation, impaired bacterial clearance, and reduced survival in systemic infection, associated with dysregulated macrophage polarization and diminished neutrophil recruitment. In contrast, CB2R-KO mice showed increased susceptibility in both systemic and mucosal infection models, marked by a pro-inflammatory macrophage profile, enhanced neutrophilia, and microbiota dysbiosis. Shotgun metagenomic analysis revealed a reduced abundance of specific protective commensals and altered microbial metabolic pathway profiles in CB2R-KO mice, suggesting a role for CB2R in maintaining mucosal immune-microbiota homeostasis. Collectively, these findings highlight non-redundant roles for CB1R and CB2R in regulating immune dynamics and salmonellosis disease severity, and they point to the ECS as a potential target for host-directed immunomodulatory therapies.IMPORTANCEEffective immunity against bacterial pathogens requires a delicate balance between microbial clearance and the containment of inflammatory damage encountered during many infections. The molecular pathways that regulate this equilibrium remain incompletely defined, and the involvement of bioactive lipid signaling mechanisms also needs to be better described. Here, we show that the endocannabinoid receptors CB1R and CB2R play non-redundant roles in host defense against Salmonella infection. CB1R deficiency results in exacerbated systemic inflammation, defective bacterial clearance, and dysregulated macrophage polarization. In contrast, CB2R deficiency leads post-infection to gut dysbiosis and has been found to negatively affect the outcome for the host in both systemic and mucosal infection with Salmonella. By describing cannabinoid receptor-specific contributions to immune regulation and microbiota dynamics, our findings reveal a previously underappreciated axis of host-pathogen interaction. This study broadens our understanding of lipid-mediated immune modulation and identifies CB1R and CB2R as potential targets for therapies aimed at restoring immune homeostasis and improving infectious disease outcomes.},
}

Animals
Mice
*Disease Susceptibility/microbiology
Salmonella typhimurium
*Salmonella Infections/genetics
Mice, Knockout
Host-Pathogen Interactions
*Receptor, Cannabinoid, CB2/genetics
*Receptor, Cannabinoid, CB1/genetics
Disease Models, Animal
Inflammation
Immunity, Mucosal
Homeostasis
Gastrointestinal Microbiome
Macrophages/microbiology
Mice, Inbred C57BL
Male
Female
Dysbiosis

@article {pmid41602774,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Correction: Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1766907},
doi = {10.3389/fmicb.2025.1766907},
pmid = {41602774},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1671267.].},
}

@article {pmid41602101,
year = {2025},
author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H},
title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1730098},
pmid = {41602101},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Nanopore Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; *Precision Medicine/methods ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Metagenomics/methods ; Microbiota ; Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.

METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.

RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.

CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.},
}

Humans
*Lung Neoplasms/complications/microbiology
*Nanopore Sequencing/methods
Male
Female
Middle Aged
Aged
Sputum/microbiology
*Precision Medicine/methods
High-Throughput Nucleotide Sequencing
*Respiratory Tract Infections/diagnosis/microbiology/drug therapy
Metagenomics/methods
Microbiota
Bacteria/genetics/isolation & purification/classification
Sensitivity and Specificity
Adult
Aged, 80 and over

@article {pmid41601218,
year = {2025},
author = {Li, CT},
title = {[Applications and challenges of forensic microbiomics].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {441-442},
doi = {10.12116/j.issn.1004-5619.2025.551105},
pmid = {41601218},
issn = {1004-5619},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Forensic Medicine/methods ; *Gastrointestinal Microbiome ; China ; Genomics ; Human Genome Project ; *Forensic Sciences ; Metagenome ; },
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Forensic Medicine/methods
*Gastrointestinal Microbiome
China
Genomics
Human Genome Project
*Forensic Sciences
Metagenome

@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020330},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}

*Gastrointestinal Microbiome/drug effects
*Carotenoids/pharmacology/chemistry
*Computational Biology
Humans
Fermentation
Lycopene/pharmacology
Lutein/pharmacology
Bacteria/drug effects/genetics/classification
beta Carotene/pharmacology

@article {pmid41599039,
year = {2026},
author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z},
title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010055},
pmid = {41599039},
issn = {2076-0817},
support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Tuberculosis/microbiology/diagnosis/blood ; Microbiota/genetics ; *Cell-Free Nucleic Acids/blood/genetics ; *Coronary Artery Disease/microbiology/diagnosis/blood ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Female ; Cohort Studies ; },
abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.},
}

Humans
*Metagenomics/methods
*Tuberculosis/microbiology/diagnosis/blood
Microbiota/genetics
*Cell-Free Nucleic Acids/blood/genetics
*Coronary Artery Disease/microbiology/diagnosis/blood
Mycobacterium tuberculosis/genetics/isolation & purification
Male
Female
Cohort Studies

@article {pmid41597665,
year = {2026},
author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N},
title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010146},
pmid = {41597665},
issn = {2076-2607},
support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; },
abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.},
}

@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020157},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}

Animals
*Carps/virology/microbiology
*Fish Diseases/virology/microbiology/genetics
*Intestinal Mucosa/virology/pathology/microbiology
Gastrointestinal Microbiome
Metagenomics
Transcriptome
Multiomics

@article {pmid41597216,
year = {2026},
author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP},
title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020141},
pmid = {41597216},
issn = {2073-4409},
support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Homeostasis/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Azoxymethane ; Dextran Sulfate ; *Antineoplastic Agents/pharmacology ; Male ; Humans ; },
abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
*Homeostasis/drug effects
*Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology
RNA, Ribosomal, 16S/genetics
Mice, Inbred C57BL
Azoxymethane
Dextran Sulfate
*Antineoplastic Agents/pharmacology
Male
Humans

@article {pmid41596659,
year = {2026},
author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA},
title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021014},
pmid = {41596659},
issn = {1422-0067},
support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy ; Male ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Azoxymethane ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; },
abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy
Male
Rats
Rats, Sprague-Dawley
Disease Models, Animal
Azoxymethane
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Dextran Sulfate
*Plant Extracts/pharmacology
Bacteria/genetics/classification

@article {pmid41596486,
year = {2026},
author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C},
title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020838},
pmid = {41596486},
issn = {1422-0067},
support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; },
mesh = {Humans ; *Psoriasis/microbiology ; *Pemphigus/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Adult ; *Hidradenitis Suppurativa/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification ; Aged ; },
abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.},
}

Humans
*Psoriasis/microbiology
*Pemphigus/microbiology
Female
Male
*Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Middle Aged
Adult
*Hidradenitis Suppurativa/microbiology
Feces/microbiology
*Bacteria/genetics/classification
Aged

@article {pmid41595535,
year = {2026},
author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y},
title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010116},
pmid = {41595535},
issn = {2073-4425},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; Animals ; Genomics/methods ; Probiotics ; },
abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods
Animals
Genomics/methods
Probiotics

@article {pmid41595438,
year = {2025},
author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D},
title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010018},
pmid = {41595438},
issn = {2073-4425},
mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pilot Projects ; *Cervix Uteri/microbiology ; Greece ; *Lactobacillus/genetics/isolation & purification/classification ; Adult ; Middle Aged ; Vagina/microbiology ; },
abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.},
}

Female
Humans
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Pilot Projects
*Cervix Uteri/microbiology
Greece
*Lactobacillus/genetics/isolation & purification/classification
Adult
Middle Aged
Vagina/microbiology

@article {pmid41595429,
year = {2025},
author = {Wu, H and Li, J and Long, J and Liao, H and Zhan, K and Chen, H and Lei, F},
title = {Enhancing Ecological Functions in Chinese Yellow Earth: Metagenomic Evidence of Microbial and Nitrogen Cycle Reassembly by Organic Amendments.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010009},
pmid = {41595429},
issn = {2073-4425},
support = {Grants 2022YFD1901500 and 2022YFD1901505//the National Key R&D Program of China/ ; Grant U2420626//the National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen Cycle/genetics ; Metagenomics/methods ; Nitrogen/metabolism ; China ; Zea mays/growth & development ; Fertilizers ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification ; Charcoal ; },
abstract = {BACKGROUND: Chinese Yellow Earth is a key subtropical agricultural resource in southwestern China; however, its productivity is limited by acidity and poor nutrient retention. This study examined how reduced nitrogen plus organic amendments affect its soil microbial structure and maize yield.

METHODS: A field experiment with four treatments evaluated reduced nitrogen fertilization amended with rice husk plus rapeseed cake (RS) or RS with biochar (BC). Soil properties (pH, nitrogen, organic matter) and maize yield were analyzed. Metagenomic analysis (NR database) characterized microbial communities, and correlation analysis with Mantel tests identified key relationships.

RESULTS: Combined organic amendments under reduced N significantly increased soil pH, nitrogen components, and organic matter, increasing maize yield by 4.41-8.97%. Metagenomics revealed enriched beneficial genera including Sphingomonas and Bradyrhizobium. Yield positively correlated with nitrate nitrogen and a beneficial microbial cluster containing Lysobacter and Reyranella, whereas Steroidobacter negatively correlated with key fertility indicators. Mantel tests revealed nitrate nitrogen as the primary correlate of functional gene community succession.

CONCLUSIONS: This study reveals that reduced nitrogen with organic amendments promotes soil improvement and microbial modulation, demonstrating potential as a sustainable practice to maintain crop productivity in Chinese Yellow Earth. The observed trend toward yield improvement underscores its promise and warrants further validation through additional trials. Overall, the findings highlight the beneficial effects of these amendments on soil health and their role in supporting sustainable subtropical agriculture under reduced nitrogen input.},
}

*Soil Microbiology
Soil/chemistry
*Nitrogen Cycle/genetics
Metagenomics/methods
Nitrogen/metabolism
China
Zea mays/growth & development
Fertilizers
*Microbiota/genetics
Metagenome
Bacteria/genetics/classification
Charcoal

@article {pmid41594879,
year = {2026},
author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L},
title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/biology15020144},
pmid = {41594879},
issn = {2079-7737},
support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; },
abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.},
}

@article {pmid41594560,
year = {2025},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.},
journal = {Biomolecules},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/biom16010018},
pmid = {41594560},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Amyloid beta-Peptides/metabolism ; Aged ; Feces/microbiology/chemistry ; Middle Aged ; Alzheimer Disease/metabolism ; Cognition ; },
abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.},
}

Humans
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism
Female
Male
*Amyloid beta-Peptides/metabolism
Aged
Feces/microbiology/chemistry
Middle Aged
Alzheimer Disease/metabolism
Cognition

@article {pmid41593747,
year = {2026},
author = {Lin, L and Zheng, X and Tao, Y and Zhu, W and Guan, LL and Mao, S},
title = {Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03960-z},
pmid = {41593747},
issn = {1474-760X},
support = {U2202203//NSFC-Regional Innovation and Development Joint Fund/ ; 3236114378//NSFC-International (Regional) Cooperation Research and Exchange Programme/ ; },
abstract = {BACKGROUND: The ruminant gastrointestinal epithelium harbors a diverse and functionally critical remains poorly characterized microbial community due to persistent host-derived DNA contamination in metagenomic studies.

RESULTS: We develop Dilute-MetaSeq (dilution-based metagenomic sequencing), a novel, metagenomic workflow integrating gradient dilution with multiple displacement amplification. Dilute-MetaSeq reduces host DNA interference by 52.4-fold and achieves > 90% microbial sequencing efficiency to assess gastrointestinal epithelium-associated microbiome. This enables the construction of the microbial genome atlas of gastrointestinal epithelium (MGA-GE). This comprehensive resource, comprising 1,907 nonredundant prokaryotic and 5,603 viral genomes, reveals extraordinary microbial diversity and novelty, with 41.4% of prokaryotic and 99.9% of viral genomes representing taxonomically unclassified lineages. Spatial profiling identifies the rumen and reticulum as a biodiversity hotspot dominated by epithelium-adapted Butyrivibrio and methylotrophic Methanomassiliicoccales, while functional annotation uncovers 1,200 biosynthetic gene clusters (primarily RiPPs and NRPSs) and 1,212 viral auxiliary metabolic genes linked to host metabolism modulation. Pangenome analysis of 987 strains, including a novel Butyrivibrio clade with reduced genome sizes, elevated GC content, and butyrate synthesis from amino acid-derived substrates (e.g., glutarate, lysine), highlights metabolic adaptations to the nutrient-scarce epithelial niche compared to digesta-associated microbes.

CONCLUSIONS: Collectively, the MGA-GE provides transformative insights into host-microbe-virus interactions and establishes a foundation for developing microbiome-based intervention strategies to enhance ruminant health, agricultural productivity, and bioactive discovery.},
}

@article {pmid41591867,
year = {2026},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70215},
doi = {10.1002/mbo3.70215},
pmid = {41591867},
issn = {2045-8827},
support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; },
mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; },
abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.},
}

*Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
*Databases, Genetic
Microbiota/genetics
Environmental Pollutants/metabolism
Metagenome
Metagenomics

@article {pmid41591576,
year = {2026},
author = {Robayo, MIG and Armijo, JHC and Rosa, LH and Passarini, MRZ},
title = {Metagenomic analysis of the fungal community present in unimpacted and oil-impacted soil, South Shetland Islands, maritime Antarctica.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {62},
pmid = {41591576},
issn = {1573-0972},
support = {440218/2023-3//CNPq PROANTAR/ ; PRPPG Nº 118/2024//Institutional Program to Support Research Groups/ ; CNPq 18/2024//National Council for Scientific and Technological Development/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Mycobiome/genetics ; Soil/chemistry ; Islands ; Phylogeny ; Biodiversity ; Nitrogen/analysis ; },
abstract = {We assessed the fungal diversity and functional profile of two soils collected in contrasting environments: one unimpacted soil, Hennequin Point, King George Island, and the other impacted by whale oil, Whalers Bay, Deception Island, Maritime Antarctica, using metagenomic approaches. Taxonomic assignment revealed a predominance of Ascomycota in both soils. A total of 20 and 23 fungal genera were identified at King George and Deception islands, respectively. The rare genera Thermothielavioides, Pyricularia, Fulvia, and Coccidioides were detected in the Antarctic environment. The highest fungal diversity was observed in the soil of Deception Island. Canonical analysis of King George Island soil displayed higher values of total organic carbon, sulfur, and lead, which may have favored the presence of the genera Puccinia, Lachancea, and Akanthomyces. The soil of Deception Island presented correlations with higher levels of nitrogen, chromium, and iron, with a predominance of genera such as Aspergillus, Trichoderma, and Malassezia. Functional analysis revealed distinct adaptive strategies among the soils. Domains related to translation, gene regulation, and metabolic efficiency were observed for fungi in Hennequin Point soil, King George Island, suggesting resource optimization in a cold, moss-covered environment. In Deception Island soil, fungal redox metabolism, iron acquisition, and the degradation of nitrogen compounds were highlighted, reflecting adaptation to an anthropogenic soil rich in metal oxides. Both soils exhibited functional fungal networks involved in hydrolytic enzymatic pathways that may act in the decomposition of organic compounds. New sequencing must be performed due to the insufficient depth of the data. Our results indicated that the soil from Hennequin Point and Whalers Bay exhibited distinct fungal communities, which can be influenced by environmental and ecological factors such as moss, oil, and heavy metals encountered in pristine and oil-impacted soils resulting from anthropogenic activities over the years.},
}

Antarctic Regions
*Soil Microbiology
*Fungi/genetics/classification/isolation & purification
*Metagenomics/methods
*Mycobiome/genetics
Soil/chemistry
Islands
Phylogeny
Biodiversity
Nitrogen/analysis

@article {pmid41590723,
year = {2026},
author = {Atak, E and Tavčar Verdev, P and Petek, M and Coll, A and Bosch, D and Dolinar, M and Komarysta, V and Glavaš, N and Rotter, A},
title = {Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia.},
journal = {Marine drugs},
volume = {24},
number = {1},
pages = {},
doi = {10.3390/md24010026},
pmid = {41590723},
issn = {1660-3397},
support = {L4-4564//The Slovenian Research and Innovation Agency/ ; Euro-MED 0200514//Interreg Euro-MED Program/ ; },
mesh = {*Cyanobacteria/isolation & purification/genetics/metabolism ; *Microalgae/isolation & purification/genetics ; Salinity ; Slovenia ; Metagenomics/methods ; Biodiversity ; Biotechnology/methods ; Ecosystem ; },
abstract = {Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats.},
}

*Cyanobacteria/isolation & purification/genetics/metabolism
*Microalgae/isolation & purification/genetics
Salinity
Slovenia
Metagenomics/methods
Biodiversity
Biotechnology/methods
Ecosystem

@article {pmid41589896,
year = {2026},
author = {Conrad, RE and Tsementzi, D and Meziti, A and Hatt, JK and Montoya, J and Konstantinidis, KT},
title = {Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0258925},
doi = {10.1128/aem.02589-25},
pmid = {41589896},
issn = {1098-5336},
abstract = {Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.},
}

@article {pmid41586370,
year = {2025},
author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L},
title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1718782},
pmid = {41586370},
issn = {1664-302X},
abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.

METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.

RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-α level in Dahl salt-sensitive rats.

DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.},
}

@article {pmid41586308,
year = {2025},
author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L},
title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695928},
pmid = {41586308},
issn = {2235-2988},
mesh = {Humans ; Cross-Sectional Studies ; *Metagenomics ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Microbiota/genetics ; Aged ; Severity of Illness Index ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Inflammation/microbiology ; *Abscess/microbiology ; },
abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.

METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.

RESULTS: Although α-diversity did not differ significantly among severity groups, β-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.

CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.},
}

Humans
Cross-Sectional Studies
*Metagenomics
Male
Female
Retrospective Studies
Middle Aged
*Microbiota/genetics
Aged
Severity of Illness Index
*Bacteria/classification/genetics/isolation & purification
Adult
*Inflammation/microbiology
*Abscess/microbiology

@article {pmid41582618,
year = {2026},
author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J},
title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {1},
pages = {e70212},
pmid = {41582618},
issn = {2190-6009},
mesh = {Humans ; Male ; Female ; Aged ; *Gastrointestinal Microbiome/drug effects ; *Soybean Proteins/administration & dosage/pharmacology ; Aged, 80 and over ; *Muscle, Skeletal/physiology ; *Meals ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; *Sarcopenia/diet therapy ; },
abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.

METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10 g of soy protein (totalling 30 g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).

RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56 ± 0.22 cm; Control, -0.91 ± 0.26 cm, p(interaction) < 0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42 ± 0.21%, Control: -0.06 ± 0.16, p(interaction) < 0.05; Agathobaculum butyriciproducens, Intervention: 0.02 ± 0.007%, p(time) < 0.01, Control: -0.04 ± 0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88 ± 0.40%, Control: 0.62 ± 0.63, p(interaction) < 0.05; Eubacterium_sp_CAG_38, Intervention: -0.64 ± 0.28%, Control: 0.10 ± 0.22, p(interaction) < 0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004 ± 0.002; Control: 0.001 ± 0.001, p(interaction) < 0.05). Interaction (group × time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74 ± 0.34 mg/g, p(time) < 0.05, Control: 0.12 ± 0.43 mg/g; isobutyric acid, Intervention: 0.14 ± 0.08 mg/g, p(time) < 0.05, Control: 0.08 ± 0.10 mg/g; isovaleric acid, Intervention: 0.27 ± 0.14 mg/g, p(time) < 0.05; Control: 0.16 ± 0.20 mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.

CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.},
}

Humans
Male
Female
Aged
*Gastrointestinal Microbiome/drug effects
*Soybean Proteins/administration & dosage/pharmacology
Aged, 80 and over
*Muscle, Skeletal/physiology
*Meals
Feces/microbiology
Fatty Acids, Volatile/metabolism
*Sarcopenia/diet therapy

@article {pmid41535719,
year = {2026},
author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L},
title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.},
journal = {Cell research},
volume = {36},
number = {2},
pages = {103-120},
pmid = {41535719},
issn = {1748-7838},
support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/immunology/microbiology/complications ; Risk Factors ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.},
}

Humans
*Dysbiosis/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Neoplasms/immunology/microbiology/complications
Risk Factors
Immune Checkpoint Inhibitors/therapeutic use
Animals

@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {39},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andalucía/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Plant Leaves/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Salt-Tolerant Plants/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; Metagenome ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}

*Plant Leaves/microbiology
*Bacteria/genetics/classification/isolation & purification
*Microbiota
*Salt-Tolerant Plants/microbiology
Soil Microbiology
Plant Roots/microbiology
Metagenome

@article {pmid41501250,
year = {2026},
author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X},
title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3801},
pmid = {41501250},
issn = {2045-2322},
support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Myositis/microbiology ; Middle Aged ; Adult ; China ; Feces/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; Bacteria/genetics/classification ; Virome ; Machine Learning ; Case-Control Studies ; Metagenome ; Asian People ; Aged ; East Asian People ; },
abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
Female
Male
*Myositis/microbiology
Middle Aged
Adult
China
Feces/microbiology
Metagenomics/methods
Dysbiosis/microbiology
Bacteria/genetics/classification
Virome
Machine Learning
Case-Control Studies
Metagenome
Asian People
Aged
East Asian People

@article {pmid41493379,
year = {2026},
author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA},
title = {A mathematical framework to correct for compositionality in microbiome data sets.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0112625},
doi = {10.1128/aem.01126-25},
pmid = {41493379},
issn = {1098-5336},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.},
}

Humans
*Metagenomics/methods
*Microbiota
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid41457319,
year = {2026},
author = {Smith, DDN and Subasinghe, RM and Kehoe, C and Grégoire, DS},
title = {Multi-omics provides functional insights and underscores practical challenges in assessing the composition and performance of a nitrifying microbial consortium.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0198425},
pmid = {41457319},
issn = {1098-5336},
support = {GRDI-AMR2 One Health,STAGE//Environment and Climate Change Canada/ ; 2022-04891//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Microbial Consortia ; Ammonia/metabolism ; *Nitrification ; Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification ; Multiomics ; },
abstract = {UNLABELLED: Microbial consortia show promise for bioremediation of environmental pollution, but performance optimization and risk assessment remain challenging due to unculturable species and limitations of traditional biochemical and sequencing tools. This study demonstrates how a multi-omics approach can provide deeper insight into the performance and risks of using a model aerobic ammonia-oxidizing consortium under conditions representative of wastewater treatment. Long-read DNA sequencing recovered several high-quality genomes, revealing dominance by an unclassified Nitrosospira species with expected ammonia oxidation capabilities. Lower-abundance taxa with nitrogen cycling potential were also detected, though species-level identification was limited by poor taxonomic database representation. Multi-omics and nitrogen analyses showed shifts in community composition and nitrogen cycling activity when the consortium was grown along a redox gradient typical of wastewater. All cultures accumulated ammonia over 4 weeks, with only aerobic cultures reducing ammonia levels thereafter. The dominant Nitrosospira population declined in abundance and activity in aerobic cultures while shifting toward nitrogen reduction under anoxic conditions. This metabolic shift would not have been detected using amplicon sequencing alone. Multi-omics also supported risk assessment through detection of waterborne pathogens from the Legionella genus and other lineages harboring virulence genes resembling those from known pathogens. This study highlights the value of multi-omics for optimizing microbial consortia and assessing biosafety risks but also underscores challenges related to effective data analyses and the feasibility of risk assessment under realistic conditions. Addressing these challenges will be essential to support the broader adoption of multi-omics strategies by stakeholders working with microbial consortia across diverse environmental applications.

IMPORTANCE: Microbial consortia are increasingly used to advance a sustainable bioeconomy. Optimizing consortia for environmental applications and ensuring regulatory compliance remains challenging, largely due to reliance on culturing microbes with unknown physiology. In this study, we apply cutting-edge sequencing to a consortium designed for ammonia removal from wastewater. Long-read DNA sequencing enabled complete genome recovery and revealed that populations integral to nitrogen cycling are poorly represented in taxonomic databases. By integrating multi-omics with biochemical assays, we uncovered how environmental conditions drive off-target nitrogen reactions and the potential risks of exposure to pathogens carrying virulence genes. Our findings underscore how whole-community approaches provide insights that are not obtainable with traditional amplicon sequencing and biochemical analysis methods. However, our study also provides recommendations on how hurdles related to data integration and environmental representation must be addressed to support stakeholders adopting such approaches in the context of commercializing microbial consortia.},
}

*Microbial Consortia
Ammonia/metabolism
*Nitrification
Wastewater/microbiology
*Bacteria/metabolism/genetics/classification
Multiomics

@article {pmid41443199,
year = {2026},
author = {Lucas, TN and Biehain, U and Gautam, A and Gemeinhardt, K and Lass, T and Konzalla, S and Ley, RE and Angenent, LT and Huson, DH},
title = {MMonitor for real-time monitoring of microbial communities using long reads.},
journal = {Cell reports methods},
volume = {6},
number = {1},
pages = {101266},
doi = {10.1016/j.crmeth.2025.101266},
pmid = {41443199},
issn = {2667-2375},
mesh = {Humans ; *Metagenomics/methods ; *Software ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Whole Genome Sequencing ; },
abstract = {Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source software platform for real-time analysis and visualization of metagenomic Oxford Nanopore Technologies (ONT) sequencing data. MMonitor includes two components: a desktop application for running bioinformatics pipelines through a graphical user interface (GUI) or command-line interface (CLI) and a web-based dashboard for interactive result inspection. The dashboard provides taxonomic composition over time, quality scores, diversity indices, and taxonomy-metadata correlations. Integrated pipelines enable automated de novo assembly and reconstruction of metagenome-assembled genomes (MAGs). To validate MMonitor, we tracked human gut microbial populations in three bioreactors using 16S rRNA gene sequencing and applied it to whole-genome sequencing (WGS) data to generate high-quality annotated MAGs. We compare MMonitor with other real-time metagenomic tools, outlining their strengths and limitations.},
}

Humans
*Metagenomics/methods
*Software
Metagenome/genetics
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Computational Biology/methods
Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing
Whole Genome Sequencing

@article {pmid41437386,
year = {2025},
author = {Aminu, S and Ascandari, A and Mokhtar, MM and Allali, AE and Benhida, R and Daoud, R},
title = {Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {45},
pmid = {41437386},
issn = {2049-2618},
mesh = {*Microbiota/genetics ; Humans ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Sewage/microbiology ; Cities ; Metagenomics/methods ; Machine Learning ; Genome, Bacterial ; },
abstract = {BACKGROUND: Human-built environment microbiomes mediate pathogen persistence and antimicrobial resistance (AMR) circulation, yet their ecological organization and resilience remain poorly quantified. Hospitals, sewage systems, ambulances, and public transport form interconnected microbial networks where contamination potential and compositional stability define biosurveillance risk. Understanding these dynamics requires genome-resolved frameworks capable of linking community composition to ecological behavior.

METHODS: We analyzed 767 publicly available Illumina metagenomes from four urban environments using the GRUMB workflow. Quality-filtered reads were assembled into 10,834 metagenome-assembled genomes (MAGs) and dereplicated into 1542 species-level representatives. Functional annotation with CARD and VFDB identified ARG- and VF-carrying species, producing a genome-resolved abundance matrix used for ecological and predictive modeling. Alpha and beta diversity, indicator taxa, and prevalence were assessed in R, while machine learning (Random Forest, scikit-learn) achieved a nested cross-validation balanced accuracy of 0.97 ± 0.01. Synthetic donor-recipient simulations (α = 0-1) implemented in Python modeled compositional blending, entropy-based uncertainty, and Minimal Detectable Contamination (MDC) thresholds.

RESULTS: Microbial communities exhibited strong environment-specific structure (PERMANOVA R[2] = 0.12, p < 0.001). Hospital sewage contained the highest richness and compositional heterogeneity, whereas ambulances and hospital environments showed low-diversity, surface-filtered microbiomes. Machine learning identified consistent ecological predictors (Pseudomonas_E fragi, Sphingomonas sp000797515, Acinetobacter variabilis, Roseomonas mucosa) that delineated environmental identity. Synthetic blending revealed a directional source-sink hierarchy with hospital sewage acting as the primary donor (MDC = 0.2-0.3), while hospital environments displayed the greatest compositional resilience (MDC ≥ 0.8). Entropy-based uncertainty analysis identified tipping zones (α = 0.3-0.5), and dominance mapping highlighted hospital environments as stabilizing ecological nodes. WHO-priority pathogens (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli) occupied central positions in the network, bridging environmental and clinical compartments.

CONCLUSIONS: This genome-resolved and simulation-driven framework reveals a directional microbial continuum across urban infrastructures governed by dominance, resilience, and clinical connectivity. Hospital sewage functions as a microbial donor, while hospital environments act as ecological stabilizers anchoring built-environment microbiomes. These findings advance biosurveillance from descriptive profiling to predictive ecological modeling, offering quantitative metrics for risk-informed infrastructure design. Video Abstract.},
}

*Microbiota/genetics
Humans
*Bacteria/genetics/classification/isolation & purification
Metagenome
Sewage/microbiology
Cities
Metagenomics/methods
Machine Learning
Genome, Bacterial

@article {pmid41423629,
year = {2025},
author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM},
title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {954},
pmid = {41423629},
issn = {2041-1723},
support = {109105z/15/a//Wellcome Trust (Wellcome)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; },
mesh = {Humans ; Malawi ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Adult ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics/drug effects ; Female ; Male ; Bayes Theorem ; Antimicrobial Stewardship ; Bacteria/drug effects/genetics/classification ; Sepsis/drug therapy/microbiology ; Metagenomics ; Young Adult ; },
abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.},
}

Humans
Malawi
*Gastrointestinal Microbiome/drug effects/genetics
*Anti-Bacterial Agents/pharmacology/therapeutic use
Adult
Feces/microbiology
*Drug Resistance, Bacterial/genetics/drug effects
Female
Male
Bayes Theorem
Antimicrobial Stewardship
Bacteria/drug effects/genetics/classification
Sepsis/drug therapy/microbiology
Metagenomics
Young Adult

@article {pmid41422269,
year = {2025},
author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y},
title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {22},
pmid = {41422269},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects ; Metagenomics ; Virulence Factors/genetics ; Animal Migration ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics ; Metagenome ; Sequence Analysis, DNA ; },
abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.},
}

*Gastrointestinal Microbiome/genetics
Animals
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects
Metagenomics
Virulence Factors/genetics
Animal Migration
Phylogeny
*Drug Resistance, Bacterial/genetics
DNA, Bacterial/genetics
Metagenome
Sequence Analysis, DNA

@article {pmid41408356,
year = {2026},
author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH},
title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.},
journal = {Rheumatology (Oxford, England)},
volume = {65},
number = {1},
pages = {},
doi = {10.1093/rheumatology/keaf668},
pmid = {41408356},
issn = {1462-0332},
support = {202330//National Clinical Key Speciality Capacity Building/ ; 2021818//Hainan Province Clinical Medical Center/ ; YSPTZX202313//The Innovation Platform for Academicians of Hainan Province/ ; WSJK2024MS150//Joint Project on Health Science and Technology Innovation in Hainan Province/ ; Qhyb2022-133//Hainan Provincial Postgraduate Innovation Research/ ; hnjg2024-67//Hainan Province Education Reform/ ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; *Metabolome/physiology ; Feces/microbiology ; Metabolomics ; Adult ; Aged ; Case-Control Studies ; Metagenomics ; Tandem Mass Spectrometry ; Multiomics ; },
abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.

METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted liquid chromatography-tandem mass spectrometry metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.

RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae and Parabacteroides distasonis were noticed. Conversely, Phocaeicola plebeius, Blautia hansenii and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate and glutamate metabolism, arginine and proline metabolism, and glycine, serine and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.

CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.},
}

Humans
*Scleroderma, Systemic/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
*Metabolome/physiology
Feces/microbiology
Metabolomics
Adult
Aged
Case-Control Studies
Metagenomics
Tandem Mass Spectrometry
Multiomics

@article {pmid41395968,
year = {2026},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0198525},
pmid = {41395968},
issn = {1098-5336},
support = {4421050//USDA-Evans-Allen/ ; 2021-38821-34583//USDA-CBG/ ; },
mesh = {Animals ; *Microbiota ; *Aquaculture/methods ; *Ostreidae/microbiology ; *Vibrio parahaemolyticus/genetics/isolation & purification ; *Vibrio vulnificus/genetics/isolation & purification ; *Vibrio ; Population Dynamics ; Metagenomics ; },
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}

Animals
*Microbiota
*Aquaculture/methods
*Ostreidae/microbiology
*Vibrio parahaemolyticus/genetics/isolation & purification
*Vibrio vulnificus/genetics/isolation & purification
*Vibrio
Population Dynamics
Metagenomics

@article {pmid41366061,
year = {2026},
author = {Deng, JW and Zhou, YL and Zhang, YX and Zhou, CB and Fang, JY},
title = {The relationship between gut microbiota, lifestyle habits, and early-onset colorectal cancer: shedding light on early prediction.},
journal = {British journal of cancer},
volume = {134},
number = {3},
pages = {469-476},
pmid = {41366061},
issn = {1532-1827},
support = {82203224, 81830081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/epidemiology/diagnosis/etiology ; *Life Style ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Diet ; Adult ; Aged ; Cohort Studies ; Age of Onset ; },
abstract = {BACKGROUND: The development of early-onset colorectal cancer (EO-CRC) is linked to environmental exposures and gut microbiota alterations. We aimed to discover the connection and develop prediction strategies.

METHODS: In the observational study, we performed 16S rRNA sequencing and metagenomic sequencing on 76 samples from discovery cohort and validation cohort, and qPCR analysis of selected microbiota, along with lifestyle and dietary assessment on 298 samples from validation cohort. Mediation analysis was employed to investigate the mediating role of gut microbiota. Logistic regression analysis evaluated the optimal prediction model for EO-CRC, with the area under the receiver operating characteristic curves (AUC) assessing diagnostic value.

RESULTS: Dysbiosis of the EO-CRC gut microbiota was characterised by evaluated abundance of F. nucleatum, P. micra, Pks[+] E. coli, and F. Plautii. Mediation analysis showed that Pks[+] E. coli mediated the relationship between fried food, processed meat and coffee to EO-CRC, while F. nucleatum mediated the adverse effects of snacks. A combination of three bacterial markers along with lifestyle and diet demonstrated strong diagnostic potential (AUC = 0.95, 95% CI = 0.92-0.98).

CONCLUSIONS: Our data suggested that the EO-CRC-enriched bacteria may mediate the effects of lifestyle and dietary factors on disease development. A predictive model combining diet, lifestyle, and gut bacteria demonstrated promising early predictive capabilities.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/microbiology/epidemiology/diagnosis/etiology
*Life Style
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
Diet
Adult
Aged
Cohort Studies
Age of Onset

@article {pmid41363534,
year = {2026},
author = {Ren, M and Liu, Y and Wang, Y and Tu, Y and Guo, Y and Sun, X and Niu, G and Wang, Y},
title = {Virome diversity and molecular characterization of two emerging RNA viruses in mosquito populations from Yantai, China.},
journal = {mSphere},
volume = {11},
number = {1},
pages = {e0053925},
pmid = {41363534},
issn = {2379-5042},
mesh = {Animals ; China ; *Virome/genetics ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; *Culicidae/virology ; Metagenomics ; *Mosquito Vectors/virology ; High-Throughput Nucleotide Sequencing ; *Genetic Variation ; Culex/virology ; },
abstract = {Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.},
}

Animals
China
*Virome/genetics
Phylogeny
*RNA Viruses/genetics/classification/isolation & purification
*Culicidae/virology
Metagenomics
*Mosquito Vectors/virology
High-Throughput Nucleotide Sequencing
*Genetic Variation
Culex/virology

@article {pmid41358839,
year = {2026},
author = {Li, Y and Fu, X and Sun, F and Dong, M and Wang, Y and Wang, Y and Liu, Q},
title = {Metabolomic and metagenomic insights into WFBG-mediated regulation of gut microbiota and metabolism in broilers.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0189025},
pmid = {41358839},
issn = {1098-5336},
mesh = {Animals ; *Chickens/microbiology/metabolism/growth & development ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/analysis ; *Animal Feed/analysis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metabolomics ; Metagenomics ; Fermentation ; },
abstract = {UNLABELLED: The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.

IMPORTANCE: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (≤20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.},
}

Animals
*Chickens/microbiology/metabolism/growth & development
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics/analysis
*Animal Feed/analysis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metabolomics
Metagenomics
Fermentation

@article {pmid41318814,
year = {2026},
author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C},
title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.},
journal = {British journal of cancer},
volume = {134},
number = {3},
pages = {439-446},
pmid = {41318814},
issn = {1532-1827},
mesh = {Humans ; *Stomach Neoplasms/therapy/immunology/pathology/drug therapy ; Male ; Female ; Middle Aged ; Aged ; Retrospective Studies ; *Immunotherapy, Adoptive/methods ; *Claudins/immunology ; Gastrointestinal Microbiome/drug effects ; Adult ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Granulocyte Colony-Stimulating Factor/administration & dosage/therapeutic use ; Antibodies, Monoclonal, Humanized/administration & dosage/therapeutic use ; Adrenal Cortex Hormones/administration & dosage/therapeutic use ; Treatment Outcome ; },
abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.

METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.

RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P < 0.001) and overall survival (OS) (3.9 vs. 9.5 months; P < 0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.

CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.

TRIAL REGISTRATION: NCT03874897.},
}

Humans
*Stomach Neoplasms/therapy/immunology/pathology/drug therapy
Male
Female
Middle Aged
Aged
Retrospective Studies
*Immunotherapy, Adoptive/methods
*Claudins/immunology
Gastrointestinal Microbiome/drug effects
Adult
Anti-Bacterial Agents/therapeutic use/administration & dosage
Granulocyte Colony-Stimulating Factor/administration & dosage/therapeutic use
Antibodies, Monoclonal, Humanized/administration & dosage/therapeutic use
Adrenal Cortex Hormones/administration & dosage/therapeutic use
Treatment Outcome

@article {pmid41015044,
year = {2025},
author = {Mukherjee, A and Mazumder, M and Verma, A and Tikariha, H and Bhattacharya, R and Ooi, QE and Swarup, S},
title = {A bacterial signal coordinates plant-microbe fitness trade-off to enhance sulfur deficiency tolerance in plants.},
journal = {Cell host & microbe},
volume = {33},
number = {10},
pages = {1748-1764.e6},
doi = {10.1016/j.chom.2025.09.007},
pmid = {41015044},
issn = {1934-6069},
mesh = {*Sulfur/deficiency/metabolism ; *Rhizosphere ; Soil Microbiology ; Microbiota ; *Glutathione/metabolism ; *Arabidopsis/genetics/growth & development/microbiology ; Brassicaceae/genetics/growth & development/microbiology ; Genetic Fitness ; Metagenome ; Plant Roots/microbiology ; },
abstract = {Plant-associated microorganisms interact with each other and with host plants via intricate chemical signals, offering multiple benefits, including enhanced nutrition. We report a mechanism through which the rhizosphere microbiome improves plant growth under sulfur (S) deficiency. Disruption of plant S homeostasis caused a coordinated shift in the composition and S-metabolism of the rhizosphere microbiome. Leveraging this, we developed an 18-membered synthetic rhizosphere bacterial community (SynCom) that rescued the growth of Arabidopsis and a leafy Brassicaceae vegetable under S-deficiency. This beneficial trait is taxonomically widespread among SynCom members, with bacterial pairs providing both synergistic and neutral effects on host growth. Notably, stronger competitive interactions among SynCom members conferred greater fitness benefits to the host, suggesting a trans-kingdom (plant-microbe) fitness trade-off. Finally, guided chemical screening, deletion knockout mutants, and targeted metabolomics identified and validated microbially released glutathione (GSH) as the necessary bioactive signal that coordinates the trans-kingdom fitness trade-off and improves plant growth under sulfur limitation.},
}

*Sulfur/deficiency/metabolism
*Rhizosphere
Soil Microbiology
Microbiota
*Glutathione/metabolism
*Arabidopsis/genetics/growth & development/microbiology
Brassicaceae/genetics/growth & development/microbiology
Genetic Fitness
Metagenome
Plant Roots/microbiology

@article {pmid41582543,
year = {2026},
author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF},
title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {1},
pages = {26-35},
doi = {10.3967/bes2025.089},
pmid = {41582543},
issn = {2214-0190},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Blood Pressure ; *Hypertension/microbiology ; Prospective Studies ; Aged ; Blood Pressure Monitoring, Ambulatory ; China ; Adult ; },
abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).

METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between α-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.

RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).

CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Blood Pressure
*Hypertension/microbiology
Prospective Studies
Aged
Blood Pressure Monitoring, Ambulatory
China
Adult

@article {pmid41581932,
year = {2026},
author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK},
title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.},
journal = {Advances in protein chemistry and structural biology},
volume = {149},
number = {},
pages = {171-201},
doi = {10.1016/bs.apcsb.2025.08.002},
pmid = {41581932},
issn = {1876-1631},
mesh = {*Biotechnology/economics ; *Antimicrobial Peptides/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; Humans ; Animals ; Delivery of Health Care/economics ; *Anti-Bacterial Agents/pharmacology/chemistry ; },
abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.},
}

*Biotechnology/economics
*Antimicrobial Peptides/chemistry/pharmacology
*Aquatic Organisms/chemistry
Humans
Animals
Delivery of Health Care/economics
*Anti-Bacterial Agents/pharmacology/chemistry

@article {pmid41581112,
year = {2026},
author = {Lett, JM and Scussel, S and Chéhida, SB and Hoareau, M and Filloux, D and Fernandez, E and Roumagnac, P and Parvedy, E and Quirin, E and Clain, C and Minatchy, J and Roux, E and Teycheney, PY and Lefeuvre, P},
title = {Metagenomic screening of the virome of symptomatic tomato plants from La Réunion Island uncovers a complex of viruses including a newly identified whitefly-transmitted polerovirus.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {62},
pmid = {41581112},
issn = {1432-8798},
mesh = {*Plant Diseases/virology ; *Solanum lycopersicum/virology ; *Hemiptera/virology ; Animals ; Phylogeny ; *Virome/genetics ; Reunion ; Metagenomics ; *Luteoviridae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; },
abstract = {Using unbiased high-throughput sequencing for metagenomic screening of viruses in diseased tomato plants, we identified a viral complex that includes viruses previously reported in tomato crops on La Réunion Island as well as a novel polerovirus, tentatively named "tomato necrotic yellowing virus" (ToNYV, proposed species, "Polerovirus ToNYV"). Molecular characterization and phylogenetic analysis revealed that ToNYV is closely related to two recently described poleroviruses from Africa and the Middle East, one of which is transmitted by the whitefly Bemisia tabaci, a trait uncommon among poleroviruses. Our transmission experiments demonstrated that ToNYV is also transmitted by B. tabaci and is prevalent across major tomato-growing regions of La Réunion. These findings highlight the value of metagenomic virome analysis in diseased plants for identifying novel viruses potentially involved in emerging plant diseases, either individually or as components of viral complexes.},
}

*Plant Diseases/virology
*Solanum lycopersicum/virology
*Hemiptera/virology
Animals
Phylogeny
*Virome/genetics
Reunion
Metagenomics
*Luteoviridae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing
Genome, Viral

@article {pmid41578762,
year = {2025},
author = {Shen, F and Xu, C and Wang, C},
title = {Gut Microbiome Diagnostic Biomarkers for Colorectal Cancer.},
journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology},
volume = {37},
number = {1},
pages = {62-74},
pmid = {41578762},
issn = {2148-5607},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Feces/microbiology ; Female ; Middle Aged ; *Biomarkers, Tumor/analysis ; Aged ; *Adenoma/microbiology/diagnosis ; Case-Control Studies ; Disease Progression ; Early Detection of Cancer/methods ; Fusobacterium nucleatum/isolation & purification ; Adult ; },
abstract = {BACKGROUND/AIMS: Gold standard diagnostic methods, such as invasive procedures and serum biomarkers, have limited sensitivity and specificity for the detection of colorectal cancer (CRC). Thus, the development of more accurate and noninvasive detection approaches is imperative. Emerging research elucidating the intricate role of the gut microbiota in CRC pathogenesis underscores the need for precision screening tailored to high-risk cohorts to improve early detection and intervention strategies and comprehensively address this challenging clinical problem.

MATERIALS AND METHODS: Fecal metagenomic sequencing datasets were employed to identify potential bacterial biomarkers for CRC diagnosis and selected relevant microbial taxa for subsequent validation. A total of 180 participants were enrolled: 65 healthy controls (HC), 65 colorectal adenoma patients, and 50 CRC patients, and fecal samples were analyzed using fluorescence quantitative polymerase chain reaction to confirm biomarker relative abundance, culminating in the establishment of an evolutionary model for CRC progression; furthermore, a treatment efficacy and prognostication model supported by comprehensive statistical methodologies was established.

RESULTS: This study analyzed fecal microbial biomarkers associated with CRC progression and identified differentially abundant bacterial species across HCs, adenoma, and CRC patient groups. Notably, Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (P. anaerobius) showed significant correlations with CRC stage and metastasis, highlighting their potential as diagnostic biomarkers. Among individual microbes, P. anaerobius exhibited the highest diagnostic value when combined with Fn.

CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression.   Cite this article as: Shen F, Xu C, Wang C. Gut microbiome diagnostic biomarkers for colorectal cancer. Turk J Gastroenterol. 2026;37(1):62-74.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology
*Gastrointestinal Microbiome/genetics
Male
Feces/microbiology
Female
Middle Aged
*Biomarkers, Tumor/analysis
Aged
*Adenoma/microbiology/diagnosis
Case-Control Studies
Disease Progression
Early Detection of Cancer/methods
Fusobacterium nucleatum/isolation & purification
Adult

@article {pmid41485666,
year = {2026},
author = {He, H and Han, L and Ni, W and Yu, J and Liu, K and Li, W and Li, C and Hu, S and Li, C and Li, X},
title = {The horse gut microbiota genome represents a vast novel reservoir of CAZymes.},
journal = {International journal of biological macromolecules},
volume = {339},
number = {Pt 2},
pages = {150042},
doi = {10.1016/j.ijbiomac.2025.150042},
pmid = {41485666},
issn = {1879-0003},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Horses/microbiology ; Phylogeny ; *Glycoside Hydrolases/genetics/metabolism ; *Genome, Bacterial ; Metagenome ; Glycosyltransferases/genetics/metabolism ; Substrate Specificity ; },
abstract = {Herbivores represent crucial subjects for mining highly efficient carbohydrate-active enzymes (CAZymes) from gut microbiomes. Here, we analyzed 12,763 metagenome-assembled genomes (MAGs) from the horse gut, revealing that its microbial community as a rich reservoir of CAZymes diversity, with 5,204,848 glycoside hydrolases (GHs) and 4,596,191 glycosyl transferases (GTs) identified. Our findings demonstrate that Bacteroidota (5,479,287 CAZymes) and Bacillota_A (2,987,684 CAZymes) serve as the primary functional phyla for plant polysaccharide degradation. A total of 17,250 polysaccharide utilization loci (PULs) discovered in Bacteroides species. Through comparative genomic screening, a total of 12,976 hypothetical genes were predicted in PULs. These genes represent a putative novel reservoir of CAZymes. We selected and identified a putative CAZyme, which encodes 452 amino acids and is designated H113. Our research has confirmed that H113 is a metal enzyme (Zn[2+] significantly enhancing its catalytic efficiency) capable of degrading α-1,4 glycosidic bonds in maltotriose and also exhibiting activity toward mannan, demonstrating optimal activity at pH 4.8 and 35 °C (specific activity: maltotriose: 82.2 U/mg, mannan: 2.3 U/mg). Phylogenetic analysis revealed H113 belongs to a conserved enzyme family with 1866 identified homologues. This study not only provides a reference for efficient discovery of novel CAZymes but also offers valuable resources for developing novel biocatalysts.},
}

Animals
*Gastrointestinal Microbiome/genetics
Horses/microbiology
Phylogeny
*Glycoside Hydrolases/genetics/metabolism
*Genome, Bacterial
Metagenome
Glycosyltransferases/genetics/metabolism
Substrate Specificity

@article {pmid41574290,
year = {2025},
author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W},
title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719300},
pmid = {41574290},
issn = {2235-2988},
mesh = {*Feces/virology ; Animals ; Phylogeny ; *Metagenomics ; *DNA Viruses/genetics/classification/isolation & purification ; Tibet ; Cattle/virology ; *Virome ; *Picornaviridae/genetics/classification/isolation & purification ; Genome, Viral ; China ; },
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.

METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.

RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.

DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.},
}

*Feces/virology
Animals
Phylogeny
*Metagenomics
*DNA Viruses/genetics/classification/isolation & purification
Tibet
Cattle/virology
*Virome
*Picornaviridae/genetics/classification/isolation & purification
Genome, Viral
China

@article {pmid41534355,
year = {2026},
author = {He, S and Wang, Z and Zhong, Z and Shi, C and Li, D and Yin, F},
title = {Soil salinization alters biogeochemical cycles in agricultural ecosystems by reducing carbon-cycling microorganisms.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119706},
doi = {10.1016/j.ecoenv.2026.119706},
pmid = {41534355},
issn = {1090-2414},
mesh = {*Soil Microbiology ; *Salinity ; *Soil/chemistry ; *Carbon Cycle ; Ecosystem ; Agriculture ; Bacteria/genetics/metabolism ; Microbiota ; Metagenomics ; },
abstract = {Salinity stress can decline crop yield in agricultural systems. Beyond the environmental conditions that drive agricultural plant growth, the diverse roles of microbes represent a critical, often overlooked factor in shaping crop health and productivity. Salinization exerts a profound effect on soil microbial communities, with consequences for biogeochemical cycles. However, the salinity adaptation mechanisms of microorganisms participating in biogeochemical cycles remain incompletely understood, which hold considerable promise for microbial solutions in saline agriculture. In this study, metagenomics-based technology was employed to analyze agricultural soils within a region-scale irrigation area characterized by varying degrees of salinization. According to the results of generalized linear models, bell-shaped trends were observed for the diversity and abundance of biogeochemical cycling genes along the soil salinity gradient, all of which peaked at a salinity of approximately 7.5 ‰. Further comparisons indicated reduced total abundance of all biogeochemical cycling genes in high salinity soils (>7.5 ‰) compared to those in low salinity soils (<7.5 ‰). Furthermore, correlation analysis indicated the coupling of different biogeochemical cycling genes, which were observed to be possessed by similar functional microorganisms, with a predominance of Gammaproteobacteria and Alphaproteobacteria. The presence of elevated salt levels resulted in a decline in the abundance of various microorganisms that play roles in biogeochemical cycling, including members of the Alphaproteobacteria, Actinomycetia, Limnocylindira, and Gemmatimonadetes phyla. Concurrently, there was an enrichment of a limited number of salt-tolerant bacteria, predominantly classified under the Bacteroidia and Bacilli taxonomic groups. The coupling of different biogeochemical cycling genes in some metagenome-assembled genomes (MAGs) was confirmed through metagenomics binning. Three MAGs (strains of Methylophaga, Salinimicrobium, and Sediminibacterium, respectively) with diverse biogeochemical cycling functions were recognized as potential plant-growth-promoting bacteria under salinity stress. These findings contribute to the existing body of knowledge on the salinity adaptability of soil microbial communities and offer guidance for the management of saline agriculture.},
}

*Soil Microbiology
*Salinity
*Soil/chemistry
*Carbon Cycle
Ecosystem
Agriculture
Bacteria/genetics/metabolism
Microbiota
Metagenomics

@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {241},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
mesh = {*Artificial Intelligence ; *Metagenome/genetics ; *Metagenomics/methods ; Microbiota/genetics ; Computational Biology/methods ; Machine Learning ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}

*Artificial Intelligence
*Metagenome/genetics
*Metagenomics/methods
Microbiota/genetics
Computational Biology/methods
Machine Learning
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of sediment microbial community composition and function to mangrove restoration from an aquaculture pond in Southern China.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology ; China ; Aquaculture ; *Wetlands ; *Microbiota ; Ponds/microbiology ; Bacteria/classification ; *Environmental Restoration and Remediation ; },
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}