@article {pmid42182019,
year = {2026},
author = {Wu, L and Li, S and Han, F and Guo, J and Zhang, X and Xu, L},
title = {Restoring circadian disrupted gut microbial metabolite rhythms with phytochemicals: a new avenue against metabolic disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1801367},
pmid = {42182019},
issn = {1664-302X},
abstract = {The global epidemic of metabolic diseases-encompassing obesity, type 2 diabetes mellitus (T2DM), non-alcoholic fatty liver disease (NAFLD), and cardiovascular disease-represents a defining public health challenge of our era. The traditional model of simple caloric excess vs. expenditure has proven insufficient, giving way to a paradigm that acknowledges complex interactions between genetics, environment, and lifestyle, mediated by intricate physiological systems. Among these, the host circadian timing system and the gut microbiome have ascended as pivotal, deeply intertwined regulators of metabolic homeostasis. The gut microbiome, far from a static collection of microbes, constitutes a dynamic and metabolically active community whose composition and, critically, its functional output exhibit profound and predictable diurnal oscillations. The host's circadian clocks regulate microbial rhythms primarily by controlling the daily cycle of feeding and fasting. Modern life induces circadian disruption (CD) through ubiquitous exposure to artificial light at night, shift work, social jet lag, and erratic eating patterns. It perturbs the rhythmic dynamics of the gut ecosystem, leading to a fundamental dysregulation in the temporal production of key microbial metabolites. These metabolites, including short-chain fatty acids, secondary bile acids (BAs), indoles and other tryptophan derivatives, function as indispensable chemical messengers that coordinate peripheral metabolism, immune responses, and energy homeostasis in a precise, time-of-day-dependent manner. Their desynchronization-manifesting as mistimed, deficient, or incessant signaling-directly instigates the core pathologies of metabolic disease: insulin resistance, adipocyte dysfunction, hepatic lipid accumulation, and chronic low-grade inflammation. This review synthesizes current evidence to delineate the multilevel mechanisms through which CD drives the dysregulation of gut microbiome metabolite rhythms and establishes the causal pathways linking this dysrhythmia to metabolic pathogenesis. Furthermore, we undertake a critical evaluation of the promising therapeutic potential of dietary phytochemicals-a diverse class encompassing polyphenols, glucosinolates, and prebiotic fibers-to act as chrono-therapeutic agents. Through their multifaceted capacity to remodel microbial ecology, calibrate microbial enzymatic output, and reinforce host circadian-metabolic coupling, phytochemicals present a novel, physiologically aligned, and sustainable dietary strategy for the prevention and management of metabolic disorders. We conclude by outlining key translational challenges and propose future research directions essential for harnessing the potential of the "clock-microbiome-metabolite" axis within the framework of precision nutrition and medicine.},
}

@article {pmid42182034,
year = {2026},
author = {McLeish, M and Zamfir, A and Babalola, B and Mora, MÁ and Fraile, A and García-Arenal, F},
title = {Spatial scale break in ecological strategies for host use by plant viruses.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797573},
pmid = {42182034},
issn = {1664-302X},
abstract = {Processes that involve performance traits such as host range underlie pathogen diversity and infection risk. Host range performance (HRP) is expected to be distributed across spatially explicit conditions, but rarely considered in microbial ecology. Merging of spatially discrete processes in epidemiological model selection exacerbates error propagation. We combine high throughput sequencing and reverse transcriptase polymerase chain reaction approaches to test whether HRP of 18 plant virus species influences species diversity across spatial scales. The results indicated a scaling break in the effect of HRP between the individual host and community scales. Regression analyses showed weaker (i.e., random) associations between viruses in individual hosts than at broader spatial scales of cooccurrence among hosts. Contrasting variances in effect sizes between the spatial scales indicated HRP informs on disease risk at the plant community level, but is a poor predictor of infection in individual plants. The evidence of contrasting HRP between the domains of scale set in this study, suggests heterogeneity among multiple processes across scales drive virus species diversity. Epidemiological model selection should consider variation in species trait performance across scales.},
}

@article {pmid42184066,
year = {2026},
author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A},
title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42184066},
issn = {1573-0972},
support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polyphenols/pharmacology/chemistry/administration & dosage ; Rats, Sprague-Dawley ; Male ; Rats ; *Chitosan/chemistry ; *Tea/chemistry ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; *Ferric Compounds/chemistry ; Proteome ; Proteomics ; Bacteria/classification/genetics/drug effects ; },
abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Polyphenols/pharmacology/chemistry/administration & dosage
Rats, Sprague-Dawley
Male
Rats
*Chitosan/chemistry
*Tea/chemistry
*Metabolic Networks and Pathways/drug effects
Liver/metabolism/drug effects
*Nanoparticles/chemistry
*Ferric Compounds/chemistry
Proteome
Proteomics
Bacteria/classification/genetics/drug effects

@article {pmid42184815,
year = {2026},
author = {Bełkot, Z and Adamski, MG and Strzałkowska, ZJ and Domańska, ED and Kłosińska, D and Kunstman, G and Skoczek, D and Pławińska-Czarnak, J},
title = {Full-Length 16S and 18S rRNA Long-Read Sequencing Reveals Gut Microbiome Diversity in the European Brown Hare (Lepus europaeus).},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70358},
doi = {10.1111/1758-2229.70358},
pmid = {42184815},
issn = {1758-2229},
mesh = {Animals ; *Hares/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 18S/genetics ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; },
abstract = {The European brown hare (Lepus europaeus) is a declining wildlife species of ecological and epidemiological importance, yet its intestinal microbiome remains poorly characterized. Here, Oxford Nanopore long-read sequencing was used to analyse full-length 16S and 18S rRNA genes from pooled large-intestine contents of 30 healthy hares divided into three groups. Comparative taxonomic assignment at 95% and 80% sequence identity thresholds revealed striking differences in diversity estimates, with the lower threshold uncovering up to ten-fold more taxa. Across all samples, 40 phyla, 360 families, 1027 genera, and 3373 species were identified, including 30 taxa not previously reported in lagomorphs. These included Monoglobus pectinilyticus, Ruminococcus champanellensis, Odoribacter splanchnicus, Butyricimonas virosa, and Akkermansia muciniphila, associated with pectin degradation, cellulose hydrolysis, butyrate production, mucin degradation, bile acid transformation, and nitrogen recycling. Several taxa relevant to both animal and human health were also detected, supporting hares as sentinels of environmental microbiota within a One Health framework. These findings show that analytical parameter selection strongly shapes microbiome interpretation and provide the most comprehensive gut microbiome profile of the European brown hare to date. The study expands lagomorph microbial ecology and highlights long-read sequencing as a valuable tool for wildlife microbiome surveillance in undercharacterized host species globally.},
}

Animals
*Hares/microbiology
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 18S/genetics
Phylogeny
Sequence Analysis, DNA
Biodiversity

@article {pmid42185792,
year = {2026},
author = {Mirzaei, S and Tefagh, M},
title = {MOFA: microbial optimization without forced altruism.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06485-1},
pmid = {42185792},
issn = {1471-2105},
abstract = {BACKGROUND: Microorganisms typically exist in communities, where interactions among them define the complexity of these ecosystems. Developing in silico frameworks to investigate the behavior and functionality of these communities is therefore essential for advancing our understanding of microbial ecology. In recent years, several computational modeling frameworks based on genome-scale models have been developed for the community-level analysis of microbial systems.

RESULTS: Here, we introduce microbial optimization without forced altruism (MOFA), a bilevel optimization framework that considers both species-level and community-level fitness criteria. By imposing constraints on species biomass in the outer problem, it prevents the forced altruism observed in previous algorithms. We applied MOFA to a toy model and to community models of Desulfovibrio vulgaris and Methanococcus maripaludis, which exhibit a cross-feeding relationship that causes the community objective to override individual fitness goals by prioritizing the export of metabolites for other community members. For this microbial community, a comparison with the results of NECom, OptCom, and Joint-FBA shows that MOFA yields predictions that better match the experimental results. Additionally, for pairs with a cross-feeding relationship in which exported metabolite production associated with this mutual interaction competes with species biomass, such as D. vulgaris and M. maripaludis, NECom fails to predict the community growth rate, whereas our method succeeds.

CONCLUSIONS: MOFA effectively analyzes community growth rates without relying on forced altruism. In cases where NECom fails to predict community growth, MOFA successfully predicts these growth rates. Furthermore, MOFA enhances computational efficiency by eliminating the need for the binary variables required in the NECom algorithm.},
}

@article {pmid42187718,
year = {2026},
author = {Wen, F and Chen, X and Chen, Q and Li, L and Zhao, Y and You, Y and Niu, S and Xia, Z},
title = {Nutrient Supply Gradients Modulate Cultivation-Driven Restructuring of Microbial Communities in Desert Soils.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biology15100755},
pmid = {42187718},
issn = {2079-7737},
abstract = {Understanding how cultivation conditions influence the recovery of microbial diversity is critical for interpreting cultivation-derived communities in relation to in situ microbial ecology, particularly in nutrient-limited environments such as desert soils. In this study, we investigated how an oligotrophic nutrient gradient shapes cultivation outcomes and enrichment-derived bacterial community structure in soils from the Taklimakan Desert. Three enrichment treatments representing decreasing nutrient availability-standard low-nutrient medium (R2A), diluted medium (DR2A), and sterile water-were used to compare enrichment-derived communities with the original soil microbiome. Amplicon sequencing revealed that cultivation substantially altered community composition and reduced both taxonomic richness and diversity relative to the original soil. Across enrichment treatments, bacterial communities were dominated by a limited number of taxa, whereas the original soil contained a broader range of low-abundance lineages. Within the enrichment system, variation in nutrient supply influenced the relative abundance of specific taxa, with differential responses observed at the genus level. In contrast, beta diversity analysis showed only limited separation among enrichment treatments, and co-occurrence network analysis indicated generally simple and weakly connected community structures across all conditions. Overall, our results demonstrate that cultivation represents the primary selective force shaping enrichment-derived bacterial communities, while nutrient supply intensity acts as a secondary modulator of taxon-specific enrichment. These findings highlight the importance of incorporating nutrient gradients into cultivation strategies to improve ecological interpretation and facilitate the recovery of oligotrophy-associated microorganisms from desert soils.},
}

@article {pmid42187796,
year = {2026},
author = {Aramburu, A and Beltran-Sanz, N and Raggio, J and Divakar, PK and Pintado, A and de Los Ríos, A and Sancho, LG},
title = {Islands of Biodiversity: Characterization of Lichen Flora in Antarctic Nunataks.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/jof12050314},
pmid = {42187796},
issn = {2309-608X},
support = {PID2019-105469RB-C21//Ministerio de Ciencia, Innovación y Universidades/ ; CT82/20-CT83/20//Universidad Complutense de Madrid - Banco Santander/ ; PID2023-147388NB-I00//MCIN/AEI/10.13039/501100011033/FEDER, UE/ ; },
abstract = {Antarctic terrestrial photosynthetic biota is dominated by cryptogamic communities, which are largely restricted to scarce ice-free areas. Among these, nunataks constitute habitats of remarkable biogeographical interest, as they may harbor distinctive biotic assemblages worthy of investigation. This work presents a comprehensive assessment of lichen diversity on Antarctic nunataks. The lichen flora of four nunataks on the Hurd Peninsula (Livingston Island, maritime Antarctica) was investigated. Specimens were identified using an integrative approach combining morphological assessment and DNA barcoding. This survey revealed a high and potentially underestimated species richness, with 39 confidently identified and several additional taxa requiring further taxonomic resolution. A review of published records of lichen occurrence in nunatak and non-nunatak environments throughout Antarctica was used to evaluate patterns in taxonomic, biogeographical, and morphotype composition. This synthesis showed that nunataks support lower species richness than other ice-free environments. Most of their taxa occur in non-nunatak areas, consistent with patterns observed locally on the Hurd Peninsula. Floristic overlap seems greater in continental Antarctica, suggesting a stronger influence of nunatak-associated environmental constraints in the maritime region. These results underscore the ecological significance of nunataks as environmentally filtered habitats and highlight their relevance for understanding biodiversity patterns and community assembly in Antarctica's terrestrial ecosystems.},
}

@article {pmid42174303,
year = {2026},
author = {Kim, CH and Ciloglu, A and Yan, J and Mackay, A and Noel, KR and Cooper, M and Oluoch, A and Canam, T and Stone, CM},
title = {Habitat Type and Locality Structure the Midgut Microbiota of Aedes albopictus.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02792-5},
pmid = {42174303},
issn = {1432-184X},
abstract = {The mosquito midgut microbiome plays a crucial role in nutrition, reproduction, and immunity, yet how locality and urban development shape these communities and their potential relevance to mosquito-pathogen interactions remains poorly understood. Here, we investigated bacterial community composition and diversity in the midguts of adult female Aedes albopictus collected from residential and woodland habitats of Champaign-Urbana and Charleston in Illinois, USA. We sequenced the V4 region of the 16 S rRNA gene from 160 samples and analyzed the data using QIIME 2. After quality and feature filtering, 112 samples were retained, yielding 2,531 unique amplicon sequence variants assigned to 34 bacterial phyla, 246 families, and 404 genera. Because formal contaminant assessment was not possible, findings should be interpreted with appropriate caution. Woodland habitats showed significantly higher Shannon diversity, observed ASV richness, and phylogenetic diversity than residential habitats, with Charleston woodland samples exhibiting the highest richness and phylogenetic diversity. Factorial analyses showed significant associations of both city and habitat type with Shannon diversity, observed richness, and Faith's phylogenetic diversity, with significant interaction terms also detected. Beta diversity analyses revealed distinct clustering of Charleston woodland samples, and factorial PERMANOVA indicated significant associations of both city and habitat type across all four beta diversity metrics, with the strongest interaction effect observed for unweighted UniFrac. In conclusion, these results show that habitat type and locality are strongly associated with the composition and diversity of the Ae. albopictus midgut microbiota, underscoring the importance of habitat-specific microbial patterns in mosquito biology.},
}

@article {pmid42175702,
year = {2026},
author = {Meadows, NML and Delahay, RJ and McDonald, RA and Powell, S and Hopkins, K and Arnold, L and Harrison, XA},
title = {Fecal Microbiome Varies With Social Group, Age and Bovine Tuberculosis Infection in the European Badger (Meles meles).},
journal = {Molecular ecology},
volume = {35},
number = {10},
pages = {e70369},
doi = {10.1111/mec.70369},
pmid = {42175702},
issn = {1365-294X},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Mustelidae/microbiology ; *Feces/microbiology ; *Tuberculosis, Bovine/microbiology ; Cattle ; *Gastrointestinal Microbiome/genetics ; Age Factors ; Mycobacterium bovis/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Social Behavior ; Social Group ; },
abstract = {Host-associated microbes are key components of animal health and physiology, with particular importance for determining responses to pathogen infection. The gut microbiota is highly variable at the individual level, being shaped by a multitude of factors including diet, social behaviour, and age. Yet the relative influence of these traits on microbiota composition, and the consequences of this variation for host responses to pathogens remain unresolved. Here we investigate factors that shape the faecal microbiome in European badgers (Meles meles). Badgers act as a wildlife reservoir of Mycobacterium bovis, a zoonotic pathogen and the causative agent of bovine TB (bTB) in cattle, but the potential role of the microbiome in shaping patterns of infection and severity of disease is not known. Analysing 165 samples from 72 badgers over 3 years, we found that social group and age were key determinants of faecal microbiota composition and identified several bacterial genera associated with bTB infection. Investigation of microbiome dynamics at the individual level using longitudinally sampled badgers revealed marked heterogeneity in age-dependent microbiome trajectories that were not detectable from population level trends in chronological age. These data provide novel insights into the factors associated with microbial community dynamics in complex wild systems and highlight the need for individual-level and longitudinal approaches to studying host-microbiome associations.},
}

Animals
*Mustelidae/microbiology
*Feces/microbiology
*Tuberculosis, Bovine/microbiology
Cattle
*Gastrointestinal Microbiome/genetics
Age Factors
Mycobacterium bovis/pathogenicity
RNA, Ribosomal, 16S/genetics
Social Behavior
Social Group

@article {pmid42176010,
year = {2026},
author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E},
title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02785-4},
pmid = {42176010},
issn = {1432-184X},
abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.},
}

@article {pmid42176025,
year = {2026},
author = {Muhammad, N and Ansar, W and Bashir, T and Khan, HR},
title = {Bacillus-derived antimicrobial peptides as alternatives to antibiotics in poultry: mechanisms, applications, and future prospects- a review.},
journal = {Archives of microbiology},
volume = {208},
number = {8},
pages = {},
pmid = {42176025},
issn = {1432-072X},
mesh = {Animals ; *Antimicrobial Peptides/pharmacology/chemistry ; *Poultry/microbiology ; *Bacillus/chemistry/metabolism ; *Anti-Bacterial Agents/pharmacology ; Biofilms/drug effects ; *Poultry Diseases/microbiology/drug therapy ; },
abstract = {Bacterial enteric pathogens, antimicrobial resistance, and mycotoxin-associated intestinal injury remain important challenges in poultry-associated systems. In this context, Bacillus-derived antimicrobial peptides (AMPs) have attracted attention as potential alternatives to conventional antibiotics due to their structural diversity and multifunctional properties. These peptides include ribosomally synthesized bacteriocins and non-ribosomally synthesized lipopeptides, such as surfactin, iturin, and fengycin. Their amphipathic structures enable interaction with microbial membranes, leading to permeabilization and disruption of cellular homeostasis. In addition to direct antimicrobial activity, these AMPs may interfere with biofilm-associated processes, modulate host immune responses, and help protect against toxin-induced epithelial injury. This review summarizes current knowledge on the diversity, structural characteristics, biosynthesis, mechanisms of action, and microbiological relevance of Bacillus AMPs in poultry-associated environments. Emphasis is placed on membrane targeting, biofilm regulation, immunomodulation, and mycotoxin-related gut protection, as well as limitations associated with antimicrobial resistance. Available evidence indicates that these peptides have diverse mechanisms of action; however, their activity is influenced by peptide class, formulation, microbial ecology, and host physiological factors. In addition, the potential for adaptive or genetically encoded resistance should be considered. Key translational challenges include peptide instability, variability in in vivo efficacy, strain-specific differences, safety considerations, and the lack of standardized comparative models. Future progress will depend on improved delivery systems, microbiome-resolved in vivo studies, and the integration of genomic mining, synthetic biology, and computational peptide design. These approaches may support the development of AMPs with improved stability, specificity, and functional performance in poultry-associated microbial systems.},
}

Animals
*Antimicrobial Peptides/pharmacology/chemistry
*Poultry/microbiology
*Bacillus/chemistry/metabolism
*Anti-Bacterial Agents/pharmacology
Biofilms/drug effects
*Poultry Diseases/microbiology/drug therapy

@article {pmid42176189,
year = {2026},
author = {Plum-Jensen, LE and Mohr, MG and Tanabe, TS and Wang, B and Echers, SG and Madsen, NS and Thorup, C and Linhartova, M and Nielsen, LP and Dueholm, MKD and Boesen, T and Marshall, IPG and Dahl, C and Schramm, A},
title = {Distribution of a novel DsrEFH sulfur transferase suggests widespread sulfur oxidation capacity in sulfate reducers.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag130},
pmid = {42176189},
issn = {1751-7370},
abstract = {Microbial sulfur cycling is typically divided into an oxidative and a reductive branch, with microbes driving either sulfide oxidation or sulfate reduction distinguished by their genomic setup. Paradoxically, filamentous cable bacteria perform electrogenic sulfide oxidation but contain genes indicative of sulfate reduction, including the reductive type of dissimilatory sulfite reductase (DsrAB), whereas they apparently lack the canonical sulfur transferase DsrEFH essential for sulfur oxidation. AlphaFold2 structure prediction of conserved cable bacteria proteins with unknown functions identified a protein complex resembling canonical DsrEFH (hereafter termed DsrEFH type II). In vitro characterization of heterologously expressed DsrEFH type II confirmed its sulfur transferase function and, together with site-directed mutagenesis, verified that the conserved cysteine, Cys67, is the active sulfur transfer residue. Genes encoding the novel DsrEFH type II were found in 985 prokaryotic genomes. They typically co-occurred with genes for reductive DsrAB in microbes characterized as sulfate reducers or sulfur disproportionators. This study not only fills an important gap in the sulfide oxidation pathway of cable bacteria, but also suggests that a wide range of sulfate reducing bacteria may be more metabolically versatile than currently understood, representing a major shift in the perception of this globally significant physiological group of microorganisms.},
}

@article {pmid42178691,
year = {2026},
author = {Kang, Z and Huang, H and Lin, J and Niu, Y and Chen, J and Tang, J and Hu, Z and Liu, P and Qu, J},
title = {Unraveling Oral Dysbiosis: Microbial Complexity in Common Oral Diseases.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70305},
doi = {10.1002/mbo3.70305},
pmid = {42178691},
issn = {2045-8827},
support = {S202510555045//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; S202410555239//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; S202310555226//Hunan Provincial College Students' Innovation and Entrepreneurship Training Program/ ; },
mesh = {*Dysbiosis/microbiology ; Humans ; *Microbiota ; *Mouth/microbiology ; *Mouth Diseases/microbiology ; Periodontal Diseases/microbiology ; Dental Caries/microbiology ; Biofilms/growth & development ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The oral microbiome is highly intricate, hosting billions of bacteria and other microorganisms that form biofilms on various oral surfaces. An imbalanced ecological relationship between the microbial community and the host can lead to various oral diseases. This narrative review explores the current understanding of the correlation between the microbiome and oral diseases. The main body of this manuscript is divided into seven parts, including a review of current research on oral microbial colonization and early life development, an introduction to five common oral diseases related to microorganisms, and a discussion on the relationship between dental caries and periodontal disease at the microbial level. Our aim in presenting this review is to offer a valuable resource for further research on the role of oral microorganisms in diagnosing and treating oral diseases. The oral microbiome's significant impact and diversity characteristics on health and disease have been recognized; however, there remains a severe lack of systematic understanding of its functions, host interactions, and environmental factors. Comprehensive research is urgently needed to elucidate the mechanisms that maintain its ecological balance, providing a scientific foundation for the precise prevention and control of oral diseases. This review comprehensively synthesizes current knowledge regarding oral microbial dysbiosis in the context of the major oral diseases mentioned and proposes a conceptual framework grounded in microbial ecology to elucidate disease progression and guide therapeutic strategies.},
}

*Dysbiosis/microbiology
Humans
*Microbiota
*Mouth/microbiology
*Mouth Diseases/microbiology
Periodontal Diseases/microbiology
Dental Caries/microbiology
Biofilms/growth & development
Bacteria/classification/genetics/isolation & purification

@article {pmid42178776,
year = {2026},
author = {Lukan, T and Pogačar, K and Kraigher, B and Stare, K and Kovačič, TG and Zagorščak, M and Petek, M and Stefanic, P and Vozelj, A and Levak, V and Povalej, TM and García, JM and Pozo, MJ and Álvarez, E and Franco-Zorrilla, JM and Križnik, M and Baebler, Š and Mandić-Mulec, I and Gruden, K},
title = {ERF transcription factor StPti5 is a regulator of endophyte community maintenance in potato.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71240},
pmid = {42178776},
issn = {1469-8137},
support = {J4-3089//Slovenian Research and Innovation Agency/ ; J4-4550//Slovenian Research and Innovation Agency/ ; J4-9302//Slovenian Research and Innovation Agency/ ; P4-0116//Slovenian Research and Innovation Agency/ ; P4-0165//Slovenian Research and Innovation Agency/ ; P4-0463//Slovenian Research and Innovation Agency/ ; Z1-60169//Slovenian Research and Innovation Agency/ ; MCIN/AEI/PID2021-124813OBC31//"ERDF A way of making Europe" financed by the European Union/ ; },
abstract = {We have recently identified an ethylene response factor, StPti5, as a susceptibility factor that negatively regulates immune responses to diverse pathogens. Here, we investigated the role of StPti5 in the processes involved in the colonization of potato with beneficial organisms. RNA-seq showed that at the time of Bacillus subtilis biofilm establishment, immune responses in interacting roots were attenuated, and a complex transcriptional network was triggered, with ethylene signaling being a central module and StPti5 strongly induced. Interestingly, the response is intensified if plants are inoculated by two antagonistic B. subtilis strains. While StPti5 is not involved in the establishment of biofilm on roots, we show that bacterial abundance increases in shoots of StPti5-silenced plants. Remarkably, root colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis was also higher in the StPti5-silenced plants. To decipher the mechanistic basis of StPti5 function, we performed a DAP-seq experiment and showed that StRIN13, a regulator of plant immune signaling, is a direct target of StPti5. StPti5 is involved both in suppressing defense against harmful and limiting colonization by beneficial microbes. Such a mechanistic understanding of plant-microbe interaction paves the way for sustainable crop management.},
}

@article {pmid42181278,
year = {2026},
author = {De Yebra, P and Zoccarato, L and Galindo, JA and Numberger, D and Abdulkadir, N and Grossart, HP and Greenwood, AD},
title = {Diversity of antibiotic resistance genes increases in urbanized lakes: A multi-tool screening.},
journal = {iScience},
volume = {29},
number = {6},
pages = {115892},
pmid = {42181278},
issn = {2589-0042},
abstract = {Antimicrobial resistance (AMR) threatens to cause up to 10 million deaths annually by 2050 if no action is taken. Using shotgun sequencing, we examined the eco-evolutionary dynamics of AMR across urban-rural environment gradients in lake water and sediments, a farm pond and a wastewater treatment plant (WWTP). ARGs were identified using multiple databases and five bioinformatic tools, detecting up to 18 ARG classes-more than any single tool alone. ARG diversity was higher in urban lake sediments, urban waters, and wastewater compared to rural lake sediments and water. Among all environments, urban lake water showed the highest overall ARG abundance, second only to wastewater, and this pattern held across all ARG classes, except for aminoglycoside resistance, which was most prevalent in rural lake sediments. These findings highlight multi-tool ARG screening efficiency, WWTPs and urban sediments as major ARG reservoirs, and emphasize the need for enhanced urban-rural AMR surveillance.},
}

@article {pmid42181306,
year = {2026},
author = {Bhadury, P and Danda, AA and Ghosh, A and Yash, and Saini, N and Chowdhury, DR and Saha, S and Dubey, SK},
title = {Dataset of prokaryotic and eukaryotic community structures from sediment and surface water eDNA of a sustainable mangrove fisheries (SMF) aquaculture pond.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112800},
pmid = {42181306},
issn = {2352-3409},
abstract = {Sustainable mangrove fisheries (SMF) is an integrated mangrove fisheries approach used in coastal aquaculture ponds that brings sustainability to coastal aquaculture practices. To track the positive value of mangrove on the aquaculture practices, sediment and overlying surface water based environmental DNA (eDNA) biomonitoring has been initiated in SMF pond of Haroa Block (West Bengal, India), in close proximity to Sundarbans mangrove. In the post-monsoon of 2025 (January), sediment and overlying surface water samples were collected from the same SMF pond, followed by application of eDNA extraction and Oxford Nanopore Technologies (ONT) sequencing to deduce biological communities. During sampling, in-situ environmental parameters were recorded and dissolved nutrients were also measured. The dissolved nitrate and reactive silicate concentrations (320.32 and 46.85 µM respectively) were high in SMF pond reflecting effective mimicry of natural mangroves within the studied SMF pond. Using MinION platform integrating ONT, prokaryotic communities based on 16S rRNA metabarcoding revealed high abundance of Proteobacteria, followed by Firmicutes which were higher in sediment compared to surface water. There was high abundance of Bacteroidetes and Actinobacteria in sediment compared to the surface water reflecting the potential pool of complex forms of organic carbon. Microphytobenthos in the sediment was represented by members of Cyanobacteria. At the 18S rRNA level, members of Bacillariophyta dominated both sediment and water reflecting their importance in photosynthetic primary production and potential food for shrimps growing in the SMF pond. Besides, sequences representing other groups of alveolates were also encountered in sediment and surface water. The presence of Ascomycota and Basidiomycota within the eukaryotic pool reflecting their specific role in breakdown and utilization of mangrove litter, in addition to Firmicutes. This study generates key baseline information for long-term monitoring and represents the first eDNA-based dataset for sediment and surface water of prokaryotic and eukaryotic biological communities within the SMF.},
}

@article {pmid42181765,
year = {2026},
author = {Gervasi, A and Schutz, L and Cardol, P and Meyer, PE},
title = {Motilitometer: A compact modular microscope for motility and photoresponse analysis of microorganisms.},
journal = {HardwareX},
volume = {26},
number = {},
pages = {e00788},
pmid = {42181765},
issn = {2468-0672},
abstract = {In biology, cell motility is a valuable indicator, revealing how cells sense their environment, adapt to stimuli, and reflect their physiological state. In this paper, we present a modular microscopy system designed to study the motility of microorganisms. The setup is compact, assembled from low-cost 3D-printed and widely available components. It integrates programmable multispectral illumination to enable controlled photo stimulation and investigation of light-induced behavioral responses, including phototaxis. Initially developed for the investigation of photosynthetic microalgae, the system is easily adaptable to a wide range of motile microorganisms. It supports two complementary observation modes: a droplet-based chamber that minimizes sedimentation for cell speed analysis, and a deeper chamber that allows sedimentation, enabling quantitative assessment of motility fraction and orientation relative to directional light. The optical system provides a magnification of up to approximately 9×, sufficient for the precise centroid detection and tracking of single cells. This open-source, DIY (Do It Yourself) microscopy platform offers an accessible tool for photobiology, microbial ecology, and biophysics, helping democratize quantitative motility studies.},
}

@article {pmid42167281,
year = {2026},
author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC},
title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70327},
doi = {10.1111/1462-2920.70327},
pmid = {42167281},
issn = {1462-2920},
support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; },
mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; },
abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.},
}

*Wetlands
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
*Greenhouse Gases/analysis/metabolism
Congo
RNA, Ribosomal, 16S/genetics
*Plankton/genetics/classification
Ecosystem
Methane/metabolism
Phylogeny
Carbon Cycle
Biodiversity
Metagenome

@article {pmid42167521,
year = {2026},
author = {Wolacewicz, M and Decewicz, P and Valdes, ME and Iaconi, OS and Todiras, M and Ferdohleb, A and Rodriguez-Mozaz, S and Borrego, CM and Dziewit, L},
title = {The occurrence and removal of antibiotic residues and antibiotic resistance genes in the largest European constructed wetland at Orhei (Moldova).},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {402},
number = {},
pages = {128381},
doi = {10.1016/j.envpol.2026.128381},
pmid = {42167521},
issn = {1873-6424},
abstract = {Constructed wetlands (CWs) are increasingly promoted as low-cost, nature-based solutions for wastewater treatment, particularly in low- and middle-income countries (LMICs), yet their performance in removing pharmaceutical compounds, antibiotic resistance genes (ARGs), and bacterial pathogens remains insufficiently characterized under real-field-scale conditions. Here, we investigated the fate of pharmaceutical compounds (including antibiotic residues), wastewater bacterial communities, and the associated ARGs in the largest European passive treatment system, the vertical-flow CW of Orhei (Moldova), serving nearly 26,000 inhabitants. Metagenomic profiling revealed 783 bacterial families, with a reduction from 33 families in raw sewage to 25 in the final effluent and clear enrichment of autochthonous wetland taxa. A total of 150 ARG types conferring resistance to 16 antibiotic classes were detected. The cumulative ARG load decreased by approximately 78% from influent to effluent. ARGs conferring resistance to fosfomycin, nitroimidazoles, rifamycins, streptothricin, oxazolidinones, and pleuromutilins were not detected in the final effluent, suggesting effective removal to below the detection limit of the applied metagenomic method, while sulfonamide resistance genes (sul1, sul2) persisted across all stages. Out of 29 antibiotic residues analyzed, 13 (including two sulfamethoxazole metabolites) were detected, together with 14 non-antibiotic pharmaceuticals (out of 30 residues analyzed). The removal of individual antibiotics ranged between 85 and 100%, and for other pharmaceuticals between 34 and 100%, although some compounds (e.g., carbamazepine, 10,11-epoxycarbamazepine, alprazolam) showed negative removals. Environmental risk assessment (risk quotients, RQ) indicated no significant risk to freshwater biota (RQ < 0.1) for all detected compounds in the treated effluent. Results demonstrated that a large-scale CW in the LMIC context can substantially reduce antibiotic residues and ARGs, supporting its role as an effective, nature-based component of One Health-oriented wastewater management.},
}

@article {pmid42168408,
year = {2026},
author = {Maskow, T and Duong, HL and Fernández Merayo, N and Schlosser, D},
title = {Biocalorimetry for the biotechnological use of natural and synthetic macromolecules.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {42168408},
issn = {1432-0614},
mesh = {*Biotechnology/methods ; *Calorimetry/methods ; Biomass ; *Macromolecular Substances/metabolism ; Fermentation ; Plastics/metabolism ; },
abstract = {Biocalorimetry offers a powerful approach for real-time process monitoring and optimization in the biotechnological utilization of both natural and synthetic macromolecules, particularly in complex solid-state systems aiming at the valorization of plant biomass or plastics' waste. This review critically examines general strengths and limitations of biothermodynamics and calorimetry for monitoring microbial activity, which can be tracked across diverse scales and substrates via metabolic heat measurements. Metabolic heat-derived activity parameters enable the robust quantitative evaluation of the performance of microorganisms for substrate conversion, hence potentially representing valuable tools for bioprocess development and operation. While biocalorimetry is established in liquid-phase cultivation systems to some extent, its adaptation to solid-state fermentation, composting, and the biochemical breakdown of solid plastics still remains in early stages while holding promise for real-time control and upscaling. Challenges and limits of the applicability of this technology currently persist especially for mixed cultures and non-sterile processes. Nevertheless, expanding metabolic heat-based datasets to microbial functional traits could advance ecological and industrial applications. Overall, biocalorimetry is positioned as a valuable tool for advancing circular bioeconomy strategies, though further validation and methodological development are needed for broader adoption in both research and industrial contexts. KEY POINTS: • Biocalorimetry reliably quantifies microbial activity on complex solid substrates. • Biocalorimetry can support plant biomass and plastic waste valorization in a circular bioeconomy. • Biocalorimetric monitoring is applicable from the laboratory to the technical scale.},
}

*Biotechnology/methods
*Calorimetry/methods
Biomass
*Macromolecular Substances/metabolism
Fermentation
Plastics/metabolism

@article {pmid42168837,
year = {2026},
author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T},
title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05157-7},
pmid = {42168837},
issn = {1471-2180},
support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; },
abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.},
}

@article {pmid42171373,
year = {2026},
author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0030526},
doi = {10.1128/msystems.00305-26},
pmid = {42171373},
issn = {2379-5077},
abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.},
}

@article {pmid42094371,
year = {2026},
author = {Zhang, C and Sabonis, D and Cai, Y and Zang, Z and Tamulaitiene, G and Gerdt, JP},
title = {Chemical suppression of a bacterial immune system revives repressed phages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42094371},
issn = {2692-8205},
abstract = {Many antiviral immune systems have recently been discovered in bacteria. The mechanisms of several are obscure, as are their individual significance for antiphage defense. To shed light on the mechanism and significance of the two-component type I Thoeris antiphage immune system, we leveraged high-throughput phenotypic screening to identify three small molecule inhibitors. The inhibitors target the ThsA NADase component, inhibiting its 3'-cADPR-activated filamentation. The temporal control afforded by the small-molecule inhibitors allowed us to answer an outstanding question in antiviral immunity-is persistent immunity required to repress phage titers, or do immune systems become unnecessary after eradicating infectious phages? We found that Thoeris immunity must be maintained, as chemical inhibition enabled repressed phages to revive and overtake the bacterial population. Furthermore, due to the cooperative nature of antiviral immunity, we found that Thoeris must be inhibited in only 10% of the bacteria to cause phage-induced lysis of the entire population.},
}

@article {pmid42166181,
year = {2026},
author = {Hijri, M and Aliyat, FZ and Legeay, J and Lee, SJ and Idbella, M and Anwar, AF and Errafii, K and Marasco, R and Biswas, MK and Venturi, V and Zézé, A and Gemeda, M and Eziuzor, SC and Makhalanyane, T and Ahmed, B},
title = {Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag132},
pmid = {42166181},
issn = {1751-7370},
abstract = {Microbial ecology and microbiome science are increasingly central to global "One Health" efforts, a framework that recognizes the interconnected health of humans, animals, and the environment. In Africa, these fields are particularly important for addressing interconnected challenges in public health, agriculture, and ecosystem resilience. Discussions at the ISME-Africa Morocco 2025 regional meeting highlighted both progress and persistent gaps in African microbiome research. Initiatives such as the African BioGenome Project and Human Heredity and Health in Africa demonstrate the feasibility of population-representative studies, regional training, networking, and open-science frameworks; however, the research landscape remains fragmented, with limited intra-African collaboration and continued reliance on external funding and leadership. The development of Africa-specific reference genomes, population-based microbiome datasets, is essential to address these gaps and ensure global representation. This perspective synthesizes current evidence and outlines strategic priorities to transition from toward coordinated pan-African research networks and flagship programs. Key recommendations include developing Africa-specific genome reference datasets, establishing pan-continental consortia, fostering equitable African-non-African partnerships, integrating microbiome science into policy frameworks, and adopting FAIR open-science practices. Strengthening bioinformatics and computational capacity will be essential to transform fragmented data into high-impact, coordinated insights. Advancing these priorities will accelerate translation into One Health outcomes, including antimicrobial resistance surveillance, food security, climate-resilient agriculture, and precision medicine. Africa's rich microbial diversity offers significant potential for antibiotic discovery, improved crop productivity, and sustainable agricultural systems. Collectively, strengthening Africa-led, collaborative microbiome research will enable the continent's microbial diversity to drive impactful solutions with regional and global relevance.},
}

@article {pmid42166940,
year = {2026},
author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM},
title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.},
journal = {Pathology, research and practice},
volume = {285},
number = {},
pages = {156543},
doi = {10.1016/j.prp.2026.156543},
pmid = {42166940},
issn = {1618-0631},
abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.},
}

@article {pmid42153623,
year = {2026},
author = {Diaz-Colunga, J and Catalan, P and San Roman, M and Arrabal, A and Sanchez, A},
title = {Full factorial construction of synthetic microbial communities.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {42153623},
issn = {2050-084X},
support = {PID2021-125478NAI00//Spanish National Plan for Scientific and Technical Research and Innovation/ ; PID2022-142185NB-C21//Spanish National Plan for Scientific and Technical Research and Innovation/ ; PID2022-142185NB-C22//Spanish National Plan for Scientific and Technical Research and Innovation/ ; 101088469/ERC_/European Research Council/International ; },
mesh = {*Pseudomonas aeruginosa/genetics/growth & development ; *Microbial Consortia ; *Synthetic Biology/methods ; *Microbial Interactions ; Biomass ; },
abstract = {Constructing combinatorially complete species assemblages is often necessary to dissect the complexity of microbial interactions and to find optimal microbial consortia. At the moment, this is accomplished through either painstaking, labor-intensive liquid handling procedures, or through the use of state-of-the-art microfluidic devices. Here, we present a simple, rapid, low-cost, and highly accessible liquid handling methodology for assembling all possible combinations of a library of microbial strains, which can be implemented with basic laboratory equipment. To demonstrate the usefulness of this methodology, we construct a combinatorially complete set of consortia from a library of eight Pseudomonas aeruginosa strains, and empirically measure the community-function landscape of biomass productivity, identify the highest-yield community, and dissect the interactions that lead to its optimal function. This easy-to-implement, inexpensive methodology will make the assembly of combinatorially complete microbial consortia easily accessible for all laboratories.},
}

*Pseudomonas aeruginosa/genetics/growth & development
*Microbial Consortia
*Synthetic Biology/methods
*Microbial Interactions
Biomass

@article {pmid42153658,
year = {2026},
author = {Chen, X and Chen, GG and Gong, Z and Zhu, H and Liang, Z and Chan, JYK and Tong, MCF and Chen, Z and Chang, WT},
title = {The middle ear-nasopharyngeal microbiome axis associated with obstructive Eustachian tube dysfunction in chronic otitis media.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0000726},
doi = {10.1128/msystems.00007-26},
pmid = {42153658},
issn = {2379-5077},
abstract = {Obstructive Eustachian tube dysfunction (ETD) commonly complicates chronic otitis media (COM), yet microbial factors at the Eustachian tube (ET) openings remain poorly understood. In this prospective cohort study, we characterized the microbiota at both the middle ear (ME) and nasopharyngeal (NP) ET openings in COM patients undergoing ear surgery and examined associations with obstructive ETD over one year of follow-up. Using 16S rRNA gene sequencing and functional inference, we profiled microbial communities from the ME-side ET opening and the torus tubarius on both surgical-side and contralateral nasopharynx. Among 37 patients (18 with ETD, 19 without), ME and NP microbiota differed significantly in composition. Ears with ETD showed increased ME microbial diversity and enrichment of Neobacillus, Agrobacterium, and Sphingomonas. Paired NP-ME analyses indicated an altered NP-ME microbial relationship in ETD, with Neobacillus showing a nasopharyngeal source signal. Functional prediction revealed increased porphyrin metabolism and decreased pyruvate metabolism in ME microbiota with ETD, suggesting a shift toward biofilm formation and altered redox states. Anaerococcus was increased in the nasopharynx of patients with bilateral COM. These findings identify distinct microbial and metabolic features of COM with obstructive ETD, supporting a role for nasopharyngeal-microbial influence on ME pathology.IMPORTANCEChronic otitis media (COM) is a common and often persistent ear disease, especially when complicated by Eustachian tube dysfunction (ETD). By profiling microbiota at both Eustachian tube openings, this study links upper-airway microbial ecology with middle-ear microbial states in COM and helps clarify where clinically relevant signals may arise along the Eustachian tube pathway. The paired nasopharyngeal-middle ear design revealed that nasopharyngeal microbes may be linked to middle-ear community shifts in COM with obstructive ETD, consistent with a potential upper airway contribution to the middle-ear microbiota, generating testable hypotheses about microbial exchange and persistence. These findings highlight the upper airway microbiome as a potential target for developing new preventive and therapeutic strategies in COM.},
}

@article {pmid42156649,
year = {2026},
author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D},
title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {33-46},
pmid = {42156649},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; },
abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.},
}

*Microbiota/genetics
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
RNA, Ribosomal, 16S/genetics
Oceans and Seas
*Seawater/microbiology
Computational Biology/methods

@article {pmid42156652,
year = {2026},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Computational Microbial and Viral Ecology Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {83-141},
pmid = {42156652},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; },
abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.},
}

*Metagenomics/methods
*Computational Biology/methods
Metagenome
*Microbiota/genetics
*Viruses/genetics/classification
Virome
Bacteriophages/genetics
Bacteria/genetics
Archaea/genetics

@article {pmid42158881,
year = {2026},
author = {Marzi, M and Sener, G and Sener, TE},
title = {The gut-kidney axis in calcium oxalate nephrolithiasis: Nutritional and microbial insights.},
journal = {Northern clinics of Istanbul},
volume = {13},
number = {2},
pages = {252-262},
pmid = {42158881},
issn = {2536-4553},
abstract = {Calcium oxalate (CaOx) nephrolithiasis is the most common type of kidney stone disease worldwide. Recent studies show that its development cannot be explained solely by renal solute handling; instead, it reflects a broader interaction between dietary habits, the intestinal microbiota, and host metabolic responses. Intestinal absorption of calcium and oxalate-two central drivers of lithogenesis-is shaped by both microbial composition and dietary patterns. Although Oxalobacter formigenes was initially regarded as the main oxalate-degrading organism, newer studies indicate that a wider disturbance of the gut microbiota, especially the loss of short-chain fatty acid (SCFA)-producing species, may increase susceptibility to stone formation. In this review, nutritional, microbial, and mechanistic evidence is brought together to examine how diet-particularly salt, animal protein, calcium, oxalate, fruits, vegetables, and water intake-modulates the gut-kidney axis. Diets high in salt or animal protein tend to shift the microbiota toward more pro-inflammatory and acidogenic profiles, while fiber-rich, plant-based diets and adequate hydration appear to support microbial diversity, SCFA production, and epithelial barrier integrity. Probiotic and synbiotic interventions have also gained attention as potential strategies to reduce stone recurrence by targeting gut microbial function. Taken together, current findings suggest that the gut-kidney axis is a dynamic metabolic link between diet, microbial ecology, and renal physiology. Future studies combining multi-omics methods with personalized nutritional approaches may help develop more effective microbiota-based prevention and treatment strategies for CaOx nephrolithiasis.},
}

@article {pmid42160933,
year = {2026},
author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M},
title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142454},
doi = {10.1016/j.jhazmat.2026.142454},
pmid = {42160933},
issn = {1873-3336},
abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.},
}

@article {pmid42161759,
year = {2026},
author = {Chen, Y and Wilschut, RA and Garbeva, P},
title = {The legacy of soil chemistry: a hidden manipulator driving plant-soil feedbacks.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.009},
pmid = {42161759},
issn = {1878-4380},
abstract = {Plants actively reshape the soil environment through their roots and associated microbes, creating lasting changes known as soil legacies that influence future plant generations via plant-soil feedbacks. While biotic factors such as pathogens and mutualists have received much attention, the chemical legacies, including water-soluble and volatile organic compounds, remain underexplored. These metabolites, produced by plants and soil microbes, modulate microbial communities, nutrient dynamics, and plant defenses, driving positive or negative feedbacks. This opinion article synthesizes recent evidence on soil chemical diversity, their role in legacy formation and persistence, while highlighting analytical challenges and promising applications in agriculture and ecology.},
}

@article {pmid42162823,
year = {2026},
author = {Naying, L and Bo, Z and Wei-Min, W and Xin, L and Ruixi, L and Xintong, M and Xiaofeng, W and Li, Z and Shaoliang, Y and Honghui, L and Yixin, H},
title = {Simulated freeze-thaw cycles restructure plastisphere microbiomes and functional gene co-occurrence networks in alpine lake sediment microcosms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128322},
doi = {10.1016/j.envpol.2026.128322},
pmid = {42162823},
issn = {1873-6424},
abstract = {Microplastics (MPs) are increasingly recognized as dynamic ecological interfaces rather than inert contaminants, yet their role in shaping microbial functional interactions under climate-driven disturbances remains poorly understood. In particular, how climate driven freeze-thaw cycles (FTCs) influence the dynamics of mobile genetic elements (MGEs) within the plastisphere remains unclear. Here, we used controlled microcosms containing sediments from Tibetan Plateau lakes and polyethylene/polyethylene terephthalate particles to examine how simulated extreme FTCs were associated with changes in plastisphere microbial communities and functional gene co-occurrence patterns. FTCs reshaped plastisphere microbial communities, but their assembly trajectories differed between habitats. In the plastisphere, deterministic selection was pronounced at early FTC stages, whereas it did not further intensify with increasing FTC frequency. In contrast, sediment communities exhibited a progressive shift toward deterministic assembly with increasing FTCs. Concomitantly, MGEs were relatively enriched in the plastisphere and co-occurrence with genes involved in carbon metabolism, antibiotic resistance genes (ARGs), and virulence factors (VFs), forming interconnected functional networks. Notably, FTCs were associated with the enrichment of specific carbon metabolizing taxa (e.g., Comamonas and Brevundimonas) within the plastisphere that also carried relatively high abundances of MGEs, ARGs, and VFs. These patterns suggest that MPs may provide ecological niches linking carbon utilization and gene exchange potential. Collectively, this work highlights the interactive influence of climate-related disturbance and emerging pollutants on plastisphere microbial ecology, and provides a mechanistic basis for future assessment of ecological implications in fragile alpine ecosystems.},
}

@article {pmid42163999,
year = {2026},
author = {Kumar, C and Saini, N and Ghosh, A and Bhadury, P},
title = {Genome description of a potentially novel species of Rossellomorea sp. strain H39_3 isolated from the Hindon River, India.},
journal = {Access microbiology},
volume = {8},
number = {5},
pages = {},
pmid = {42163999},
issn = {2516-8290},
abstract = {In October 2024, a putative novel species, belonging to the genus Rossellomorea, designated as strain H39_3, was isolated using Luria-Bertani medium from surface water representing station H39, located on the Hindon River, in close proximity to Gautam Buddha Nagar in Uttar Pradesh, India. The 16S rRNA sequence of this isolate showed 100% identity to Rossellomorea marisflavi from the International Nucleotide Sequence Database Collaboration (INSDC) DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was undertaken using long-read sequencing with Oxford Nanopore Technologies (ONT) chemistry on the MinION platform, followed by genome annotation against the NCBI Reference Sequence Database (RefSeq) and Genome Taxonomy Database (GTDB) databases. The genome is ~4.46 Mb in size, with a G+C content of 48.64 mol%. The low average nucleotide identity (92.23%) and digital DNA-DNA hybridization (46.1%) values showed affiliation with the reference strain R. marisflavi, indicating the isolate as a potential novel species. Functional analysis of the draft genome of this isolate revealed an array of genes, including the presence of arsC (arsenate reductase), the assimilatory nitrate reduction pathway and the ability to degrade polysaccharides. The presence of nitrogen metabolizing genes such as nirB (nitrite reductase subunit B), along with the ability to break down complex forms of carbon, offers the potential of this strain for application in bioremediation of contaminated river ecosystems.},
}

@article {pmid42164315,
year = {2026},
author = {O'Connor, BRW and Allen, D and Quinn, M and Kozey, M and Léveillé, RJ and Whyte, LG},
title = {Bipolar investigation of near-surface glacial ice reveals an active microbial ecosystem driven by photosynthesis and chemolithoautotrophy.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag105},
pmid = {42164315},
issn = {2730-6151},
abstract = {Despite extreme conditions including freezing temperatures, low water activity, and few nutrients, active microorganisms are thought to inhabit glacial ice, yet little is known about their identities and methods of survival. We used flow cytometry, cultivation, metagenomics, and metatranscriptomics to characterize viable and active microbial communities from near-surface englacial ice from White Glacier in the Canadian High Arctic and Johnsons Glacier on Livingston Island, Antarctica. The ice, though low in microbial biomass (10[4] cells/ml), harbors communities capable of growth at subzero temperatures (-5°C), high salinity (12% NaCl), and low pH (pH 3). The communities of both poles were different, with metagenome-assembled genomes (MAGs) from White Glacier belonging to Cyanobacteriota and novel phyla and MAGs from Johnsons Glacier belonging to Pseudomonadota and Actinomycetota. Despite this, both glacial communities shared key metabolic functions, including aerobic respiration, aerobic carbon monoxide oxidation, sulfide oxidation, and denitrification. Metatranscriptomics from White Glacier revealed dominant Cyanobacteriota, performing oxygenic photosynthesis and carbon fixation and accompanied by active lithoautotrophs performing metabolisms such as carbon fixation via the 3-hydroxyproprionate cycle, anoxygenic photosynthesis, sulfide oxidation, and nitrate reduction/denitrification. These metabolisms appear to support an active heterotrophic community performing aerobic respiration and aerobic carbon monoxide oxidation. This study highlights the distinct but functionally similar microbial communities in Arctic and Antarctic glaciers, hinting that there may be a core set of metabolisms required for surviving in englacial ice and suggesting that similar communities could persist in glacial ice on Mars or the icy outer moons, Europa and Enceladus.},
}

@article {pmid42165578,
year = {2026},
author = {Hernández-Villamor, D and Bautista Angeli, J-R and Jeaidi, A and Joaquín-García, A and Rabaey, K and Prévoteau, A},
title = {Propionate oxidation by Geobacter sulfurreducens is electron acceptor dependent.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0006426},
doi = {10.1128/aem.00064-26},
pmid = {42165578},
issn = {1098-5336},
abstract = {UNLABELLED: The accumulation of propionate is a challenge in numerous fermentative industrial processes because its degradation is energetically unfavorable and limited to few microbial species. Here, we report for the first time the oxidation of propionate by the extracellular electron transfer (EET)-capable bacterium Geobacter sulfurreducens in axenic cultures. G. sulfurreducens was capable of utilizing propionate both as an electron donor (ED) and a source of carbon, with fumarate as an electron acceptor (EA). In contrast, propionate was metabolized only in the presence of acetate with soluble Fe(III) citrate and was not oxidized when insoluble iron oxides or glassy carbon electrodes poised at +0.1 V vs SHE served as the EA. Biomass yield (per mole of electrons available) was lower with propionate alone than with propionate and acetate together, and acetate was preferentially consumed when both were present. Transcriptomic analysis of cultures grown with either propionate or acetate (with fumarate as EA) showed significant gene expression shifts, strongly suggesting the methylmalonyl-CoA pathway as the main route for propionate degradation. Furthermore, propionate-consuming cultures exhibited an upregulation of branched-chain amino acid (BCAA) biosynthesis, as well as sulfur, nitrogen, and 2-oxocarboxylic acid metabolism.

IMPORTANCE: The accumulation of propionate is a challenge in anaerobic and fermentative processes because it inhibits methanogenesis, and few microbial species within such systems can degrade it. G. sulfurreducens is a model electroactive bacterium widely used in bioelectrochemical systems and is increasingly studied in wastewater treatment and anaerobic digestion because of its ability to enhance syntrophic metabolism via direct interspecies electron transfer. We show for the first time that G. sulfurreducens can oxidize propionate, expanding its known metabolic repertoire, and that this capability is controlled by the nature of the terminal electron acceptor. Transcriptomic analyses strongly suggest that the methylmalonyl-CoA pathway is the main pathway for propionate degradation and reveal additional associated transcriptional changes. These findings, together with insights into propionate degradation kinetics, could inform future strategies aimed at using this bacterium to mitigate propionate buildup and improve the stability of anaerobic treatment systems.},
}

@article {pmid42166056,
year = {2026},
author = {Jayaneththi, U and Sneddon, NW and Burkitt, LL and Jeyakumar, P and Anderson, CWN and Fermin, LM and Donaghy, DJ},
title = {Host Filtering Shapes the Soil-gut Microbiome Linkages in Pastoral Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02791-6},
pmid = {42166056},
issn = {1432-184X},
abstract = {Soil and ruminant gut microbiomes are linked within grazing pastoral systems, yet the strength and direction of these connections under different pasture management systems remain poorly understood. This study characterised bacterial communities in soil and faeces from cattle and sheep grazing standard and diverse pastures managed under contemporary and regenerative practices using 16 S rRNA gene sequencing. Shared bacterial taxa between soil and gut were identified, and their dominance patterns and soil-gut diversity relationships were evaluated using Spearman correlations and Procrustes analyses. Several taxa, including Prevotella copri, Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides uniformis, Clostridium perfringens and Fibrobacter succinogenes were commonly shared between soil and gut but were usually more prevalent in the gut, indicating predominant host‑associated dominance. Soil exhibited significantly greater bacterial alpha diversity than the gut across all treatments, and neither pasture diversity nor management significantly affected soil-gut alpha diversity differences or the contributions of shared taxa. Correlations between soil and gut alpha diversity were weak and non-significant, and correlations for beta diversity between soil and gut varied through time and among treatments without reaching significance. These findings indicate that, although soil-gut microbial connectivity exists, gut communities are primarily shaped by host-related ecological processes and internal filtering, with soil acting mainly as a diverse reservoir and sink for gut-derived taxa. This highlights that host-driven gut microbiomes primarily shape the soil-gut microbiome link, limiting the strong direct influence of pasture diversity or management.},
}

@article {pmid42152548,
year = {2026},
author = {Costa Júnior, PSP and Melo, DS and Buttrós, VH and Magalhães-Guedes, KT and Dias, DR and Schwan, RF},
title = {Coffea arabica Infusion as a Potential Substrate for Kombucha Fermentation Modulates Microbial Populations, Symbiotic Culture of Bacteria and Yeast Ultrastructure, and Functional Attributes: Insights From Machine Learning.},
journal = {Journal of food science},
volume = {91},
number = {5},
pages = {e71117},
doi = {10.1111/1750-3841.71117},
pmid = {42152548},
issn = {1750-3841},
support = {//CNPq/ ; //FAPEMIG/ ; //CAPES/ ; //FINEP/ ; },
mesh = {Fermentation ; *Coffea/chemistry ; *Kombucha Tea/analysis/microbiology ; Machine Learning ; *Yeasts/metabolism ; *Bacteria/metabolism ; Volatile Organic Compounds/analysis ; Lactic Acid/metabolism ; Symbiosis ; Humans ; },
abstract = {Kombucha is traditionally produced from sweetened Camellia sinensis tea fermented by a symbiotic culture of bacteria and yeasts (SCOBY). However, limited information is available on the effects of replacing tea with Coffea arabica infusion on fermentation parameters, microbial ecology, and overall quality of the beverage. This study evaluated the effects of substituting green tea with C. arabica infusion (25%-100%, v/v) during kombucha fermentation on fermentation kinetics, microbial populations, SCOBY structure, and physicochemical, functional, and sensory attributes. Coffee substitution reduced sugar consumption rates without significantly affecting final pH (2.8-3.2) or titratable acidity (∼0.4). Increasing coffee proportions markedly reshaped microbial populations, reducing acetic acid bacteria and increasing lactic acid bacteria, thereby shifting metabolism toward lactic acid production. Structural analyses revealed preserved SCOBY integrity, with a more porous cellulose network in coffee-based formulations. Total phenolic content decreased after fermentation in most treatments, whereas the 100% coffee kombucha remained stable and maintained antioxidant capacity. GC-MS analysis identified 111 volatile compounds, and multivariate and machine learning approaches revealed coffee-associated biomarkers associated with lactic acid and aroma-active compounds. Overall, C. arabica infusion proved to be a suitable alternative substrate for kombucha fermentation, enabling substrate-driven modulation of microbial dynamics and metabolic profiles while maintaining product safety and functional potential. PRACTICAL APPLICATIONS: Replacing green tea with C. arabica infusion in kombucha production enables the development of beverages with differentiated microbial, chemical, and sensory profiles while maintaining fermentation performance and safety. Coffee-based kombucha promotes a shift toward lactic acid-oriented fermentation, distinct aroma signatures, and functionality without requiring significant changes to conventional SCOBY-based processes. From a practical perspective, coffee infusion is a feasible strategy for product diversification, allowing manufacturers to modulate fermentation outcomes through raw material selection and to support the development of innovative, scalable, and consumer-oriented kombucha beverages.},
}

Fermentation
*Coffea/chemistry
*Kombucha Tea/analysis/microbiology
Machine Learning
*Yeasts/metabolism
*Bacteria/metabolism
Volatile Organic Compounds/analysis
Lactic Acid/metabolism
Symbiosis
Humans

@article {pmid42096509,
year = {2026},
author = {Kholwadwala, A and Katkov, E and Lypaczewski, P and Gonzalez, A and Barrett, RDH and Shapiro, BJ},
title = {Nutrient enrichment and connectivity jointly shape bacterioplankton taxonomic and functional diversity.},
journal = {FEMS microbiology letters},
volume = {373},
number = {},
pages = {},
doi = {10.1093/femsle/fnag056},
pmid = {42096509},
issn = {1574-6968},
support = {RGPIN-2019-04549//NSERC/ ; RGPIN-2019-05455//NSERC/ ; //Canada Foundation for Innovation/ ; },
mesh = {*Bacteria/classification/genetics/metabolism ; *Plankton/classification ; *Nutrients/metabolism ; *Biodiversity ; Fresh Water/microbiology ; Ecosystem ; Lakes/microbiology ; },
abstract = {It is increasingly important to understand the response of freshwater communities and ecosystems to fertilizers given their widespread usage and the propensity for these fertilizers to runoff into rivers and lakes. Dispersal, an important ecological factor mediated by landscape connectivity, could potentially counteract the impacts of anthropogenic stressors through the reintroduction of communities unperturbed by local stressors. However, this potential has not yet been studied in the context of nutrient stressed natural communities. Here, we investigate the impacts of nutrient enrichment and connectivity on freshwater bacterioplankton communities. We subjected mesocosms stocked with native bacterioplankton communities to different combinations of nutrient enrichment and connectivity (volumes of water transferred between mesocosms). We show that nutrient enrichment strongly structures the bacterioplankton community, favoring nutrient tolerant taxa and depressing taxonomic diversity. Connectivity, however, interacts with nutrient enrichment to restore functional diversity in communities subjected to the highest levels of nutrient stress. Despite the ameliorating effects of dispersal, nutrient enrichment leaves a consistent signature in communities, driving a shift from more heterotrophic to more phototrophic communities. Taken together, our results demonstrate that while nutrient enrichment significantly impacts freshwater bacterioplankton communities, connectivity can help restore functional diversity to a certain extent.},
}

*Bacteria/classification/genetics/metabolism
*Plankton/classification
*Nutrients/metabolism
*Biodiversity
Fresh Water/microbiology
Ecosystem
Lakes/microbiology

@article {pmid42147301,
year = {2026},
author = {Barbosa, MC and Pellegrinetti, TA and da Cunha, ICM and da Silva, AVR and Marcandalli Boleta, EH and Losovoi, LA and Mendes, R and Tsai, SM and Mendes, LW},
title = {Genotype-dependent stability and specialization of arbuscular mycorrhizal fungal communities under drought in common bean.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1786322},
pmid = {42147301},
issn = {1664-462X},
abstract = {Arbuscular mycorrhizal fungi (AMF) represent a key biological strategy for enhancing agricultural resilience under extreme climatic events such as drought. However, how AMF interact with drought-tolerant plant genotypes to sustain performance under water limitation remains poorly understood. Here, we used high-throughput DNA sequencing to investigate AMF communities associated with drought-tolerant (BAT477 and SEA5) and drought-susceptible (IAC-Milênio and IAC-80SH) common bean genotypes, integrating taxonomic, structural, and functional perspectives under contrasting water regimes. We hypothesized that drought tolerance is not simply linked to AMF presence, but rather to the ability of host genotypes to structure and stabilize their mycorrhizal communities under stress. Our results reveal genotype-specific responses to drought, with distinct community restructuring dynamics observed across individual genotypes. Drought-tolerant genotypes maintained or increased AMF relative abundance, diversity, and functional integrity under drought, whereas susceptible genotypes displayed opposing changes in the community's structure. Although most genotypes displayed high dissimilarity in AMF community structure between control and drought conditions, tolerant genotypes reorganized their communities through increase in the relative abundance of key ASVs, whereas susceptible genotypes experienced substantial reductions in abundance, diversity, and specialist ASVs. Niche occupancy and functional guild analyses further showed that AMF communities in tolerant genotypes were dominated by specialist and symbiotrophic ASVs, whereas susceptible genotypes shifted toward rare and functionally reduced assemblages. At the plant level, AMF community stability was positively associated with root biomass and negatively associated with foliar nutrient, indicating a tight coupling between mycorrhizal community structure, host nutritional status, and growth. Collectively, our findings indicate that drought tolerance in common bean emerges, at least in part, from a cooperative host-microbiome strategy in which the host actively regulates the structure and functional stability of AMF communities under water stress. These results advance our understanding of plant-mycorrhizal interactions in drought adaptation and highlight the potential of integrating mycorrhizal functionality into plant breeding strategies aimed at developing climate-resilient crops.},
}

@article {pmid42148754,
year = {2026},
author = {Heredia, MY and Kuehnert, PA and March, K and Knoll, LJ and O'Leary, CE},
title = {Competition between commensal protists shapes gut mucosal immunity in mice.},
journal = {mBio},
volume = {},
number = {},
pages = {e0080226},
doi = {10.1128/mbio.00802-26},
pmid = {42148754},
issn = {2150-7511},
abstract = {UNLABELLED: Intestinal protists are emerging as key modulators of host immunity and microbial ecology, yet their impact on mammalian hosts remains poorly defined. Here, we investigated the role of two distinct protists, the amoeba Entamoeba muris, and the parabasalid, Tritrichomonas, to determine how they shape gut immunity in vivo individually and together. Unlike the well-characterized inducer of type 2 immunity, Tritrichomonas, which activates the tuft cell-IL-25-ILC2 circuit in the small intestine, E. muris failed to elicit robust immune responses in the intestine or colon. However, the introduction of E. muris into mice naturally colonized by Tritrichomonas spp., or co-infection with E. muris and Tritrichomonas spp. reduced Tritrichomonas-induced type-2 response in the small intestine and Tritrichomonas-dependent immune activation in the colon. Our data suggest that E. muris may limit the abundance of Tritrichomonas spp., with reduced protist loads in the cecum specifically correlating with diminished tuft cell activation. We also identified sex-specific differences in the intestinal response to Tritrichomonas spp., which have not previously been reported. Taken together, these findings reveal that the presence of E. muris reduces Tritrichomonas-dependent activation of type 2 immunity in the small intestine, even when both protists can be detected in the cecum, without triggering overt inflammation. This work provides a framework for understanding how protists interact within the gut ecosystem and shape mucosal immunity in the absence of pathogenicity.

IMPORTANCE: Single-cell parasites called protists are common in mammalian intestinal tracts, yet their modulation of the host immune response and interactions with each other remain poorly defined. Here, we investigated the role of two protists, Entamoeba and Tritrichomonas, to determine how they shape gut immunity individually and together. Unlike the well-characterized inducer of type 2 immunity, Tritrichomonas, which activates the tuft cell circuit, Entamoeba failed to elicit a robust immune response. The introduction of Entamoeba into mice naturally colonized by Tritrichomonas, or co-infection with Entamoeba and Tritrichomonas, reduced the Tritrichomonas-induced immune response. Our data suggest that Entamoeba limits the abundance of Tritrichomonas, correlating with diminished tuft cell activation. We also identified sex-specific differences in the intestinal response to Tritrichomonas. These findings show that Entamoeba reduces Tritrichomonas-dependent activation of type 2 immunity without triggering much inflammation. It helps our understanding of how protists interact within the gut and shape immunity without disease.},
}

@article {pmid42150376,
year = {2026},
author = {Grzesiak, J and Brzykcy, J and Young, P and Krakowska, E and Stasiuk, R and Krakowski, K and Decewicz, P and Kiedryńska, A and Matlakowska, R and Bartosik, D},
title = {Gelidimonas denitrificans gen. nov., sp. nov., and Gelidimonas diazotrophica sp. nov. psychrophilic bacteria involved in the nitrogen cycle in tundra soils of South Spitsbergen.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126730},
doi = {10.1016/j.syapm.2026.126730},
pmid = {42150376},
issn = {1618-0984},
abstract = {Two Gram-negative, psychrophilic, denitrifying bacterial strains, D2 and D11, were isolated from ornithogenic soil collected at a breeding colony of the marine bird Alle alle on Spitsbergen Island, Svalbard (Norway; High Arctic). Complete genome sequencing revealed that each strain possesses a single circular chromosome (3.83 Mbp and 3.63 Mbp, respectively) with similar GC content (55.3% and 55.5%), as well as plasmids - one shared by both strains (26.3 kb) and one unique to strain D11 (16.3 kb). Despite their striking genetic similarity, the two strains exhibit distinct physiological characteristics. Strain D2 is a facultative chemolithoautotroph capable of using hydrogen as an energy source and assimilating carbon dioxide and dinitrogen, whereas strain D11 displays a strictly heterotrophic lifestyle. Although the 16S rRNA genes of D2 and D11 share a high level of sequence identity (99.6%), whole-genome comparative analyses, including digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), indicated that they represent two distinct species within the family Oxalobacteraceae (class Betaproteobacteria). Core proteome-based phylogenetic analysis of Oxalobacteraceae unambiguously placed both strains within the family; however, neither clustered with any currently described genus. We therefore propose that these strains represent a novel genus, Gelidimonas gen. nov., with type species Gelidimonas denitrificans sp. nov. (type strain D11[T]) and a second species Gelidimonas diazotrophica sp. nov. (type strain D2[T]).},
}

@article {pmid42150526,
year = {2026},
author = {Thompson, LR},
title = {Microbial ecology: Rise of the planet of the microbes.},
journal = {Current biology : CB},
volume = {36},
number = {10},
pages = {R432-R434},
doi = {10.1016/j.cub.2026.03.072},
pmid = {42150526},
issn = {1879-0445},
mesh = {*Microbiota/genetics ; Metagenomics ; Ecosystem ; *Bacteria/genetics ; *Metagenome ; },
abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.},
}

*Microbiota/genetics
Metagenomics
Ecosystem
*Bacteria/genetics
*Metagenome

@article {pmid42151475,
year = {2026},
author = {Kobiałka, M and Świerczewski, D and Walczak, M and Pisarek-Pacek, A and Wóycicki, RK},
title = {Complementary Microscopic and Metabarcoding Studies Allow for a Better Understanding of the Symbiotic Microbiome of Leafhopper Species Iassus lanio (Hemiptera, Cicadellidae).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02790-7},
pmid = {42151475},
issn = {1432-184X},
support = {Sonata 17, project no. 2021/43/D/NZ8/02183//National Science Centre, Poland/ ; },
abstract = {Leafhoppers' microbiome patterns were shaped by deep co-evolutionary adaptation driven by dietary specialization. Their microbiome is dominated by obligate symbionts that supplement their nutrient-poor phloem-sap diet, as well as facultative symbionts, including both bacterial and fungal microorganisms. In this study, NGS metabarcoding techniques were performed, supplemented by confocal and electron microscopy, to thoroughly investigate the symbiotic system of the Auchenorrhyncha species Iassus lanio, a representative of the poorly studied leafhopper subfamily Iassinae. The obtained results include descriptions of the composition, distribution, and ultrastructure of microorganisms, as well as the phylogeny of ancient symbionts. Two obligate symbionts were found: the ancient Auchenorrhyncha symbiont Karelsulcia bacterium and the yeast-like symbiont Ophiocordyceps. Karelsulcia bacteria occur exclusively in specialized organs called bacteriomes, while fungal microorganisms inhabit mycetocytes within the fat body. Both symbionts are transmitted transovarially from mother to offspring. The presence of Wolbachia, Sodalis and Cardinium was detected. Sodalis and Cardinium were observed in the fat body. The ultrastructure of Cardinium showed a characteristic microtubule crest inside. The obtained phylogeny of Karelsulcia bacteria indicates Iassinae affinity with the Coelidiinae and Deltocephalinae subfamily symbionts. Taxonomic profiling revealed that both sequencing methods detected the same range of bacterial taxa, while ONT exhibited improved resolution for dominant species. Differential abundance analysis emphasized platform-specific biases. These studies highlight the complementary roles of different microscopy and metabarcoding techniques, demonstrating the complexity of symbiotic systems in leafhoppers and thereby improving our understanding of the host-symbiont relationship and expanding our knowledge of the structure and localization of insect microorganisms.},
}

@article {pmid42152232,
year = {2026},
author = {Mortier, F and Bafort, Q and Bonte, D and Van de Peer, Y},
title = {Repeatability of phenotypic consequences due to whole-genome duplication in Spirodela polyrhiza.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71256},
pmid = {42152232},
issn = {1469-8137},
support = {BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; 1238124N//Fonds Wetenschappelijk Onderzoek/ ; 833522//H2020 Excellent Science/ ; },
abstract = {Whole-genome duplication (WGD) is widespread in plants, yet the extent to which it yields predictable phenotypic outcomes remains unclear. Here, we show that the phenotypic consequences of genome doubling in a duckweed model system, Spirodela polyrhiza, are highly repeatable and largely deterministic. We previously generated three independent colchicine-induced autotetraploids from each of nine globally distributed diploid genotypes and now quantified growth and morphology across a salt gradient. In benign conditions, diploids grew faster, whereas tetraploids had larger, thicker fronds. As salinity increased, the diploid growth advantage diminished, and tetraploids frequently matched or exceeded diploid growth rates. By partitioning the components of variance in growth in our experimental design, we found that ploidy per se explained a comparable amount of phenotypic variation in growth and substantially more variation in salt tolerance than the genotypic background, with evidence of rare within-genotype stochastic differences between tetraploids. These results indicate that the shifts in morphology and stress tolerance from genome doubling are predictable and can match the phenotypic effect from genetic sequence diversity.},
}

@article {pmid42140125,
year = {2026},
author = {Lv, Y and Wang, W and Liu, Z and Ji, Y and Liu, X},
title = {Divergent fates: Polystyrene microplastics alter trifloxystrobin degradation and microbial ecology differently in agricultural soil vs. river sediment.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120268},
doi = {10.1016/j.ecoenv.2026.120268},
pmid = {42140125},
issn = {1090-2414},
abstract = {This study investigates the effects of polystyrene microplastics (PS-MPs) on trifloxystrobin (TRI) degradation behavior and microbial community structure in agricultural soil and river sediment. Degradation kinetics and machine learning modeling (R[2] > 0.95) revealed that PS-MPs significantly inhibited TRI dissipation, with biological degradation identified as the primary driver. Specifically, the half-life of TRI was prolonged from 2.7 to 9.7 days to 4.0-18.1 days in soil, and from 3.1 to 8.3 days to 4.8-9.7 days in sediment. Trifloxystrobin acid remained the major transformation product overall, though a unique cyanide-containing compound appeared exclusively in sediment, suggesting distinctive metabolic routes. 16S rRNA sequencing showed that TRI and PS-MPs significantly altered the bacterial community structure. The PS-MPs treatment significantly reduced the relative abundance of potential TRI degrading bacteria, such as Sphingomonas and Pseudomonas, which is related to the observed delayed degradation. Microbial network analysis further revealed that TRI simplified the soil microbial network, reducing the number of nodes and connections by about 7%, while PS-MPs increased the complexity of the sediment network, increasing the number of nodes and connections by about 36%. These findings provide quantitative insights into the comprehensive ecological risks of microplastics and fungicides in different environmental matrices.},
}

@article {pmid42140850,
year = {2026},
author = {Fagundes, D and Costa, LMS and Cagliari, A and de Vargas, DP and Rieger, A},
title = {Microbial Community Shifts and Plant Performance Improvements Driven by Bacillus firmus in Pampa Agroecosystems.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70315},
pmid = {42140850},
issn = {1758-2229},
mesh = {*Bacillus/physiology ; *Soil Microbiology ; *Microbiota ; Rhizosphere ; *Glycine max/growth & development/microbiology/parasitology ; Plant Roots/growth & development/microbiology ; Animals ; Fungi/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Nematoda ; Ecosystem ; Soil ; },
abstract = {The impact of Bacillus firmus-based bionematicides on rhizosphere microbiota and plant performance remains poorly understood in complex agroecosystems. This study evaluated the effects of B. firmus application on soil microbial communities, nematode dynamics, and soybean productivity in the Pampa biome. Our results demonstrate that B. firmus significantly modulates the composition and diversity of soil microbiota, with effects varying across locations and over time. Treated areas exhibited shifts in bacterial communities, including increased abundance of beneficial taxa, while fungal diversity tended to decrease, likely due to the combined effect of the fungicide used in seed treatment. Despite persistent populations of target nematodes such as Pratylenchus brachyurus and Heterodera glycines, treated areas showed reduced root infestation in specific stages and locations. Importantly, the application of B. firmus consistently enhanced soybean shoot and root growth, resulting in productivity gains of 6%-7% across all sites. These findings reveal that B. firmus not only contributes to plant growth promotion but also induces significant, yet context-dependent, shifts in rhizosphere microbial communities. The study highlights the ecological complexity of microbial responses to biocontrol agents and underscores the importance of integrating microbiome dynamics into sustainable nematode management strategies in agroecosystems.},
}

*Bacillus/physiology
*Soil Microbiology
*Microbiota
Rhizosphere
*Glycine max/growth & development/microbiology/parasitology
Plant Roots/growth & development/microbiology
Animals
Fungi/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification
Nematoda
Ecosystem
Soil

@article {pmid42141775,
year = {2026},
author = {Zhou, F and Wang, L and Zhao, Y and Hu, C and Meng, Y and Fan, J and Fraser, WD and Baillargeon, JP and Ouyang, F and Lye, SJ and Dennis, CL and Shen, J and Wu, Y and Huang, H},
title = {Antenatal depressive symptoms impair offspring neurodevelopment by inducing maternal gut microbiota dysbiosis during pregnancy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2672188},
doi = {10.1080/19490976.2026.2672188},
pmid = {42141775},
issn = {1949-0984},
mesh = {Female ; Pregnancy ; Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; *Depression/microbiology/complications ; Fecal Microbiota Transplantation ; Adult ; Case-Control Studies ; *Pregnancy Complications/microbiology/psychology ; Prospective Studies ; Butyrates/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Prenatal Exposure Delayed Effects ; Feces/microbiology ; Infant ; Brain/growth & development/metabolism ; *Neurodevelopmental Disorders/etiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The effects of maternal antenatal depression (AND) across different stages of pregnancy on offspring neurodevelopment remain poorly understood, and the underlying microbiota-related mechanisms are largely unknown. In a multicenter prospective cohort of 2053 pregnant women, we found that elevated depressive symptoms at any trimester were significantly associated with delayed infant neurodevelopment. Using a nested case‒control design with 16S rRNA sequencing of 504 maternal fecal samples, we identified a consistent reduction of butyrate-producing bacteria and disruption of amino acid metabolism in women with AND symptoms - features that correlated with poorer infant cognitive outcomes. To establish causality, fecal microbiota transplantation (FMT) from women with AND symptoms was administered to germ-free dams, resulting in impaired intestinal barrier integrity, heightened neuroinflammatory signaling, and altered polyunsaturated fatty acid and amino acid metabolism in fetal brains at E18.5, leading to postnatal cognitive deficits in the offspring. Remarkably, maternal butyrate supplementation partially rescued these molecular and neurodevelopmental abnormalities. Together, these findings reveal a mechanistic link between maternal mood, gut microbial ecology, and fetal brain development, and identify the maternal gut microbiota and its metabolites as potential therapeutic targets to prevent the intergenerational effects of antenatal depression.},
}

Female
Pregnancy
Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
*Depression/microbiology/complications
Fecal Microbiota Transplantation
Adult
Case-Control Studies
*Pregnancy Complications/microbiology/psychology
Prospective Studies
Butyrates/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism
*Prenatal Exposure Delayed Effects
Feces/microbiology
Infant
Brain/growth & development/metabolism
*Neurodevelopmental Disorders/etiology
RNA, Ribosomal, 16S/genetics

@article {pmid42143132,
year = {2026},
author = {Rescan, M and Dachs Rojo, M and Borrego, CM},
title = {Gene expression plasticity under multiple stresses drives higher tolerance to a macrolide in saline and warmer environments.},
journal = {npj antimicrobials and resistance},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44259-026-00214-7},
pmid = {42143132},
issn = {2731-8745},
support = {101062450//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; },
abstract = {The widespread presence of antibiotics in the environment at sub-inhibitory concentrations imposes a selective pressure that promotes the spread of resistance. In the field, antibiotics interact with diverse physicochemical parameters that can attenuate or intensify their fitness effects. Gene expression is a central plastic trait that governs phenotypes at a higher level of integration and modulates the strength of selection, yet how synergistic or antagonistic fitness effects arise from interactions among transcriptional responses remains poorly understood. Here, we characterized gene-expression interactions underlying fitness-level interactions previously identified between a macrolide, temperature and salinity, and proposed a general methodological framework for assessing the impact of multiple stressors on gene expression. We analyzed the transcriptional response of Escherichia coli to azithromycin (AZI) across two salinity and temperature conditions. De novo and antagonistic interactions were prevalent, with evidence of cross-regulations between salt and AZI. High salinity increased tolerance by two orders of magnitude and, similarly to AZI, induced a downregulation of carbon metabolism. Reduced temperature, which canceled the salinity protective effect, enhanced carbon metabolism and counteracted this shift. Salinity additionally restored stress-response pathways, largely repressed by AZI. Third-order interactions attenuated the contribution of salinity relative to AZI, but the number of affected genes declined exponentially with interaction order, suggesting that higher-order interactions at the gene-expression level should play a minor role in the responses to multiple stressors. By modulating transcriptional responses to AZI, simple environmental parameters could reshape the adaptive landscape of antibiotic resistance, potentially altering the spectrum of resistance mutations likely to spread.},
}

@article {pmid42143576,
year = {2026},
author = {Xu, X and Tan, Y and Xiecun, S and Wang, J and Zhao, W and Wang, L and Dai, R and Tang, L and Li, X and Jin, D and Fan, Y},
title = {Galactosaminogalactan orchestrates Verticillium dahliae virulence and rhizosphere microbial ecology through multi-partite interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag123},
pmid = {42143576},
issn = {1751-7370},
abstract = {The infection of plants by soil-borne fungal pathogens is a complex process and depends on their adhere ability to host surfaces and interactions with the rhizosphere bacteria. In this study, we identify galactosaminogalactan (GAG) as a pivotal virulence determinant in the pathogenesis of Verticillium dahliae. By characterizing the VdGAG biosynthetic gene cluster, we show that the glycosyltransferase VdGtb is essential for GAG synthesis. The knockout of GAG increased fungal sensitivity to the cell wall-perturbing agent calcofluor white (CFW) and reduced mycelial ball formation in liquid culture. The absence of GAG polysaccharides reduced root-binding capacity by 50% and increased cotton immune responses 1 day post fungal infection. The ΔVdGtb mutant exhibited a significant 30.5% decrease in the pathogenicity toward cotton seedlings compared with the wild type V991. Microbiome and bacterial enrichment analysis indicate that the GAG polysaccharides promote the enrichment of soil bacteria and alter the bacterial community structure in the plant rhizosphere. Several bacteria enriched by GAG-contained fungal cells, including Achromobacter animicus, Pseudomonas aeruginosa, and Acinetobacter pittii exhibited strong growth-inhibitory effects against V. dahliae and showed distinct effects on fungal virulence in a GAG-dependent manner. Together, these results reveal that GAG is not merely a cell wall component but a multi-functional molecule that orchestrates fungal protection, host infection, and inter-kingdom microbial communication.},
}

@article {pmid42144578,
year = {2026},
author = {Pinheiro, Â and Martins, TM and Varela, A and Domingos, P and Escórcio, R and Bento, A and Martins, I and Afonso, CAM and Silva Pereira, C},
title = {Extremotolerant fungi in resinous soils: a unique diversity of generalists and specialized hydrocarbon degraders.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05128-y},
pmid = {42144578},
issn = {1471-2180},
support = {CENTRO-01-0247-FEDER-072630//European Regional Development Fund/ ; },
abstract = {Filamentous fungi are ubiquitous and constitute more than 75% of the soil biomass. Fungal diversity increasingly emerges as a key factor in soil ecosystem resilience against climate change and pollution, yet much of this diversity remains hidden and potentially in decline. While investigations have primarily focused on fungal tolerance to extreme physical conditions, such as temperature and salinity, chemically stressed environments remain underexplored reservoirs of novel fungal diversity. These habitats may harbor strains with significant biotechnological potential. This study tested the hypothesis that long-term contamination of soil with Pinus resin alters fungal diversity and promotes the growth of specialized fungal lineages enriched in hydrocarbon-degrading capabilities. We analyzed a resinous soil sample collected from an inactive resin processing site undisturbed for nearly 50 years. Initial physicochemical and microscopy analyses confirmed the presence of viable fungi despite extreme environmental constraints. High-throughput sequencing of fungal ITS2 regions revealed a fungal community composition highly distinct from adjacent forest soil, characterized by unusual taxonomic profiles and a high proportion of poorly classified or novel lineages. Functional inference and taxonomic analyses identified hydrocarbon-associated taxa including Sorocybe resinae (one of the most abundant OTUs) and Amorphotheca resinae (detected at low abundance). These fungi are known resinicolous and extremophilic species, illustrating the unique ecological adaptation of fungi within resin-rich, chemically stressful soils.},
}

@article {pmid42146037,
year = {2026},
author = {Sun, L and Wang, X and Long, Y and Wang, X and Niu, X and Li, H and Taethaisong, N and Meethip, W and Paengkoum, S and Paengkoum, P},
title = {A review on the use of coconut oil to mitigate methane emissions in ruminants: mechanisms of action and research progress.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1774322},
pmid = {42146037},
issn = {2297-1769},
abstract = {Methane (CH4) generated during ruminal fermentation in ruminants is a major contributor to greenhouse gas emissions and represents a substantial loss of dietary energy. Therefore, mitigating enteric CH4 emissions through safe and efficient nutritional strategies is of considerable ecological and economic significance. Coconut oil (CO) has received increasing attention due to its distinctive fatty acid profile. Accumulating evidence indicates that the medium-chain fatty acids (MCFA) abundant in CO exert direct inhibitory effects on rumen protozoa and methanogenic archaea, thereby conferring strong antimethanogenic potential. However, the CH4 mitigation efficacy of CO is often accompanied by trade-offs related to rumen microbial ecology, animal productive performance, and the nutritional quality of animal-derived products, particularly at higher doses where fiber digestibility and dry matter intake (DMI) may decline. Consequently, a clearer definition of safe and effective inclusion levels across different ruminant species and production stages is needed. This review systematically summarizes the physicochemical properties and safety of CO, with particular emphasis on its mechanisms of action within the rumen. Furthermore, current application studies and future research prospects of CO in ruminant production are discussed, providing a scientific reference for its use in nutritional strategy to lower methane in ruminant systems.},
}

@article {pmid42146303,
year = {2026},
author = {Maity, A and Bhowmik, R and Das, A and Trivedi, S and Mondal, SK and Gupta, AD and Paul, P and Das, S and Chakraborty, P and Tribedi, P},
title = {Cuminaldehyde potentiates antimicrobial efficacy of gentamicin and ciprofloxacin against Escherichia coli: a response surface methodology (RSM) based study.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {193},
pmid = {42146303},
issn = {2190-572X},
abstract = {UNLABELLED: The increasing prevalence of antibiotic resistance poses a serious threat to public health, significantly reducing the effectiveness of conventional antibiotics against bacterial infections, particularly those caused by multidrug-resistant Escherichia coli (E. coli). As monotherapy becomes increasingly unreliable due to the rapid evolution of resistance, combination therapy has emerged as a promising strategy to address this challenge. In this context, the present study aimed to evaluate the effect of cuminaldehyde (CA) in combination with two conventional antibiotics, gentamicin (GN) and ciprofloxacin (CF), against five drug-resistant clinical strains of E. coli. In silico analyses using PASS Online, SwissADME, ProTox 3.0, and Osiris predicted the potential antimicrobial properties of the test compounds. In vitro investigations further demonstrated significant antimicrobial activity, with minimum inhibitory concentration (MIC) values ranging from 400 to 450 µg/mL for CA, 6-8 µg/mL for GN, and 2-3 µg/mL for CF against different E. coli strains. Furthermore, fractional inhibitory concentration index (FICI) analysis revealed that diverse interaction patterns, including synergistic effects, exist between CA and the conventional antibiotics. To optimize these combinations, response surface methodology (RSM) was employed to determine the optimal doses of the test compounds. The experimental validation of the RSM model showed high predictive accuracy (98-99%), confirming its robustness and reliability. Overall, the present findings successfully identified potent synergistic triple-drug combinations exhibiting significant inhibitory effects against drug-resistant E. coli, thereby proposing a promising approach for developing effective therapeutic strategies to combat antibiotic resistance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04832-w.},
}

@article {pmid42137812,
year = {2026},
author = {Pane, M and De Prisco, A and Amoruso, A and Deusebio, G and Marzorati, M and Corazzari, M and Monzani, R and Saverio, V and Bron, PA},
title = {Probiotic detoxification of heavy metals: functional assessment in simulated intestinal and ex vivo models.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821114},
pmid = {42137812},
issn = {1664-302X},
abstract = {INTRODUCTION: Bioremediation is an emerging, sustainable strategy that relies on microbial processes to detoxify environmental pollutants. Among these pollutants, heavy metals (HMs) are pervasive, non-degradable toxic elements that pose serious risks to human health. In this study, we individually evaluated three probiotic lactobacilli strains-Lactiplantibacillus plantarum LP14, Lactobacillus crispatus LCR04, and Lactobacillus acidophilus LA12-for their capacity to detoxify cadmium, chromium, mercury, and lead in the gastrointestinal (GI) tract, as well as their capacity to mitigate heavy metal-induced intestinal damage, with a single-strain product strategy in mind.

METHODS: After initial selection of the strains for their in vitro detoxifying potential, we employed a dynamic Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) model and each strain's survival, growth, and heavy metal detoxification capacity was assessed under sequential gastric, small-intestinal, and colonic conditions.

RESULTS: Strain- and metal-specific differences in HMs sequestration emerged: L. plantarum LP14 and L. crispatus LCR04 showed robust persistence and significantly reduced HMs bioavailability, whereas L. acidophilus LA12 displayed minimal detoxification under GI simulation. Mechanistically, only the strains that proliferated in the colonic phase achieved substantial HM removal, underscoring the importance of metabolic activity in situ. In a gut ex vivo system (GEVS), heavy metal exposure alone compromised epithelial barrier integrity and triggered pro-inflammatory responses. Pre-incubation of the HMs with each of the probiotic strains markedly alleviated these effects, restoring intestinal permeability and cytokine profiles.

DISCUSSION: Overall, the results demonstrate a novel probiotic-based intestinal bioremediation strategy and highlight the translational potential of targeted single-strain probiotic interventions, reducing heavy metal exposure to protect gut health.},
}

@article {pmid42139623,
year = {2026},
author = {Khudhair, HM and Alhamdani, ASH and Al Tameemi, AMH},
title = {Microbiology of dental decay and periodontal disease: A review.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {4},
pages = {829-846},
doi = {10.36740/WLek/216932},
pmid = {42139623},
issn = {0043-5147},
mesh = {Humans ; *Periodontal Diseases/microbiology/therapy ; *Dental Caries/microbiology/therapy ; Biofilms ; Porphyromonas gingivalis/pathogenicity ; Mouth/microbiology ; },
abstract = {OBJECTIVE: Aim: This review attempts to examine the microbiology, pathogenesis and current therapeutic approaches of dental caries and periodontal diseases with a special focus on the role of polymicrobial biofilms, the host-microbe interaction and the major pathogenic species involved in disease progression.

PATIENTS AND METHODS: Materials and Methods: A thorough literature review was performed using major scientific databases such as PubMed, Scopus, Web of Science and Google Scholar. Studies that were published between 2000 and 2025 were included. Relevant experimental, clinical and review articles that focused on the etiology, microbial composition, virulence mechanisms, host immune responses and therapeutic approaches of dental caries and periodontal disease were analyzed.

CONCLUSION: Conclusions: The oral cavity harbors over 700-800 bacterial species, of which the primary cariogenic pathogen is Streptococcus mutans and Porphyromonas gingivalis has been implicated as a major cause of periodontal disease. Dental caries progression is mostly attributed to acid production and demineralization of enamel, whereas periodontal disease is a result of dysbiotic shift in the subgingival microbiome with destructive host inflammatory responses. The "red complex" (P. gingivalis, Treponema denticola and Tannerella forsythia) has a high degree of synergistic virulence in advanced periodontitis. Biofilm formation, production of extracellular polysaccharide (EPS) matrix, quorum sensing and immune components (neutrophils, macrophages and matrix metalloproteinases or MMPs) are all factors that contribute to disease formation. Prevention strategies include oral hygiene measures, fluoride exposure, dietary modification, and antimicrobial agents, whereas treatment measures include mechanical debridement, systemic antibiotics, antimicrobial peptides, probiotics, and photodynamic therapy. Dental caries and periodontal diseases are the result of complex interactions between polymicrobial biofilms and immune responses by the host. A better understanding of the microbial ecology, virulence pathways and host-pathogen interactions is crucial in the process of improving prevention and treatment. Advances in targeted antimicrobial therapies and innovative therapeutic approaches hold promise for enhancing global oral health outcomes.},
}

Humans
*Periodontal Diseases/microbiology/therapy
*Dental Caries/microbiology/therapy
Biofilms
Porphyromonas gingivalis/pathogenicity
Mouth/microbiology

@article {pmid42136267,
year = {2026},
author = {Saraswati, BD and Wicaksono, AW and Valles, SL and Poeggeler, B and Singh, SK},
title = {Exploring the Gut Microbiome as a Promising Frontier in Alzheimer's Disease Therapy.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X444975260408044214},
pmid = {42136267},
issn = {1875-6190},
abstract = {Alzheimer's Disease (AD) is a major global health challenge, particularly in ageing populations, and current therapies offer limited modification of disease progression. Emerging evidence indicates that the gut microbiome contributes to AD pathogenesis through metabolic, immune, and neuroendocrine mechanisms. Microbial metabolites, including Short-Chain Fatty Acids (SCFAs), bile acids, and trimethylamine-N-oxide (TMAO), regulate neuronal signalling and blood-brain barrier integrity, and dysbiosis has been linked to amyloid-β (Aβ) accumulation, tau hyperphosphorylation, chronic neuroinflammation, oxidative stress, and synaptic dysfunction. Host genetic factors, particularly APOE ε4 and immune-regulatory variants such as TREM2 and CD33, further influence microbial composition and susceptibility to metabolite-driven pathology. This review provides a deeper synthesis of current evidence by integrating findings across multi-omics studies and identifying key unresolved issues in the microbiome-AD field. The discussion evaluates whether microbiome alterations act as early initiators or downstream consequences of neurodegeneration, examines sources of heterogeneity in microbiome-targeted interventions, and considers how inter-individual variability in host genetics and microbial ecology may inform precision therapeutics. Conceptual frameworks presented here, including a two-phase dysbiosis trajectory and a metabolite "tipping-point" network, aim to reconcile conflicting results and support the development of testable mechanistic hypotheses. Microbiome-directed strategies, such as probiotics, prebiotics, dietary modulation, faecal microbiota transplantation, and antiviral therapies, demonstrate promise but require rigorous mechanistic validation and methodological standardisation. Continued advancement in longitudinal, genotype-stratified, and multi-omics research will be essential for translating microbiome science into clinically actionable approaches. Overall, current evidence positions the gut microbiome as a compelling frontier for the development of personalised, diseasemodifying strategies in AD.},
}

@article {pmid42128003,
year = {2026},
author = {Gutsfeld, S and Wray, C and Schweiger, N and Röhrig, A and Paschke, H and Fu, Q and Kasmanas, JC and Abdulkadir, N and Kader, S and Rocha, U and Ebert, A and Tal, T},
title = {N-Ethyl Perfluorooctane Sulfonamide (N-EtFOSA) Exposure Alters Microbiome Composition and Causes Microbiome-Dependent Behavior Effects in Larval Zebrafish.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16330},
pmid = {42128003},
issn = {1520-5851},
abstract = {We hypothesized that host-associated microorganisms can alter host behavior by modifying perfluorooctane sulfonamides to produce perfluorooctanesulfonic acid (PFOS) or other potentially neuroactive metabolites. Zebrafish larvae (Danio rerio) were exposed to PFOS (0.28-5 μM), N-ethyl perfluorooctane sulfonamide (N-EtFOSA, 0.07-1.25 μM), or perfluorooctane sulfonamido ammonium iodide (PFOSAmS, 0.83-15 μM) from 5 to 6 days post fertilization (dpf). This resulted in altered dark-phase swimming behavior at 8 dpf. Exposure to PFOS, or N-EtFOSA, but not PFOSAmS caused a similar shift in community structure. We exposed microbiome-depleted (axenic, AX), conventionally colonized (CC), or axenic conventionalized on day 1 (AC1) zebrafish larvae to N-EtFOSA (0.22-0.7 μM) from 5 to 6 dpf. In comparison to CC and AC1 larvae, AX-larvae did not exhibit concentration-dependent hypoactivity at 8 dpf. Chemical analysis at 7 dpf revealed a significant increase in N-EtFOSA levels in AX-larvae and AX-water samples, relative to colonized cohorts. The main metabolite detected was perfluorooctane sulfonamide (FOSA), which was not microbiome-dependent. Perfluorooctane sulfonamidoacetic acid (FOSAA) was detected at lower levels in AX-larvae, relative to colonized groups. This study revealed that the presence of the microbiome enhanced N-EtFOSA-dependent behavior effects at the level of the host. This supports the concept that chemical-microbiome interactions can influence host phenotypic outcomes.},
}

@article {pmid42129350,
year = {2026},
author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D},
title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01626-2},
pmid = {42129350},
issn = {2730-664X},
abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.

OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.

DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n = 197) received either de-chlorinated drinking water via benchtop filtration (treatment, n = 99), or regular chlorinated water (control, n = 98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.

RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p = 0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p = 0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p = 0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p < 0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.

CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.

TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.},
}

@article {pmid42129646,
year = {2026},
author = {Mannan, SJ and Roqunuzzaman, M and Mannan, ABA and Begum, K and Yasmin, M and Yihune, E and Al-Mutairi, AA and Zaki, MEA and Ahsan, CR},
title = {Exploring genetic variations and plasmid diversity in Escherichia coli strains isolated from Hospital Wastewater.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42129646},
issn = {1471-2164},
mesh = {*Wastewater/microbiology ; *Escherichia coli/genetics/isolation & purification/pathogenicity/classification ; *Plasmids/genetics ; *Genetic Variation ; Hospitals ; Polymorphism, Single Nucleotide ; Phylogeny ; Drug Resistance, Multiple, Bacterial/genetics ; beta-Lactamases/genetics ; Whole Genome Sequencing ; },
abstract = {The multidrug-resistant (MDR) Escherichia coli, particularly β-lactamase producing strains, has become a global health challenge, where wastewater systems, specially from hospitals, serve as critical reservoirs for the dissemination of resistance genes. The objectives of the study were to investigate the whole genome sequence diversity and genetic variations focusing on their evolutionary relationships, genetic similarity, and single nucleotide polymorphisms (SNPs) of pathogenic β-lactamase producing E. coli strains. A total of four β-lactamase producing E. coli strains, from differently located tertiary care hospitals, were included in this study. A heatmap of genetic similarity revealed near-identical genetic makeup among the strains. A number of genes including AcrAB-TolC, β-lactamases, and resistance determinants such as glpT, gyrA, msbA, and tet(M) were identified in these strains. However, the presence of virulence genes of the aerobactin synthesis gene (iucA, iutA) and type III secretion systems (espX1, espX4, espX5) in the strain has the potential for pathogenicity. These resistance genes were identified at the genomic level; however, their transcriptional expression was not evaluated and the detection of virulence-associated genes suggests that the isolates have the potential to cause disease and pathogenicity. These findings provide insights into the whole genome sequence diversity of E. coli in urban based tertiary care hospital wastewater, emphasizing the genetic variation and plasmid diversity in these E. coli strains, which may have implications in public health and microbial ecology of the environment.},
}

*Wastewater/microbiology
*Escherichia coli/genetics/isolation & purification/pathogenicity/classification
*Plasmids/genetics
*Genetic Variation
Hospitals
Polymorphism, Single Nucleotide
Phylogeny
Drug Resistance, Multiple, Bacterial/genetics
beta-Lactamases/genetics
Whole Genome Sequencing

@article {pmid42133112,
year = {2026},
author = {S, S and V, SP and B, R and C, S and N, S and P, C},
title = {Impact of lifestyle on salivary microbiota composition and antibiotic resistance in adult periodontitis patients.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42133112},
issn = {1572-9699},
support = {RGP/2019-20/BDU/HECP-0042//Tamil Nadu State Council for Higher Education/ ; },
mesh = {Humans ; *Saliva/microbiology ; Adult ; *Life Style ; *Periodontitis/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Male ; Female ; *Microbiota/drug effects ; Middle Aged ; *Bacteria/drug effects/classification/isolation & purification/genetics ; Microbial Sensitivity Tests ; *Drug Resistance, Microbial ; *Drug Resistance, Bacterial ; Dysbiosis/microbiology ; },
abstract = {Adult periodontitis is a chronic inflammatory disease characterized by microbial dysbiosis and host-microbe imbalance in the oral cavity. In this study, the composition and antibiotic susceptibility of the salivary microbiota in adults with mild periodontitis were analyzed to emphasize the influence of lifestyle factors on microbial ecology and resistance trends. Saliva samples collected from clinically diagnosed individuals were analyzed using selective culture-based methods and the Kirby-Bauer disc diffusion assay. Statistical analyses were performed to evaluate interspecies growth variability and antimicrobial responses. It revealed distinct salivary microbial profiles in patients with periodontitis compared to those of healthy individuals. Fusobacterium nucleatum exhibited the highest optical density, indicating increased proliferation and potential involvement in disease progression. Lifestyle variables, particularly smoking and dietary habits, significantly influenced microbial composition (r = 0.73 for smoking; r = 0.59 for tobacco use). Antibiotic susceptibility testing has revealed substantial interspecies variation, with ciprofloxacin and tetracycline showing the highest inhibitory efficacy, whereas azithromycin and clindamycin were largely ineffective. Moderate positive correlations between Prevotella, Clostridium, and F. nucleatum (r = 0.61-0.65) suggest possible shared resistance mechanisms or ecological adaptation. Overall, combined effects of behavioral and microbial factors can shape early periodontal dysbiosis and antibiotic resistance.},
}

Humans
*Saliva/microbiology
Adult
*Life Style
*Periodontitis/microbiology/drug therapy
Anti-Bacterial Agents/pharmacology
Male
Female
*Microbiota/drug effects
Middle Aged
*Bacteria/drug effects/classification/isolation & purification/genetics
Microbial Sensitivity Tests
*Drug Resistance, Microbial
*Drug Resistance, Bacterial
Dysbiosis/microbiology

@article {pmid42135341,
year = {2026},
author = {Huang, Y and Hong, L and Li, S and Zhang, L and Guo, X and Han, J and Yu, W and Chen, H and Luo, N and Chen, J and Peng, W and Zhou, Y and Hong, S and Yan, W and Jiang, S and Cao, Y},
title = {Neonatal intensive care unit exposures reprogram microbiome-metabolome trajectories and modulate host calprotectin in preterm infants: a longitudinal multi-omics study.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01008-5},
pmid = {42135341},
issn = {2055-5008},
support = {82402017//National Key Research and Development Program of China/ ; 82402017//National Key Research and Development Program of China/ ; },
abstract = {Early-life gut microbiota development is critical for orchestrating mucosal barrier function and immune priming, as disruptions in this process can increase susceptibility to life-threatening diseases such as necrotizing enterocolitis (NEC) and sepsis. This longitudinal multi-omics study of 186 preterm infants (<32 weeks of gestation or <1500 g birth weight) explores the impact of early-life exposures in the neonatal intensive care units (NICUs) on gut microbiota, metabolism, and immune responses. We analyzed 1153 stool samples using quantitative microbial profiling, untargeted metabolomics, and fecal S100A8/A9 (calprotectin) levels. Antibiotic exposure suppressed anaerobic colonization and microbial diversity in a cumulative exposure-dependent manner, with breastmilk feeding partially mitigating these effects. The stool metabolome correlated with microbial colonization, showing antibiotic-driven disruptions in polyamine metabolism linked to anaerobe abundance. Host calprotectin levels followed a biphasic pattern, correlating with microbial diversity and polyamine metabolites. Mediation analysis identified anaerobe suppression and polyamine depletion as key drivers of antibiotic-associated reductions in calprotectin. This study reveals that NICU interventions, particularly antibiotics, reprogram the preterm gut ecosystem and immune response, with anaerobes and polyamines being key mediators linking microbial ecology to immune maturation during early life.},
}

@article {pmid42123938,
year = {2026},
author = {Chiang, CK and Lai, CL and Chiu, MH and Huang, CJ},
title = {The Gut-Lung Axis in Allergic Asthma: A Narrative Review of Microbial Dysbiosis, Immune Regulation, and Nutritional Modulation.},
journal = {Nutrients},
volume = {18},
number = {9},
pages = {},
pmid = {42123938},
issn = {2072-6643},
support = {CGH-MR-B-11316//Cathay General Hospital/ ; },
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Asthma/immunology/microbiology ; *Lung/immunology/microbiology ; Animals ; Diet ; },
abstract = {Allergic asthma is a prevalent chronic inflammatory disease of the airways whose pathogenesis has traditionally been attributed to localized immune dysfunction within the lung. However, accumulating evidence from microbiome research supports a broader system-level perspective in which cross-organ interactions contribute to disease susceptibility and progression. In particular, the gut-lung axis has emerged as a key regulatory pathway linking intestinal microbial ecology, immune development, and respiratory health. This review synthesizes current epidemiological, mechanistic, and experimental evidence supporting the role of gut microbiota dysbiosis in allergic asthma. We examine how early-life environmental and nutritional exposures and gut microbiota establishment during critical developmental windows shape long-term immune tolerance and asthma susceptibility. We then summarize characteristic features of asthma-associated gut dysbiosis and discuss how microbial-derived metabolites, including short-chain fatty acids, tryptophan metabolites, pro-allergic lipid mediators such as 12,13-dihydroxy-9Z-octadecenoic acid, and bacterial-derived histamine, modulate distal airway immune responses through epigenetic, receptor-mediated, and immune trafficking mechanisms. Particular emphasis is placed on the role of diet as a key upstream regulator of gut microbiota composition and metabolic function. Finally, we evaluate experimental and translational studies targeting the gut-lung axis, including dietary modulation, microbiome-targeted interventions such as fecal microbiota transplantation, and emerging postbiotic approaches. Collectively, current evidence indicates that gut microbial composition and metabolic function are critical determinants of respiratory immune homeostasis. Targeting the gut-lung axis through nutrition- and microbiome-based strategies offers a promising avenue for the prevention and precision treatment of allergic asthma.},
}

Humans
*Dysbiosis/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Asthma/immunology/microbiology
*Lung/immunology/microbiology
Animals
Diet

@article {pmid42124636,
year = {2025},
author = {Perez, L and Cremer, J},
title = {A mismatch between slow protein synthesis and fast environmental fluctuations determines tradeoffs in bacterial proteome allocation strategies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.22.666192},
pmid = {42124636},
issn = {2692-8205},
abstract = {Microbes live in environments that fluctuate faster than they can adjust their cellular machinery. To survive these fluctuations, they must dynamically regulate protein synthesis-a resource-intensive process that is often slower than environmental changes. Here, we develop a mechanistic model coupling antibiotic kinetics with dynamic proteome allocation to understand how limitations in translational capacity shape acclimation strategies. Using translation-inhibiting antibiotics and resistance proteins, we show that the temporal mismatch between environmental perturbations (seconds) and protein synthesis responses (hours) creates a growth advantage for anticipatory strategies where cells pre-synthesize resistance proteins before antibiotic exposure. Further, we find that the largest benefits of anticipation and the largest protein fractions reserved for anticipation are realized in environments with multiple antibiotics, suggesting that anticipation is most important in complex environments. This work establishes a framework for quantifying the costs and benefits of various acclimation strategies in dynamical environments based on the fundamental constraints of protein synthesis, with implications for microbial ecology, antibiotic resistance, and biotechnology applications.},
}

@article {pmid42126160,
year = {2026},
author = {Monteiro, T and Romeiro, K and Brisson-Suárez, K and Aazzouzi-Raiss, K and Marceliano-Alves, M and Campello, A and Alves, F},
title = {Accuracy of Digital Radiography and Cone Beam Computed Tomography in Assessing Filling Material Extrusion Using Micro-Computed Tomography as Gold Standard: A Study in Human Cadavers.},
journal = {European endodontic journal},
volume = {11},
number = {2},
pages = {45-49},
doi = {10.65717/eej.2026.25090},
pmid = {42126160},
issn = {2548-0839},
mesh = {Humans ; *Cone-Beam Computed Tomography ; Cadaver ; *X-Ray Microtomography ; *Radiography, Dental, Digital ; *Root Canal Filling Materials/adverse effects ; Sensitivity and Specificity ; },
abstract = {OBJECTIVE: This study compared the accuracy of digital periapical radiography (DPR) and cone beam computed tomography (CBCT) in detecting extruded filling material, using a human cadaver model. Micro-computed tomography (Micro-CT) served as the gold standard.

METHODS: A total of 27 single-rooted teeth embedded in cadaveric mandibular segments, obtained from a prior retreatment study, were included: 25 with confirmed apical extrusion of filling material on micro-CT and 2 without extrusion serving as negative controls. The segments were imaged using both DPR and CBCT. Two calibrated endodontists independently assessed the images for visible extrusion; discrepancies were resolved by a third evaluator.

RESULTS: Although DPR demonstrated lower overall sensitivity than CBCT, both modalities showed identical specificity (100%). Diagnostic accuracy was 70% for DPR and 74% for CBCT, without statistically significant difference between them (P > .05). Moreover, the volume of extruded filling material was not a significant predictor of detection accuracy for either DPR (P > .05) or CBCT (P > .05).

CONCLUSION: In conclusion, both DPR and CBCT demonstrated low accuracy in detecting filling material extrusion, with no significant difference between them. The occurrence of false-negative results may compromise the reliable assessment of extruded filling materials. In cases of true extrusion, approximately one-third would go undetected by both methods.},
}

Humans
*Cone-Beam Computed Tomography
Cadaver
*X-Ray Microtomography
*Radiography, Dental, Digital
*Root Canal Filling Materials/adverse effects
Sensitivity and Specificity

@article {pmid41917812,
year = {2026},
author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W},
title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41917812},
issn = {1471-2180},
support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; },
abstract = {UNLABELLED: The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04923-x.},
}

@article {pmid42116847,
year = {2026},
author = {Williams, NLR and Bei, Q and Raut, Y and Fuhrman, JA},
title = {Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag081},
pmid = {42116847},
issn = {2730-6151},
abstract = {With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. While traditional amplicon sequencing provides only relative abundance data, and the strongly preferred absolute abundances can be determined from samples spiked with internal standards, few oceanographic studies with absolute abundances exist. However, many have flow cytometry (FCM) data that should allow us to retrospectively "anchor" the relative abundances into absolute abundances. We tested this hypothesis with data from the 29th Atlantic Meridional Transect (AMT29) cruise where we had FCM of Synechococcus and Prochlorococcus, amplicons corrected with internal standards, and absolute cell count estimates from single copy recA and radA metagenomics. Anchoring the AMT29 amplicon data with Synechococcus FCM (used because phycoerythrin in Synechococcus is reliably detected by FCM in surface waters) yielded results strongly correlated with amplicon data corrected with internal standards (Pearson's r = 0.94, slope = 0.73), FCM (r = 0.80, slope = 0.43), and recA-based genome counts (Pearson's r = 0.94, slope = 0.62). Seeing this method worked reasonably well, we then generated estimates of absolute rRNA gene abundances from the Global rRNA Universal Metabarcoding of Plankton (GRUMP) transects that had FCM data (Pacific ~65 N to ~40S). These FCM-anchored gene copy estimates also showed strong correlations to FCM data (i.e. anchor with Synechococcus and predict Prochlorococcus), with r values ranging from 0.48-0.86. While the results are clearly only reasonable estimates, we believe the approach has the potential to significantly enhance the value of amplicon data which have accompanying FCM data.},
}

@article {pmid42117636,
year = {2026},
author = {Chuang, Y-C and Behringer, MG and Patton, GE and Bird, JT and Mazny, JL and Gliessman, JR and Love, CE and Dalia, AB and McKinlay, JB},
title = {Reciprocal cross-feeding between bacteria can limit the emergence of metabolic dependencies.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0036326},
doi = {10.1128/aem.00363-26},
pmid = {42117636},
issn = {1098-5336},
abstract = {Cross-feeding is prevalent in microbial communities. Through time, cross-feeding is thought to enrich for loss-of-function mutations, thereby creating or reinforcing dependencies between community members. However, few studies have compared how cross-feeding affects the evolutionary trajectory of partners compared to monoculture conditions. Here, we compared mutations that were differentially enriched in bacterial monocultures versus cocultures pairing phototrophic Rhodopseudomonas palustris with fermentative Escherichia coli in an obligate cross-feeding relationship based on the exchange of nitrogen and carbon for 650-800 generations. Opposite trends for the number of differentially enriched mutations were observed for each species; R. palustris accumulated more unique mutations in monoculture, whereas E. coli accumulated more unique mutations in co-culture. Contrary to expectations, the emergence of additional dependencies was observed in monoculture, but not in coculture, even though additional layers of cross-feeding involving iron and adenine were present in coculture. We reasoned that iron and adenine cross-feeding occurred at levels sufficient to repress gene expression in the recipient, thereby promoting gene retention by lowering gene cost. We also observed that E. coli acquired mutations in coculture that were suggestive of enhanced adenine uptake, whereas R. palustris gained the ability to oxidize H2, but only in monoculture. Thus, the influence of cross-feeding on evolutionary trajectories can vary with organisms and conditions, and there are situations where cross-feeding can limit, rather than promote, emergent dependencies.IMPORTANCEBacteria commonly engage in cross-feeding, where nutrients are transferred between neighbors. Cross-feeding is thought to alleviate energy expenditures for genes whose role can be met by cross-fed nutrients, leading to eventual gene loss. However, few examples have been documented, especially in comparison to monocultures that lack a cross-feeding partner. We grew cocultures pairing phototrophic Rhodopseudomonas palustris with fermentative Escherichia coli alongside corresponding monocultures for 650-800 generations. While coculture conditions required obligate exchange of nitrogen and carbon, additional cross-feeding of adenine and iron likely occurred. Contrary to expectations, dependencies for iron and unknown compounds emerged in monocultures, but expected iron and adenine dependencies were not observed in cocultures. Low expression of iron scavenging and adenine synthesis genes in cocultures suggested that cross-feeding repressed expression, thereby lowering gene cost. Thus, although cross-feeding can sometimes make costly genes dispensable, there are also cases where cross-feeding lowers gene cost, thereby promoting gene retention.},
}

@article {pmid42118196,
year = {2026},
author = {Stewart, J and Ockert, LE and Hawke, T and Power, M and Bino, G},
title = {First insights into the Drivers of the Cloacal Microbiome of the Wild Platypus (Ornithorhynchus anatinus).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02788-1},
pmid = {42118196},
issn = {1432-184X},
abstract = {The host microbiome plays a critical role in wildlife health, reproduction, and environmental responses. The platypus (Ornithorhynchus anatinus), a semi-aquatic monotreme endemic to eastern Australia, has remained microbiologically understudied despite conservation concern. Here, we present the first characterisation of the wild platypus cloacal microbiome using 16 S rRNA amplicon sequencing of samples collected across its eastern range, including sites recently affected by drought and bushfire. We found that region, and environmental disturbances such as bushfire and drought were significant drivers of bacterial community structure and composition, with influence from sex and breeding season also. Bushfire and drought both disrupted microbial community structure. The microbiome partially recovered following low-severity fires, but not after severe fire or prolonged drought, suggesting that microbiome resilience is linked to disturbance intensity. These findings suggest that the platypus microbiome is sensitive to environmental pressures and may offer a minimally invasive indicator of individual and ecosystem health. In addition to these ecologically important findings, across all sampled regions the platypus cloacal microbiome was consistently dominated by Campylobacterota and Fusobacteriota, with Pseudomonadota and Bacillota also prominent in the core microbiomes. Our results provide a critical baseline for integrating microbial health into conservation planning for this unique mammal.},
}

@article {pmid42119198,
year = {2026},
author = {Lemos, ACF and da Cruz, ILS and Mello, IS and Cruz, IF and Soares, MA},
title = {Free-living amoeba diversity in river waters of western Brazil and their in vitro and in vivo pathogenic potential.},
journal = {Protist},
volume = {181},
number = {},
pages = {126164},
doi = {10.1016/j.protis.2026.126164},
pmid = {42119198},
issn = {1618-0941},
abstract = {Free-living amoebae (FLA) are key components of aquatic and terrestrial ecosystems, but their diversity and distribution in central-western Brazil remain poorly characterized. Some FLA are pathogenic and may harbor bacteria of public health relevance. We aimed to identify and to characterize the FLA biodiversity in the Cuiabá River basin and to infer their pathogenic potential. Water samples were collected at eight sites across two hydrological periods, and physicochemical and microbiological parameters were quantified. FLA were isolated on non-nutrient agar seeded with heat-inactivated Escherichia coli and identified by using morphology and molecular markers. We obtained 39 isolates (six genera and 14 species); Acanthamoeba (51.3%), Vannella (23.1%), and Vermamoeba (12.8%) were predominated. Only V. vermiformis was detected during both the high-water (when four exclusive species were detected) and low-water (when nine exclusive species were detected) periods. Seventeen FLA strains (n = 35) killed zebrafish larvae (Danio rerio); 11 of these strains (64.7%) were Acanthamoeba species, and the remaining strains belonged to the genera Flamella, Naegleria, Ptolemeba, Vannella, and Vermamoeba. Thermo- and osmotolerance did not correlate with zebrafish larval mortality. These findings expand current knowledge of FLA biodiversity in Brazil and reinforce that integrated FLA monitoring in the Cuiabá River basin is needed.},
}

@article {pmid42119482,
year = {2026},
author = {Paula, MPO and Varani, AM and da Silva, VLC and Roesch, LFW and Tótola, MR and Ramos, AC and Pylro, VS},
title = {Genome-resolved characterization of microbial consortia driving glyphosate degradation in soil.},
journal = {Chemosphere},
volume = {405},
number = {},
pages = {144948},
doi = {10.1016/j.chemosphere.2026.144948},
pmid = {42119482},
issn = {1879-1298},
abstract = {Glyphosate is a widely used non-selective herbicide associated with ecological and human health concerns due to its environmental persistence, highlighting the need for effective remediation strategies. Among available approaches, microbial enzyme-mediated degradation represents a promising biological solution. This study aimed to enrich and characterize glyphosate-degrading microbial consortia from coffee plantation soils, validate glyphosate and aminomethylphosphonic acid (AMPA) degradation by chromatographic analyses, and integrate genome-based functional annotation with comparative structural analyses to investigate enzymatic systems involved in C-P and C-N bond cleavage. The enrichment process, followed by metataxonomic and metagenomic analyses, revealed dynamic shifts in microbial community composition. Achromobacter and Serratia were identified as key genera, harboring genetic potential for glyphosate and AMPA degradation. High-performance liquid chromatography with diode array detection confirmed efficient transformation of both compounds, with consortia Con_CC and Con_CC-G achieving the highest removal efficiencies under carbon- and phosphorus-limited conditions. Genome-based functional annotation showed that both genera encode gene clusters associated with the C-P lyase pathway, while only Achromobacter harbors the gene encoding glyphosate oxidoreductase (GOX), linked to oxidative C-N bond cleavage. Structural modeling indicated conservation of key catalytic residues in PhnJ, whereas GOX-related sequences in Serratia corresponded to partial homologs lacking a complete catalytic site. By integrating chromatographic, genomic, and structural analyses, this study provides a multi-level framework linking microbial community dynamics, functional potential, and molecular mechanisms underlying glyphosate degradation.},
}

@article {pmid42121034,
year = {2026},
author = {Xu, P and Zhu, Z and Liu, Y and Wang, H and Li, H and Kong, Q and Tan, Z and Li, K and Liu, S and Jamal, MA and Shang, Z},
title = {Revealing growth performance in weaned Tibetan pigs along with gut microbial diversity and oxidative status under the impact of ambient temperature.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05004-9},
pmid = {42121034},
issn = {1471-2180},
support = {32260859//National Natural Science Foundation of China for Regional Foundation/ ; 32260859//National Natural Science Foundation of China for Regional Foundation/ ; },
abstract = {The physiological parameters of Tibetan piglets have been found to be significantly influenced by environmental factors particularly during the weaning period and in the context of large fluctuations in ambient temperature in plateau regions. This study was designed to examine the effects of different ambient temperatures on gut microbiota diversity, serum antioxidant status, and growth performance of weaned Tibetan piglets. The study comprised of n = 40 weaned Tibetan piglets that were randomly allocated to five temperature-controlled groups with increase in temperature as BC4 (18 °C), BD4 (22-24 °C), BE4 (25-27 °C), BF4 (28-30 °C), and BG4 (31-33 °C). The growth performance was calculated by average daily weight gain (ADG) while serum antioxidant capacity was assessed through malondialdehyde (MDA), superoxide dismutase (SOD), total antioxidant capacity (T-AOC), and glutathione peroxidase (GSH-Px) levels. Fecal samples were taken and through 16 S rRNA gene sequencing the gut microbiota profiling was checked. Microbial α- and β-diversity indices, community composition, and taxa-specific shifts were evaluated by temperature-dependent changes. Results indicated that moderate increase in ambient temperature (25 ~ 27 °C) significantly improved the growth performance with higher ADG in the BE4 group. The serum antioxidant markers SOD, T-AOC, and GSH-Px level were higher than MDA concentrations, indicating enhanced oxidative resistance. The beneficial bacterial taxa such as Paraprevotella, Limosilactobacillus, and Paralachnospira flourished and change the gut microbiota diversity and structure, whereas potentially harmful taxa (Bifidobacterium_388775 and Ligilactobacillus) were decreased at the moderate temperatures. The LEfSe and multiple t-tests determine the gut microbial ecology when temperature-dependent shifts in microbial composition indicate a regulatory effect of ambient temperature. It is concluded that the optimal growth performance and enhanced serum antioxidant capacity in weaned Tibetan piglets maintained by moderate raise of ambient temperature (25 ~ 27 °C) to support a balanced gut microbiota. These findings indicated that during the weaning period temperature played an important role in regulating oxidative status and gut microbial diversity.},
}

@article {pmid42121736,
year = {2026},
author = {Özdemir, ÖS and Ahsan, U and Raza, I and Cengiz, Ö},
title = {Effects of Calf Starter Neutral Detergent Fiber Levels and Weaning on Growth and Rumen Microbial Diversity of Holstein Calves.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091316},
pmid = {42121736},
issn = {2076-2615},
support = {VTF- 22012//Directorate of Scientific Research Projects/ ; },
abstract = {A study was conducted to evaluate the effect of neutral detergent fiber (NDF) levels of calf starter and weaning time on growth, rumen fermentation characteristics, serum metabolites, and rumen microbial diversity of Holstein calves. A total of 24 newly born male Holstein calves were randomly distributed to four groups in a completely randomized design with a 2 × 2 factorial arrangement of NDF levels (14% and 24%) and weaning time (d 44 and d 54). There was no interaction between starter NDF levels and weaning time for any trait except rumen acetic acid in the immediate post-weaning phase (p = 0.013). Starter NDF levels had no effect on growth, feed intake, and hay intake. Late-weaned calves had greater (p = 0.050) weight gain in the pre-weaning phase whereas, early-weaned calves showed greater weight gain (p = 0.004) and starter intake (p = 0.004) in the post-weaning phase although overall weight gain, and starter and hay intakes were not affected by weaning time. Rumen pH, ammonia nitrogen, and most volatile fatty acids remained unaffected by starter NDF levels and weaning except isobutyric acid which was greater in calves fed 24% NDF starter (p = 0.001) in the immediate post-weaning and isovaleric acid which was greater in early-weaned calves (p = 0.044) at the end of experiment. Serum metabolites were largely affected (p < 0.05) by starter NDF levels and weaning time in the pre-weaning phase only. Alpha diversity of rumen microbes was greater and chaotic in 14% NDF starter group (early- and late-weaned) in the pre-weaning phase which converged in the immediate post-weaning phase and diverged on starter NDF basis at the end of experiment. Microbial ecology at phylum and genus levels composition were greatly driven by starter NDF levels in the pre-weaning phase, by weaning time in the immediate post-weaning phase, and two distinct bifurcated microbial ecologies based on starter NDF levels appeared at the end of experiment. In conclusion, the comparable growth with distinct microbial diversity but largely in favor of 24% NDF starter suggests that calves can be subjected to early weaning with 24% starter NDF levels for smooth transition from liquid to solid feed in Holstein calves.},
}

@article {pmid41918091,
year = {2026},
author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J},
title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41918091},
issn = {1471-2180},
support = {2022YFC26023002//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Understanding microbial adaptation to extreme environments remains a key challenge in microbial ecology. Geothermal hot springs, characterized by temperature gradients and varying geochemical conditions, represent valuable natural laboratories for studying microbial diversity, adaptive strategies, and evolutionary mechanisms. However, despite many studies of hot spring communities, how temperature gradients shape key microbial adaptation strategies remains insufficiently understood, limiting our ability to explain survival and function in extreme environments.

RESULTS: Our study investigated microbial community composition and functional profiles across a natural thermal gradient (50–93 °C) in six hot springs on the Western Sichuan Plateau using optimized contig- and MAG-based metagenomic strategies. Enhanced annotation approaches significantly improved taxonomic resolution in these extreme environments. Metagenomic analyses revealed distinct shifts in microbial communities along the thermal gradient: moderate-temperature springs (50–70 °C) were dominated by Pseudomonadota and Bacteroidota, exhibiting heterotrophic flexibility and utilizing the Calvin–Benson–Bassham cycle and diverse nitrogen reduction pathways; high-temperature springs (70–90 °C) were enriched in Chloroflexota, which primarily employed the Wood–Ljungdahl pathway coupled with enhanced sulfur metabolism; and extreme-temperature springs (≥ 90 °C) were characterized by Aquificota and Thermoproteota, relying on specialized autotrophic pathways (rTCA, DH/HH cycles), streamlined nitrogen assimilation, and sulfur oxidation pathways. These thermophilic lineages showed genome streamlining, reduced regulatory complexity, and specialized metabolic strategies, reflecting narrower ecological niches and deeper phylogenetic branches.

CONCLUSIONS: This metagenomic investigation across a temperature gradient in western Sichuan hot springs highlights temperature as an essential driver of microbial community structure, genome evolution, and adaptive specialization. Thermophilic lineages in extreme-temperature environments exhibited streamlined genomes, specialized metabolic functions, and narrower ecological niches, consistent with adaptation to persistent thermal stress. The findings enhance understanding of microbial evolutionary strategies and underscore the ecological significance of temperature-driven adaptation in extreme environments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04921-z.},
}

@article {pmid42112348,
year = {2026},
author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H},
title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1782828},
pmid = {42112348},
issn = {1664-3224},
mesh = {Humans ; *Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Autoimmunity ; },
abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.},
}

Humans
*Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology
Dysbiosis/immunology
Animals
*Microbiota/immunology
*Gastrointestinal Microbiome/immunology
Autoimmunity

@article {pmid42112445,
year = {2026},
author = {Furuya, R and Nishikawa, Y and Ota, Y and Prah, I and Mahazu, S and Kifushi, M and Yoshida, M and Suzuki, M and Hoshino, Y and Suzuki, T and Takeyama, H and Ablordey, A and Saito, R},
title = {Single-cell genomic profiling of antimicrobial resistance in Escherichia coli from the Densu River, Ghana.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797725},
pmid = {42112445},
issn = {1664-302X},
abstract = {INTRODUCTION: River water serves as a natural reservoir for antimicrobial resistance (AMR) factors. Although environmental AMR poses a global threat to public health as it spreads to local communities through the microbiome in aquatic environments, the actual situation remains unclear, especially in developing countries. In this study, we sought microbiome data, including AMR information, for multiple bacterial strains from river water samples using a single-cell genomics platform.

METHODS AND RESULTS: After antimicrobial selection of samples from the Densu River in Ghana, 16S rRNA amplicon sequencing revealed a high proportion of the genus Escherichia-Shigella with ampicillin and sulbactam selection. Single-cell genomic analysis revealed differences in AMR and virulence factor profiles among the same species of Escherichia coli, including the CTX-M-15 extended-spectrum β-lactamase-producing ones. Pan-genome analysis predicted 4,814 gene clusters, of which 2,264 were accessory, including 605 singletons. Phylogenetic tree analysis using the maximum likelihood method showed the heterogeneity of single-cell amplified genomes (SAGs), and cluster of orthologous gene analysis for each SAG confirmed the difference in the ratio of each functional group.

CONCLUSION: This study demonstrates the potential of single-cell genomics using the single-cell amplified genome in gel method to enhance environmental AMR surveillance with high resolution and accuracy. It also represents the first application of this approach to aquatic environments in Ghana, thereby contributing to the development of microbial ecology and genomic resources.},
}

@article {pmid42112933,
year = {2026},
author = {Gee, M and Sharp, C},
title = {Bacterial weaponry and the ecological factors of competitive success.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250028},
pmid = {42112933},
issn = {1744-1358},
support = {N/A//University of Reading (UoR)/ ; },
abstract = {Bacteria have evolved complex protein systems known as bacterial weapons to inhibit or kill their competitors. These bacterial weapons are a remarkably diverse arsenal that influence the composition and function of important microbial communities such as the human microbiome. In turn, the spatial constraints, nutrient availability, environmental stressors, and the presence of competitors determine not only whether weapons are expressed, but which weapons provide the greatest advantage. While bacterial weaponry is widespread, the types, mechanisms, and abundance of these systems vary between, and even within, species. Recent research has highlighted the importance of bacterial weaponry in community invasion and pathogenicity. Their potency and narrow killing spectrum have also generated interest in exploiting bacterial weapons to engineer microbial communities or develop therapeutics that avoid the disruption of broad-spectrum antibiotics. Understanding how ecological context affects weapon efficacy could reveal new virulence mechanisms used by pathogens and inform the design of novel treatments and microbiome-based therapies. This review outlines three of the best-studied bacterial weapon systems (protein bacteriocins, the type VI secretion system, and contact-dependent inhibition), highlighting their roles in microbial ecology, pathogenicity and their potential as therapeutics.},
}

@article {pmid42114326,
year = {2026},
author = {Esen, S},
title = {An update on heat stress impacts on rumen microbiome composition, fermentation parameters, and mitigation approaches in ruminants.},
journal = {Journal of thermal biology},
volume = {139},
number = {},
pages = {104480},
doi = {10.1016/j.jtherbio.2026.104480},
pmid = {42114326},
issn = {0306-4565},
abstract = {Over the past decade, there has been an increasing amount of literature on heat stress (HS) effects on ruminant production systems, yet much uncertainty still exists about the relationship between HS and rumen microbial ecology across species. This narrative review synthesizes peer-reviewed evidence from 2020 to 2025, with the aim of providing a critical appraisal of HS effects on rumen microbiome composition and fermentation parameters in cattle, buffalo, sheep, and goats. A convergent pattern emerges from the available data: HS consistently reduces cellulolytic bacteria (Fibrobacter, Ruminococcus) while increasing lactate-producing and starch-fermenting taxa. Acetate proportions declined by 29-33% in buffalo and beef cattle, whereas total VFA in sheep increased during mild HS, reflecting species-dependent fermentation responses. A strong relationship between breed-level heat tolerance and rumen microbiome diversity has been reported in several recent studies, providing converging evidence that heat tolerance may be characterized as a holobiont phenotype. It has been demonstrated that HS extends beyond classical VFA changes to disrupt B-vitamin synthesis, amino acid metabolism, biogenic amine homeostasis, and bile acid biotransformation. Nutritional interventions, including probiotics, chromium, herbal supplements, and rumen-protected amino acids, have been shown to partially restore microbial balance, although responses vary with HS severity and host genotype. Notwithstanding these findings, the generalisability of much published research on this topic is limited by methodological heterogeneity across studies. Taken together, these findings highlight the need for standardized experimental protocols, multi-omics integration, and microbiome-targeted intervention strategies.},
}

@article {pmid42115446,
year = {2026},
author = {Huang, M and Zhou, H and Du, X and Xia, P},
title = {Nitrogen Application Under Integrated Water-Fertilizer Management Regulates Rhizosphere Nitrogen Dynamics, Microbial Communities, and Maize Productivity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02784-5},
pmid = {42115446},
issn = {1432-184X},
support = {2025JC-YBMS-645//Shaanxi Provincial Department of Science and Technology/ ; },
abstract = {Nitrogen management strongly regulates rhizosphere nutrient availability, microbial ecological processes, and maize productivity in fertigation-based systems. Yet, the mechanisms by which nitrogen application gradients shape rhizosphere nitrogen transformations and microbial community stability remain insufficiently understood. In this study, a field experiment with four nitrogen levels (N0 0 kg·hm[-2], N1 100 kg·hm[-2], N2 140 kg·hm[-2], and N3 180 kg·hm[-2]) was conducted to clarify how nitrogen inputs influence rhizosphere nitrogen forms, microbial community assembly, and yield performance in maize under an integrated water-fertilizer regime. Moderate nitrogen application (N2) significantly enhanced rhizosphere nitrogen availability throughout the jointing, silking, and grain-filling stages. Nitrate-N and dissolved organic nitrogen (DON) reached 297.15 mg·kg[-1] and 152.14 mg·kg[-1] at jointing-substantially higher than N0-and remained elevated during subsequent stages, indicating sustained nitrogen supply. This improved nutrient status promoted plant growth and resulted in the highest grain yield (5281.85 kg·hm[-2]), representing a 25.7% increase compared with N0. In contrast, excessive nitrogen input (N3) failed to further elevate nitrogen fractions and may have reduced nitrogen-use efficiency. Nitrogen application influenced rhizosphere microbial communities. Moderate nitrogen (N2) increased bacterial richness and altered community composition, with several dominant bacterial and fungal taxa showing changes in relative abundance. Core microbial taxa remained largely stable, whereas transient taxa exhibited modest variations. Co-occurrence network analysis indicated increased cohesiveness in bacterial networks and reduced connectivity in fungal networks under nitrogen input. Functional predictions revealed that nitrogen application reduced bacterial chemoheterotrophy, aerobic-chemoheterotrophy, and nitrogen-cycling-related functions, while enhancing aromatic-compound-degradation potential. Predicted abundance of potential plant pathogenic fungi decreased following nitrogen application. Overall, moderate nitrogen input optimized rhizosphere nitrogen fractions, influenced microbial community composition and functional potential, and improved maize productivity, providing insight into microbiological responses to nitrogen management in semi-arid fertigation systems.},
}

@article {pmid42107798,
year = {2026},
author = {Song, Z and Rawat, A and Herrmann, C and Kabelitz, T and Yi, Q and Amon, B and Janke, D and Mehmood, T and Vieira, S and Overmann, J and Amon, T},
title = {Inoculation effects on microbial and methane dynamics in daily filled dairy manure storage.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134831},
doi = {10.1016/j.biortech.2026.134831},
pmid = {42107798},
issn = {1873-2976},
abstract = {Liquid manure storage is one of the major global sources of agricultural methane (CH4) emissions, and storage tanks on livestock farms are rarely emptied completely. Although the effects of residual slurry acting as an inoculum on subsequent microbial activity and CH4 generation have been examined previously, most studies have used batch or static storage systems that do not reflect the continuously filled conditions typical of dairy farms. To address this, this study for the first time simulated farm-like daily continuous filling by incubating dairy cattle manure for 92 days in laboratory-scale storage tanks with inoculum (WI) and without inoculum (WOI). Microbial community dynamics were assessed using 16S rRNA gene sequencing, while physicochemical properties and methane emissions were monitored simultaneously. Within this continuously fed system, inoculation reshaped microbial succession, leading to the early enrichment (day 8) of hydrolytic bacteria and methanogens in WI tanks. These shifts corresponded to distinct physicochemical trajectories: WI tanks maintained stable pH (7.0-7.6), accumulated fewer volatile fatty acids, reached peak daily CH4 emissions much earlier (day 31) than WOI tanks (day 79), and exhibited 17.9% higher cumulative CH4 emissions. Modified Gompertz modelling showed that inoculation shortened the apparent methanogenic lag phase by 20.64 days, confirming its accelerating effect on system-level CH4 emission dynamics under continuous filling. This study provides the first investigation of inoculation effects in daily filled manure storage, linking microbial community dynamics with CH4 emission patterns and offering a framework for identifying CH4 emission trajectories and key control windows.},
}

@article {pmid42108251,
year = {2026},
author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J},
title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52077-7},
pmid = {42108251},
issn = {2045-2322},
support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; },
abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.},
}

@article {pmid42108292,
year = {2026},
author = {Guo, JX and Gao, YZ},
title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {91-103},
pmid = {42108292},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.},
}

*Microbiota/genetics
*Bacteria/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/methods
Humans
DNA, Bacterial/genetics
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid42108299,
year = {2026},
author = {Wang, F and Zhang, H},
title = {Microbial Omics Analysis for Multispecies Symbioses in Staple and Traditional Fermented Foods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {217-240},
pmid = {42108299},
issn = {1940-6029},
mesh = {*Fermented Foods/microbiology ; *Food Microbiology/methods ; Fermentation ; *Symbiosis ; *Microbiota ; *Metabolomics/methods ; Humans ; Genomics/methods ; },
abstract = {Fermented foods represent a cornerstone of global culinary traditions, underpinned by intricate microbial communities that drive flavor development and preservation. This chapter examines the microbial ecology and functional interactions across representative staple and traditional fermented foods, including fermented vegetables (sauerkraut, kimchi), fermented condiments (soy sauce, vinegar, miso, doubanjiang), and fermented alcoholic beverages (Chinese baijiu, wine, sake, Huangjiu). Recent meta-omics advances have revealed dynamic community succession, cross-feeding networks, quorum-sensing mechanisms, and key microorganisms contributing to flavor metabolites and health-promoting compounds. Furthermore, synthetic microbial communities and starter engineering are discussed as strategies to standardize fermentation, enhance quality, and develop novel functional products.},
}

*Fermented Foods/microbiology
*Food Microbiology/methods
Fermentation
*Symbiosis
*Microbiota
*Metabolomics/methods
Humans
Genomics/methods

@article {pmid42108422,
year = {2026},
author = {Shetty, P and Vuong, T and Li, C and Wagner, V and Myrzakhmetova, D and Peng, CC and Li, W and Ching, J and Zander, A and Weiser, S and Rosenbaum, MA and Allen, RJ and Lakemeyer, M and Mittag, M},
title = {Multi-omics studies reveal how ambient temperature changes govern cellular responses of Chlamydomonas.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koag136},
pmid = {42108422},
issn = {1532-298X},
abstract = {Photosynthetic protists, known as microalgae, face increasing temperatures due to climate change. The green biflagellate alga Chlamydomonas reinhardtii (Chlamydomonas) serves as a model for thermoregulation. While responses to thermal stress are well characterized, much less is known about the impact of ambient temperature shifts. Understanding microalgal responses to environmental temperature changes is critical, as these primary producers drive ecosystem productivity and food web dynamics. Here, Chlamydomonas grew mixotrophically at ambient temperatures from 18 °C to 33 °C. Transcriptomic profiling revealed extensive reorganization, with over 5,000 transcripts significantly affected, including those involved in algal-bacterial interactions, photoreception, lipid metabolism, photosynthesis, cilia formation, and the secretome. CO2 transfer rates and acetate levels measured at 18 °C and 28 °C suggest decreased photoautotrophic algal growth at 28 °C at first. Antagonistic bacterial activity was sustained longer at lower temperatures. Proteomic analyses of isolated cilia and secreted proteins corroborate major abundance changes within these sub-proteomes, particularly in ciliary intraflagellar transport complexes and mating-related proteins in the secretome. Together, these molecular alterations resulted in pronounced changes in growth, the lengths of cells and cilia swimming behavior, mating ability and bacterial antagonism. These data reveal major cellular responses caused by ambient, even short-term temperature shifts.},
}

@article {pmid42110957,
year = {2026},
author = {Skidmore, AM and Goodfellow, SM and Nofchissey, RA and Jiang, L and Dunnum, J and Cook, JA and Guo, Y and Mali, I and Bradfute, SB},
title = {Characterization of the gut microbiome of wild Peromyscus sonoriensis in New Mexico, USA.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1672092},
pmid = {42110957},
issn = {2813-4338},
abstract = {The microbiome is highly important to the physiologies of all multicellular organisms, particularly metazoans. However, the microbiomes of many wild animals remain understudied and poorly understood. Peromyscus mice are commonly used as models of adaptation, mental health, and human disease in biomedical research, and are also common in the environment across North America, frequently coming into close contact with humans. Additionally, Peromyscus sonoriensis are implicated as the primary reservoir for Sin Nombre hantavirus, a rare but severe disease of high morbidity and mortality in humans. Here we characterize the fecal microbiomes of 311 Peromyscus sonoriensis, the western deer mouse, collected from across New Mexico, USA, which will further their usefulness as models of disease and behavior as well as increase our understanding of their ecology. The animals used in this study are geographically diverse, collected from multiple ecoregions, and encompass mice of all ages and sexes. We sequenced the entire 16S rRNA gene in a PCR independent approach and characterized the microbiomes with Shannon entropy, Faith phylodiversity, and weighted UNIFRAC. We found that these mice have diverse microbiomes, with individuals varying in the presence and proportions of various identified bacteria. We analyzed the total population of mice according to age, sex, and trapping location, and found that trapping location was the only condition to significantly impact the microbiome. When the mice were subdivided by the location of collection, there were mild effects of age and sex. When comparing mice from archival museum storage, storage of samples in 95% ethanol resulted in significant alterations to the microbiome when compared to cryopreservation. Differential bacterial family presence was determined using ANCOMBC at the 0.05 significance threshold, and there were many differentially abundant families across all groups of mice. This data set can now be used as a reference for further research into the microbiomes of related Peromyscus species, enhance the use of P. sonoriensis as model laboratory animals, and as a source of novel research questions regarding the physiology of these rodents.},
}

@article {pmid42111288,
year = {2026},
author = {Sanches, P and Mescher, MC and De Moraes, CM},
title = {Endosymbionts affect plant virus transmission by winged and wingless aphids.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag096},
pmid = {42111288},
issn = {2730-6151},
abstract = {Vector-borne pathogens frequently modify host-vector interactions, and their influence can be modulated by other microbial symbionts. We recently documented endosymbiont effects on aphid traits involved in plant virus transmission, showing that facultative endobacteria-particularly Hamiltonella defensa-enhanced transmission of pea enation mosaic virus. Here, we examine transmission steps and associated molecular signatures in winged and wingless aphid morphs. Consistent with our previous findings, we observed enhanced pea enation mosaic virus transmission, as well as elevated viral titer in wingless aphids harboring H. defensa. However, winged aphids with this endosymbiont displayed similar effects on virus titer but not transmission. Furthermore, whereas wingless aphids exhibited higher transmission than winged aphids when H. defensa was present, this pattern was reversed for aphids harboring only the obligate endosymbiont Buchnera aphidicola; in parallel, we observed no differences between morphs of lines harboring other facultative endosymbionts. Subsequent experiments comparing lines harboring H. defensa versus the obligate symbiont alone revealed divergent effects on winged and wingless morphs on (i) virus inoculation efficiency (i.e., delivery of acquired virus; H. defensa), (ii) key salivary proteins (carbonic anhydrases, CAs; both lines), and (iii) plant defense-related marker transcripts (PR-1, salicylic acid pathway; LOX, jasmonic acid pathway; both lines). The correspondence of these patterns to the observed transmission effects suggests that endosymbiont-mediated effects on transmission may reflect changes in salivary secretions and related feeding traits. Our findings highlight the role of vector endosymbionts in disease transmission and provide insights into candidate processes by which they may influence virus-vector-host interactions.},
}

@article {pmid42111323,
year = {2026},
author = {Belarbi, H and Kebede, F and Lambrecht, F and Lampaert, H and Grootaert, C and De Leyn, I and Van Bockstaele, F and Van de Wiele, T and Cakmak, I and Du Laing, G},
title = {Food-gut continuum of biofortified micronutrients: Influence of breadmaking processes on iodine, selenium, and zinc bioaccessibility and epithelial responses in an in vitro intestinal model.},
journal = {Food chemistry: X},
volume = {36},
number = {},
pages = {103882},
pmid = {42111323},
issn = {2590-1575},
abstract = {Micronutrient malnutrition affects over 3 billion people worldwide. This study evaluated biofortified wheat breads with iodine, selenium, and zinc, applied individually or in combination, and examined mineral retention, bioaccessibility, and intestinal epithelial responses. Mineral concentrations in wheat and their changes after baking unfermented flatbread and fermented sourdough were quantified, while intestinal bioaccessibility and epithelial effects were assessed using in-vitro digestion and cell culture models. Biofortification significantly increased mineral concentrations in wheat; however, retention during baking varied by mineral and product. Flour composition and baking method influenced iodine and zinc levels, whereas selenium retention was primarily affected by wheat cultivar and fermentation. In biofortified Bezostaja-1, Se bioaccessibility reached 68% in flatbread, while iodine and zinc reached 49% and 12% in sourdough. Selenium enhanced mitochondrial activity in intestinal cells in both bread types, and zinc-enriched sourdough increased epithelial integrity by 15% and reduced cellular permeability by 30%.},
}

@article {pmid42101887,
year = {2026},
author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Rocha, GS and Cheng, X and Raaijmakers, C and de Boer, W and Bodelier, PLE},
title = {Unraveling underlying mechanisms and responsible microbes of organic residue-stimulated atmospheric methane uptake in agricultural soils.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag048},
pmid = {42101887},
issn = {1574-6941},
abstract = {It has been reported that compost amendment improves atmospheric CH4 uptake of agricultural soils. However, microbes involved as well as the underlying mechanisms responsible for the observed effect remain unclear. Here we identified active MOB at (circum-) atmospheric CH4 concentrations in agricultural soils amended with green compost, and investigated three complementary hypotheses: (i) atmospheric CH4 consumption is driven by highly activated, flush-feeding MOB; (ii) stimulation of internal CH4 production which fuels flush-feeding methanotrophic activity; and (iii) increased availability of H2 that can serve as additional energy source for mixotrophic methanotrophy. First, we showed that MOB previously activated by exposure to high CH4 concentrations can subsequently oxidize atmospheric CH4 via the flush-feeding lifestyle. Second, no internal CH4 production in soil was observed following compost amendment, likely due to lack of suitable substrates for methanogenesis. Third, provision of elevated H2 concentrations did not affect the concurrent atmospheric CH4 oxidation. Phospholipid fatty acid-stable isotope probing (PLFA-SIP) revealed that four distinct MOB groups were active at (circum-) atmospheric CH4 concentrations in agricultural soils and green compost: Methylocaldum sp., Methylosinus sporium, Methylocystis sp./Methylosinus trichosporium, and USCα. These findings enhance our understanding of methanotroph ecology and can be used to craft more effective strategies of creating "climate-smart" soils.},
}

@article {pmid42102504,
year = {2026},
author = {IJdema, F and Broeckx, L and Deruytter, D and Frooninckx, L and van Miert, S and De Smet, J},
title = {Short communication: The persistent influence of host lineage on the gut microbiomes of black soldier fly and yellow mealworm.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {5},
pages = {101828},
doi = {10.1016/j.animal.2026.101828},
pmid = {42102504},
issn = {1751-732X},
abstract = {Production insects such as the black soldier fly (BSF) and yellow mealworm (YM) are increasingly recognised as sustainable protein sources, and selective breeding of genetically distinct lines offers opportunities to improve production efficiency. However, insect performance is also influenced by the gut microbiome, which provides essential metabolic and protective functions. Despite this, current breeding programmes typically focus on host genetics and phenotypes, assuming that microbiome composition remains stable under consistent rearing conditions. However, this hypothesis remains largely untested. We examined gut bacterial communities in ten distinct BSF and YM populations reared for multiple generations under identical conditions. Each species shared a distinct set of ten zero-radius operational taxonomic units (zOTUs) across all populations, but their relative abundances varied, indicating host-specific effects on microbiome composition. Strain-specific zOTUs also persisted despite uniform environments. These findings suggest that host genetic background exerts a more persistent influence on gut microbiome composition than previously assumed.},
}

@article {pmid42104021,
year = {2026},
author = {De Lara-Del Rey, IA and Pérez-Fernández, M and Magadlela, A},
title = {The Interplay of Light and Microbial Symbiosis in Shaping Plant Economic Spectrum Strategies.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02777-4},
pmid = {42104021},
issn = {1432-184X},
abstract = {Legume-rhizobia symbiosis are fundamental drivers of nitrogen cycling and plant performance, yet their role in facilitating species strategies along the Plant Economic Spectrum (PES) remains insufficiently understood. We conducted a field experiment with four legume species subjected to light and shade treatments, with and without rhizobial inoculation, to assess plant survival, biomass accumulation, nodulation, nitrogen acquisition, and isotopic signatures, alongside microbial community diversity and shifts in vegetation composition. Results demonstrate that inoculation significantly enhanced survival, growth rates, nitrogen accumulation, and nodulation across species, particularly under light conditions, indicating that microbial symbiosis promotes acquisitive strategies within the PES framework. Contrary, shaded environments consistently favoured higher survival and root allocation but reduced growth, nodulation, and nitrogen fixation, reflecting more conservative resource-use strategies. Species-specific responses revealed differential PES positioning: Trifolium repens L. exhibited high acquisitive capacity under light, while Coronilla juncea L. showed poor survival and growth under both conditions, highlighting the interaction between phylogenetic identity and resource availability. Additionally, δ[15]N and %Ndfa values confirmed that inoculation increased nitrogen fixation efficiency, whereas microbial diversity analyses indicated strong shifts in soil bacterial communities associated with inoculated plants, suggesting feedback between symbiosis and soil microbiota. These findings support two main hypotheses: (i) rhizobial inoculation acts as a biotic driver promoting acquisitive strategies by enhancing resource acquisition and growth efficiency, and (ii) light availability serves as an abiotic axis that modulates species positions along the PES continuum. Together, our study provides novel evidence that both microbial interactions and resource availability jointly determine legume strategies within the PES.},
}

@article {pmid42104085,
year = {2026},
author = {Tan, S and Wang, J and Luciano, A and Li, J and Huo, Y and Ma, Y and Yang, J and Guo, J and Zhang, B and He, X and Zhao, M and Meng, F},
title = {Medium- and Large-sized Mammals on the Plateau: An Evolutionary Crucible for Zoonotic Pathogens - Ecological Drivers, Adaptive Evolution, and One Health Control.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02772-9},
pmid = {42104085},
issn = {1432-184X},
support = {32370554 and 32460248//the National Natural Science Foundation of China/ ; },
abstract = {Plateau regions have emerged as pivotal epicenters of diverse zoonoses because of their distinctive ecological conditions and rich biodiversity. Against the backdrop of intensifying climate change, escalating interactions between wildlife, livestock, and humans, and expanding human activities, these regions now face formidable challenges. To assess public health threats within plateau ecosystems and establish targeted prevention frameworks, this review systematically synthesizes the prevalence and potential cross-species transmission risks of zoonotic pathogens-spanning parasites, viruses, and bacteria-carried by large- and medium-sized wild mammals across China's four major plateaus (Tibetan Plateau, Yunnan-Guizhou Plateau, Loess Plateau, and Inner Mongolia Plateau). Critical issues, including ecological fragility, complexity of pathogen transmission networks, and delayed responsiveness of control measures, are comprehensively analyzed. Future strategies must embrace the One Health concept to construct a multidimensional, coordinated prevention system. By integrating pathogen surveillance, ecological regulation, and technological innovation, a refined zoonosis control framework anchored in safeguarding plateau biosafety and public health can be systematically advanced.},
}

@article {pmid42104451,
year = {2026},
author = {Zhao, R and Huang, P and Pu, C and Zhu, F and Wang, C and Cai, C and Xiang, N and Ren, M and Ma, Q and Li, J},
title = {Azolla reshapes rhizosphere microbiomes and nutrient cycling in paddy fields.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00903-w},
pmid = {42104451},
issn = {2524-6372},
support = {1+9KJGG008//Sichuan Academy of Agricultural Sciences/ ; NKYRCZX2024024//Sichuan Academy of Agricultural Sciences/ ; 5+1QYGG006//Science and Technology Program of Sichuan Academy of Agricultural Sciences/ ; 2024NSFSC1229//National Natural Science Foundation of Sichuan Province of China/ ; },
abstract = {BACKGROUND: Soil quality is a critical determinant of agricultural productivity and sustainability. The symbiotic nitrogen fixation by Azolla plays a key role in enhancing soil quality. However, despite its potential as a green manure for enhancing soil quality, the role of Azolla in paddy systems remains inadequately characterized. This study aims to elucidate the effects of Azolla on soil quality by examining nutrient cycling dynamics and microbial community composition, along with their interactions.

RESULTS: We integrated soil physicochemical analyses, enzyme activity assays, bacterial community profiling, co-occurrence network analysis, and correlation assessments to evaluate the effects of Azolla on soil microbial ecology. Rice monoculture (R) and rice-Azolla co-cultivation (RA) systems were established. RA significantly increased activities of carbon- and nitrogen-cycle-related enzymes by 3-44% (P < 0.05), while phosphorus-cycle-related enzyme activities decreased by 12-42%. Under high nitrogen fertilization, Azolla altered bacterial community structure and reduced alpha diversity. Notably, Azolla recruited specific functional taxa-including Haliangium, SC-I-84, Candidatus_Solibacter, Anaerolinea, and Sphingomonas-whose relative abundances were 1.03-1.33 times higher in RA than in R.

CONCLUSIONS: This study elucidates the interactions between soil properties and microbial communities under Azolla application and uncovers the mechanisms by which Azolla enhances soil quality through nutrient cycling. Our findings demonstrate that Azolla, as a green manure, not only elevates soil nutrient content but also improves soil quality by driving microbe-mediated nutrient recycling. These results underscore the potential of Azolla as a sustainable alternative to conventional fertilization practices, offering novel insights into biofertilizer strategies for agricultural soil enhancement.},
}

@article {pmid42105173,
year = {2026},
author = {Prasad, H and Song, S and Jang, MJ and Kim, H and Razzak, MA and Haque, MA and Ahn, J and Ku, S},
title = {A Multidisciplinary Review of the Microbial, Functional, and Consumer Advancement of Indian Lassi.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42105173},
issn = {1867-1314},
support = {8000-0//Hatch program of USDA/ ; },
abstract = {Indian Lassi, a traditional yogurt-based fermented beverage, holds cultural, nutritional, and technological relevance, yet remains comparatively underrepresented in indexed scientific literature. This review synthesizes current evidence on Lassi's composition and fermentation characteristics, emphasizing its probiotic potential and nutrient profile while clearly distinguishing findings derived from Lassi-specific studies from those extrapolated from related matrices such as yogurt and buttermilk. Potential health-related effects, including support for gut and immune function and contributions to cardiometabolic risk modulation, are discussed as hypothesized benefits inferred largely from broader fermented dairy research rather than confirmed Lassi clinical trials. The diverse variations of Lassi, from sweet and salty formulations to spiced desi buttermilk style beverages, are examined alongside regional and global adaptations and their implications for microbial ecology, sensory properties, and consumer acceptance. A bibliometric and text-mining analysis of indexed Lassi-related publications maps prevailing research themes, highlighting a concentration on product formulation, quality, and safety, with comparatively sparse human and mechanistic health studies. Emerging technological developments, including precision fermentation, starter culture optimization, and innovative preservation and packaging strategies, are evaluated in relation to microbial stability, regulatory expectations, and cultural authenticity. Collectively, the review identifies critical gaps, particularly the limited experimental validation of Lassi-specific functional and health outcomes, and outlines priorities for future work.},
}

@article {pmid42105759,
year = {2026},
author = {Chen, H and Almeida-Silva, F and Logghe, G and Maere, S and Bonte, D and Van de Peer, Y},
title = {The rise of polyploids during environmental upheaval.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.04.008},
pmid = {42105759},
issn = {1097-4172},
abstract = {Polyploidy, or whole-genome duplication (WGD), serves as both a significant evolutionary force and a potential evolutionary dead end, particularly among angiosperms. Despite the prevalence of polyploid organisms, instances of ancient polyploidy are surprisingly rare, presenting a paradox that remains poorly understood. In this study, we constructed a comprehensive genomic dataset of 470 angiosperm species and dated 132 ancient WGD events that are non-randomly distributed, revealing a clustering around pivotal periods of environmental upheaval and extinction. Notably, our findings highlight a strong correlation between waves of paleopolyploidization and significant events such as the Middle Miocene Disruption, the Eocene-Oligocene Transition (EOT), the Paleocene-Eocene Thermal Maximum (PETM), the Cretaceous-Paleogene (K-Pg) extinction, and different oceanic anoxic events (OAEs). We propose that polyploid organisms have an increased chance of survival during times of great environmental turmoil, a conclusion with important implications in the context of contemporary climate change and rapid global warming.},
}

@article {pmid42092154,
year = {2026},
author = {Yu, XA and Strachan, CR and Herbold, CW and Lang, M and Gasche, C and Makristathis, A and Segata, N and Pollak, S and Tett, A and Polz, MF},
title = {Genome-wide sweeps create ecological units in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42092154},
issn = {1476-4687},
abstract = {The human gut microbiome is shaped by diverse selective forces that originate from host and environmental factors and it substantially influences health and disease. Whereas the association of microbial lineages with various health conditions has been shown at different taxonomic levels[1-5], the extent to which unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations remains poorly understood. Here we show that genome-wide selective sweeps are a pervasive mechanism that differentiates bacteria in the microbiome. This mechanism leads to population structures akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others in its niche followed by rediversification, and they manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes. Indeed, we show that genome-wide sweeps originate under a wide range of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest that sweep clusters can spread globally within decades and that this process has occurred throughout human history. Sweep clusters are associated with different host conditions-such as age, colorectal cancer, inflammatory bowel diseases and type 2 diabetes-as an indication of their ecological differentiation. Our results reveal an evolutionary mechanism for the observation of stably inherited strains with differential associations and provide a theoretical foundation for analysing adaptation among microbial populations.},
}

@article {pmid42092264,
year = {2026},
author = {Vargas-Robles, D and Santos Agrait, JL and Suárez-Pérez, J and Vázquez, F and Dominicci-Maura, A and Sariol, CA and Zorrilla, C and Romaguera, J and Godoy-Vitorino, F},
title = {Oral Microbiome Resilience During SARS-CoV-2 Infection and Diversity Shifts After COVID-19 Vaccination in a Hispanic Population.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70310},
pmid = {42092264},
issn = {2045-8827},
support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; U54GM133807/GM/NIGMS NIH HHS/United States ; 1P20GM156713-01/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; U01CA260541/CA/NCI NIH HHS/United States ; COVID-19 RAPID GRANT #2020-00269//Puerto Rico Science, Technology and Research Trust/ ; P20 GM103475/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/prevention & control/microbiology/immunology/virology ; *Microbiota ; Hispanic or Latino ; Female ; Male ; SARS-CoV-2 ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; *Mouth/microbiology ; *COVID-19 Vaccines/administration & dosage/immunology ; Longitudinal Studies ; Vaccination ; Bacteria/classification/genetics/isolation & purification ; Aged ; White ; },
abstract = {The relationship between SARS-CoV-2 infection and the oral microbiome remains poorly understood, particularly in the Hispanic population. Oral samples from 62 individuals (38 SARS-CoV-2 positive, 24 negative) were analyzed using 16S rRNA sequencing, comparing diversity and taxa by infection and symptoms. Longitudinal data from 11 participants assessed microbiome changes as the infection resolved over time. To assess the impact of vaccination, we further examined 68 consistently SARS-CoV-2-negative individuals with paired samples collected before and after vaccination. SARS-CoV-2 infection was not significantly associated with alpha diversity, while beta diversity showed a non-significant but marginal trend (p = 0.051). Prevotella nanceiensis was consistently depleted in infected individuals, even after excluding recent antibiotic users, suggesting a reproducible association with infection status rather than a diagnostic marker. Among infected participants, mucosa-related symptoms were associated with lower Veillonella parvula abundance. Longitudinal data revealed stable microbiome profiles with slightly reduced variance in alpha diversity following viral clearance. In contrast, COVID-19 vaccination in consistently negative individuals was associated with significant increases in Shannon (p = 0.050) and Simpson diversity (p = 0.017), indicating greater evenness without expansion of richness. Beta diversity analyses showed vaccination-related shifts in community composition (PERMANOVA p = 0.026), with increases in Treponema, Campylobacter, Oribacterium, and Selenomonas, and a decrease in Haemophilus. The oral microbiome of Hispanics with mild SARS-CoV-2 infection appeared resilient, with only subtle taxonomic alterations. In contrast, COVID-19 vaccination was associated with short-term increases in diversity and compositional shifts, highlighting its influence on oral microbial ecology.},
}

Humans
*COVID-19/prevention & control/microbiology/immunology/virology
*Microbiota
Hispanic or Latino
Female
Male
SARS-CoV-2
RNA, Ribosomal, 16S/genetics
Middle Aged
Adult
*Mouth/microbiology
*COVID-19 Vaccines/administration & dosage/immunology
Longitudinal Studies
Vaccination
Bacteria/classification/genetics/isolation & purification
Aged
White

@article {pmid42095322,
year = {2026},
author = {Liu, Q and Xu, P and Zhang, C},
title = {LL-37: Biological Mechanisms and Emerging Therapeutic Applications in Intestinal Disease.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {5},
pages = {e70451},
pmid = {42095322},
issn = {2050-4527},
support = {2024JH2/102600293//Liaoning Provincial Joint Program of Science and Technology/ ; },
mesh = {Humans ; *Cathelicidins ; *Antimicrobial Cationic Peptides/therapeutic use/metabolism ; Animals ; Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/immunology/drug therapy ; Immunity, Innate ; *Colorectal Neoplasms/immunology/drug therapy ; *Intestinal Diseases/immunology/drug therapy ; Immunity, Mucosal ; },
abstract = {Human cathelicidin peptide LL-37 is encoded by the CAMP gene and plays a key role in innate immunity. It maintains intestinal homeostasis through antibacterial, immunomodulation, and tissue repair functions. This paper reviews the multiple functions of LL-37 in the intestinal-immune axis and its contribution to intestinal immune homeostasis. A large amount of evidence shows that the biological effect of LL-37 is highly dependent on the environmental background, and its effects vary with peptide concentration, receptor binding status, disease stage, and local microenvironment. This article reviews the latest findings of the dual role of LL-37 in inflammatory bowel disease (IBD) and colorectal cancer (CRC), and focuses on the conditional mechanism of the transformation of its activity from protective to pathogenic. We also discuss the interaction between LL-37 and intestinal microbiota, focusing on how microbial signals and host peptides can coordinate to regulate mucosal immunity. At the same time, this article examines the key obstacles to the therapeutic application of LL-37 and its clinical promotion: cytotoxicity, rapid degradation by proteases, and drug resistance. We have further explored new strategies to overcome these challenges in the near future, including peptide engineering, nanocarrier delivery systems, and combined therapy. These findings together position LL-37 at the intersection of intestinal immunity and microbial ecology, providing a theoretical basis for its therapeutic application in IBD, CRC and infectious colitis.},
}

Humans
*Cathelicidins
*Antimicrobial Cationic Peptides/therapeutic use/metabolism
Animals
Gastrointestinal Microbiome/immunology
*Inflammatory Bowel Diseases/immunology/drug therapy
Immunity, Innate
*Colorectal Neoplasms/immunology/drug therapy
*Intestinal Diseases/immunology/drug therapy
Immunity, Mucosal

@article {pmid42095931,
year = {2026},
author = {da Cruz, MO and Montoya, QV and de Sousa, RL and Pennachioni, GGP and Rodrigues, A},
title = {Unraveling Culturable Microfungal Communities Associated with Colonies of the Fungus-Farming Ant Mycetomoellerius urichii (Forel, 1893).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02776-5},
pmid = {42095931},
issn = {1432-184X},
support = {2022/16087-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/04706-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/03746-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 126804/2024-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Microfungal communities inhabit the fungus gardens of fungus-growing ants (Formicidae: Myrmicinae: Attini: Attina, the "attines") and may play cryptic yet important ecological roles within this symbiosis. While the diversity and composition of these microorganisms are relatively well characterized in leaf-cutting ant colonies, they remain poorly understood in non-leaf-cutting attine species, including Mycetomoellerius urichii. To address this gap, we investigated the microfungal communities in colonies of M. urichii using culture-dependent methods. Based on analyses of four independent molecular loci, we identified 94 microfungal species, with Trichoderma spirale, Syncephalastrum sp., and Cladosporium sp. as the most abundant taxa. Several of the microfungi found in this study have also been reported from leaf-cutting ant colonies. The microfungal communities were dominated by fungi exhibiting a multitrophic lifestyle (pathotroph-saprotroph-symbiotroph). Community composition showed considerable variation among colonies, with no consistent species co-occurrence patterns detected. Together, these findings provide the first community-level characterization of culturable microfungi inhabiting the fungus gardens of M. urichii and offer new insights into the microbial communities associated with the fungus-farming ant symbiosis.},
}

@article {pmid42096486,
year = {2026},
author = {Colorado Gómez, MA and Melo-Bolívar, JF and Ruíz Pardo, RY and Junca, H and Alzate, JF and Villamil Díaz, LM},
title = {Anaerobic bacteria Cetobacterium sp. nov C33 plays a crucial role in the intestinal microbial balance and regulation of gene expression to immune and metabolic responses in Nile tilapia.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0344851},
pmid = {42096486},
issn = {1932-6203},
mesh = {Animals ; *Cichlids/microbiology/immunology/metabolism/genetics ; *Gastrointestinal Microbiome ; Probiotics ; RNA, Ribosomal, 16S/genetics ; *Bacteria, Anaerobic/physiology/genetics ; Aquaculture ; Gene Expression Regulation ; },
abstract = {Aquaculture ranks among the largest global food production industries, with Nile tilapia (Oreochromis niloticus) being one of the most widely farmed species. However, increasing consumer demand and higher stocking densities place considerable stress on aquaculture systems, often leading to a rise in fish diseases. Probiotics have emerged as valuable tools in this sector, promoting fish health by modulating physiological functions such as metabolism, digestion, immune responses, stress tolerance, and disease resistance. Here, the probiotic potential of Cetobacterium sp. nov C33, an anaerobic bacterium isolated from the intestine of Nile tilapia, was evaluated on short-term dietary supplementation in fingerlings in laboratory conditions. Using 16S rRNA amplicon sequencing, we assessed the impact of Cetobacterium sp. nov C33 on gut microbiota, while transcriptomic analysis of the head kidney provided insights into immune system modulation. Results indicate that dietary inclusion of this anaerobic bacterium significantly alters the gut microbiota structure in tilapia fingerlings and regulates genes associated with key metabolic pathways, including the immune system, underscoring its potential as a probiotic for enhancing tilapia health. Our results offer promising evidence of its potential as a probiotic to improve tilapia health.},
}

Animals
*Cichlids/microbiology/immunology/metabolism/genetics
*Gastrointestinal Microbiome
Probiotics
RNA, Ribosomal, 16S/genetics
*Bacteria, Anaerobic/physiology/genetics
Aquaculture
Gene Expression Regulation

@article {pmid42100688,
year = {2026},
author = {Yadav, J and Gehlot, P and Soni, P and Jain, T},
title = {Plant microbiome engineering: from inoculation to genome editing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1781381},
pmid = {42100688},
issn = {1664-302X},
abstract = {Plant-associated microbiomes are central to crop productivity, nutrient efficiency, and stress resilience, yet conventional microbiome manipulation strategies, largely based on microbial inoculation and agronomic management, often suffer from inconsistent field performance and limited persistence. Although several recent reviews have discussed CRISPR-mediated plant-microbe engineering and synthetic microbial community (SynCom) design separately, few reviews integrate genome editing, ecological stability of microbiomes, and climate-resilient agricultural applications within a unified conceptual framework. Recent advances in molecular biotechnology are transforming this landscape by enabling precision engineering of plant-microbe interactions at genetic, metabolic, and community levels. In particular, synthetic biology tools including CRISPR/Cas genome editing, RNA interference, and synthetic microbial communities (SynComs), now allow targeted modification of plant traits governing microbial recruitment, microbial pathways underpinning nutrient cycling and stress tolerance, and community-level functional complementarity. This review integrates molecular genetics, microbial ecology, and systems-level microbiome design to frame the plant and its microbiome as an engineerable holobiont. We integrate insights from genome editing in plants and microbes, omics-guided SynCom design, climate-resilience mechanisms, and emerging AI-assisted decision frameworks, including machine learning and ecological modeling approaches used to analyze multi-omics datasets, and predict plant-microbiome interactions across experimental and field-based studies. Importantly, we critically assess limitations related to ecological stability, trait trade-offs, biosafety, and regulatory challenges that constrain large-scale deployment. By bridging genome-enabled microbiome manipulation with ecological design principles, this review proposes an integrative framework for climate-smart microbiome engineering and identifies key research priorities required to transition from empirical inoculation toward predictive, sustainable, and socially responsible agricultural biotechnology.},
}

@article {pmid42101618,
year = {2026},
author = {Nguyen, PN and Rehan, SM},
title = {Microbial Communities Across Social Roles in Small Carpenter Bee Nests.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02787-2},
pmid = {42101618},
issn = {1432-184X},
abstract = {Bee microbiota form important symbiotic relationships with their hosts, but microbial communities vary across bee species, sociality, and environment. Comparing the microbiome of bees with different social roles and foraging behaviours may uncover the ways in which microbiota are environmentally acquired and subsequently introduced and spread into the nest environment. Here, we performed metabarcoding of the 16S rRNA, ITS, and ribulose biphosphate carboxylase large (rbcL) regions on mothers, dwarf eldest daughters, and regular daughters in nests of the facultatively social, small carpenter bee, Ceratina calcarata, contrasting bacteria, fungi, and plant associates. We also performed two different sampling types by characterizing the microbiome using whole-guts and whole-bodies. Social role in nest impacted the microbial community composition and mothers were found to demonstrate increased plant diversity compared to their daughters, more specifically in whole-bodies, highlighting the ability to determine plants that bees are visiting during foraging through DNA metabarcoding. We also found that metabarcoding of the whole-body recovered increased fungal and plant diversity compared to whole-guts, suggesting that including microbiota from beyond the gut offers an opportunity to characterize uncommon associates that bees encounter, particularly through plant-pollinator relationships. As the transmission of beneficial symbionts and pathogens between individuals are studied for its impact on bee health, microbial analyses of bees across different environments and levels of sociality provides unique biomonitoring that can indicate the health of the larger bee community.},
}