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PubMed2025

Clinical and Microbiological Insights into Caseous Lymphadenitis in Sheep and Goats in Khorasan Razavi, Iran.

INTRODUCTION: Caseous lymphadenitis (CLA), a chronic bacterial disease caused by Corynebacterium pseudotuberculosis, significantly impacts small-ruminant health and productivity worldwide, causing economic losses through reduced wool and milk yields, reproductive issues, and carcass condemnation. Despite its importance, CLA prevalence and microbial dynamics remain under explored in Iran, where small ruminants are vital to rural economies. This study assessed the prevalence, clinical manifestations, and bacteriological profile of CLA in Khorasan Razavi Province, northeast Iran, to inform regional control strategies and address potential zoonotic risks. MATERIALS & METHODS: We examined 15 flocks totaling 4,733 animals (4,640 sheep, 93 goats) through clinical inspections and microbiological analysis of pus samples from affected lymph nodes. RESULTS: The results revealed a lymphadenitis prevalence of 11.59% (95% CI, 10.58%, 12.66%), with 8.62% of sheep (400/4640) and 8.60% of goats (8/93) affected, varying across flocks from 0% to 28.57%. Submandibular lymph nodes were most commonly affected (51.35%), followed by retropharyngeal (18.02%) and parotid (15.32%) nodes, with peak incidence in the 2-3-year age group (38.24%), likely linked to shearing practices. Bacteriological analysis of 102 pus samples identified C. pseudotuberculosis in 19.6% (20/102) of cases, characterized by small, dry, white colonies with β-hemolysis on Columbia blood agar. A diverse microbial profile included Actinobacillus spp. (7.8%), Trueperella pyogenes (3.9%), and novel isolates like Acinetobacter spp. and Yersinia spp. (1.0% each), with 43.14% of samples sterile, suggesting chronicity or sampling challenges. CONCLUSION: These findings indicate CLA etiology is complex, extending beyond a single pathogen and influenced by local husbandry practices. The study underscores CLA's economic burden and zoonotic potential, given rare but documented human cases. Integrated control measures-enhanced molecular diagnostics, recombinant phospholipase D (PLD) vaccine trials, and improved biosecurity-are urgently needed. Future research should prioritize genomic strain typing and environmental reservoir analysis to refine CLA management in Northeast Iran, offering insights applicable to similar agroecosystems globally.

Animals↗

PubMed1977

Nose, throat, and fecal flora of beagle dogs housed in "locked" or "open" environments.

The microbial flora of the nose, throat, and feces of male beagle dogs housed in a "locked environment" (i.e. confined to germfree-style isolators and supplied with sterile food, air, and water) or an open environment were assessed between 26 and 30 months into the study. Forty-five genera and 170 different species or types of microorganisms were cultured from the nose, throat, and feces of the beagles. Clostridia, eubacteria, corynebacteria, bacteroides, lactobacilli, and anaerobic, gram-positive cocci accounted for most of the microbial diversity in the flora. Some of the facultative anaerobes, especially streptococci and lactobacilli (in feces), occurred in numbers that were comparable to the most numerous anaerobic species. Confinement to the locked environment resulted in an increased diversity of microorganisms in the flora, but the total microbial counts did not increase to any great extent. Even with the increased diversity of bacteria in the flora of confined dogs, some bacteria seemed to favor certain areas of the gastrointestinal tract over others. The increased diversity of bacteria observed in these confined dogs may pose some infectious disease problems for other mammals (including humans) that may be confined to a locked, ultra-clean environment for a prolonged period of time.

Aerobiosis↗

PubMed2026

Metagenomic insights into antibiotic resistance genes and virulence factors in sediments of river Yamuna.

Riverine sediments serve as critical reservoirs of microbial diversity and functional genes, reflecting both natural ecological processes and anthropogenic impacts. In the present study, we employed a shotgun metagenomic approach to investigate microbial community composition, antimicrobial resistance (AMR) genes, and virulence factors in sediments collected from three environmentally distinct locations of the Yamuna River near Agra, India, representing BSA, TGY, and YEA. The sediment DNA was subjected to high-throughput Illumina sequencing, followed by quality control, assembly, and open reading frame prediction. Taxonomic classification and diversity analyses were performed using MEGAN6 and R-based statistical tools, while AMR genes were identified from predicted metagenomic proteins using the Resistance Gene Identifier (RGI) against the CARD database, with high-confidence perfect and strict hits retained; ARGs were interpreted independently of species-level host assignment. Virulence factors were assessed through presence-absence profiling of functionally relevant gene categories. The results revealed pronounced spatial heterogeneity in microbial communities, with increasing taxonomic diversity, functional complexity, and evenness from BSA to TGY and YEA. TGY and YEA composite samples showed greater observed representation of high-confidence AMR gene predictions spanning multiple drug classes and resistance mechanisms, alongside a diverse repertoire of virulence-associated genes linked to motility, adhesion, and secretion systems. In contrast, the BSA site harbored a comparatively simpler resistome and virulome. Overall, this study highlights Yamuna River sediments as important reservoirs of resistance and virulence determinants and underscores the need for long-term genomic surveillance to inform risk assessment, pollution control, and sustainable river management strategies.

AMR↗

PubMed2026

Airway microbiome diversity, intramucosal bacteria, and spatial immunity in asthmatic adults and controls.

RATIONALE: Asthma is characterized by disruption of the thoracic airway mucosae and loss of microbial diversity. Spatial profiling of the mucosal transcriptome may systematically discover mechanisms for microbial influences on immunity. OBJECTIVES: We investigated relationships between clinical measures, microbial communities, and the host mucosal transcriptome within different strata of bronchial biopsies in subjects with and without asthma. METHODS: We performed bronchoscopy in 65 asthmatic adults and 44 healthy controls, quantifying bacterial operational taxonomic units (OTUs) in bronchial brushings by 16S ribosomal RNA (rRNA) gene amplicon sequences. Biopsy histologic features were scored blind to diagnosis. Following 16S rRNA in situ hybridization of 44 biopsies, bacterial foci were scored in epithelium, basement membrane, and stroma. Global human gene expression was quantified in epithelial and stromal compartments using digital spatial profiling. MEASUREMENTS AND MAIN RESULTS: Clinical asthma was independently predicted by basement membrane abnormalities (BaseMA), endobronchial bacterial diversity, and circulating eosinophil counts, but not by specific OTU abundances. 16S rRNA staining revealed bacteria within epithelium and mucosa of all biopsies. Intramucosal bacteria counts correlated negatively with spatially organized coexpression networks encoding antigen-specific immunity, neutrophil functions, and matrix activation, whereas BaseMA correlated positively with the adaptive immunity module. Eosinophil counts correlated with epithelial bacterial counts and senescence pathways. Clinical asthma was accompanied by upregulation of a regulatory T-cell network. CONCLUSIONS: Asthma and its related phenotypes are accompanied by complex mucosal events that extend beyond eosinophilic pathways. Components of diverse airway microbiota may modify immunity by beneficial interactions within the mucosa.

Humans↗

PubMed2026

Ecological Filtering by Tuber Compartments Shapes Stable Core Microbiomes That Underpin Potato Plant Growth Across Environments.

Harnessing plant microbiomes for sustainable agriculture requires understanding not only whether they can boost crop performance, but also how ecological processes govern their assembly, stability, and functional contributions across environments. While we previously showed that seed tuber microbiomes can predict potato vigour using machine learning, it remained unclear how ecological processes shape tuber microbiome stability and functionality across host genotypes, tuber compartments, soil types, and years. Here, we analyzed the national-scale dataset of 240 field-collected potato seedlots, spanning six genotypes, two soil types, and two growing years, with a focus on the spatially distinct heel and eye compartments of the potato tuber. By profiling over 1200 bacterial and fungal communities and linking microbiome composition to plant performance, we show that plant genotype and tuber compartment are the strongest determinants of microbial diversity and composition. Compartment-specific enrichment of functional traits revealed spatial partitioning of microbial functions, with organic compound conversion and nitrogen cycling dominant in the heel, and energy metabolism enriched in the eye. Applying a macroecological abundance-occupancy framework, we identified a stable core microbiome of bacterial and fungal taxa that persisted across all environments and years. These core members were more strongly associated with plant growth-related traits than non-core taxa, and core taxa in different tuber compartments showed distinct correlations with taxa of potential pathogenic relevance. Together, our findings demonstrate that tuber compartments act as ecological filters that structure persistent, functionally specialised microbiomes linked to plant growth-related traits across environments. By providing an ecological and functional framework for compartment-resolved, stable core microbiomes, this study advances mechanistic understanding of plant-microbe interactions and identifies stable microbial partners as promising targets for improving potato resilience and productivity.

Journal Article↗

PubMed2026

Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.

Bacteriophages (phages) are being explored as alternatives or complements to antibiotics because of their ability to selectively kill bacterial pathogens. However, phages that infect many oral bacteria remain undiscovered. Here, we discovered that dental wastewater harbors previously underexplored phage diversity. Viral particles concentrated from dental wastewater displayed diverse morphologies, including abundant filamentous phage-like particles. Deep long-read metagenomic sequencing of concentrated viral particles generated 7.4 billion bases of sequence data and yielded 255 medium- to high-quality viral operational taxonomic units (vOTUs), including 46 predicted complete genomes. Comparison with large phage databases revealed that 63 of these 255 vOTUs had no detectable match, indicating that extensive sequencing of dental wastewater substantially expands the number of potential bacteriophages associated with the human oral microbiome. Host prediction linked many vOTUs to oral-associated bacterial taxa, including species with few or no previously reported phages, such as Porphyromonas gingivalis, Tannerella forsythia, and Candidatus Saccharibacteria. Functional annotation identified diverse genes associated with antiphage defense systems within a subset of vOTUs, suggesting that oral phages may contribute to the movement of genes encoding bacterial immune functions within the oral microbiome. Together, these findings expand the known oral phageome and show that dental wastewater contains a largely untapped diversity of phages.IMPORTANCEThe human oral cavity contains a diverse microbial community, but the bacteriophages (phages) that infect many oral bacteria remain poorly characterized. This gap limits our understanding of how phages shape oral microbial communities. Here, we show that dental wastewater is an underexplored source of oral phage diversity. Deep long-read metagenomic sequencing revealed 255 medium- to high-quality phage operational taxonomic units, many of which are not present in existing oral phage databases. These genomes include predicted phages of periodontal disease-associated bacteria and other oral taxa with few or no known phages. Dental wastewater therefore expands the known human oral phageome and reveals candidate phages linked to bacteria associated with oral health and disease.

Bacteriophages↗

PubMed2026

Microbial and functional shifts between flare and remission in a single-center cohort of children with inflammatory bowel disease.

BACKGROUND: Gut microbial dysbiosis is central to the pathogenesis of inflammatory bowel disease (IBD). While gut microbiome differences between patients with and without IBD are well established, microbiome changes associated with disease activity and remission remain limited, particularly in paediatric populations. AIM: To examine intra-individual taxonomic and functional gut microbiome changes during transition from active flare to remission under maintenance immunosuppression in a pilot single-center Singapore cohort of children with IBD. METHODS: Paired stool samples and clinical data were collected from seven patients with paediatric IBD [5 Crohn's disease (CD), 2 ulcerative colitis; ≤ 18 years] during active disease/flare (visit 1; Pediatric CD Activity Index/Pediatric Ulcerative Colitis Activity Index ≥ 10) and subsequent clinical remission (visit 2; Pediatric CD Activity Index/Pediatric Ulcerative Colitis Activity Index < 10). Samples underwent shotgun metagenomic sequencing for high-resolution taxonomic profiling and functional annotation of Kyoto Encyclopaedia of Genes and Genomes pathways. RESULTS: Gut microbial diversity was reduced during flare compared to remission, with Actinobacteria abundance significantly higher in remission. Two distinct microbial clusters differentiated flare and remission states: The remission cluster was enriched with Bifidobacterium adolescentis, Bifidobacterium dentium, Lactobacillus gasseri, Faecalibacterium prausnitzii, while the flare state showed increased Klebsiella pneumoniae. Remission was further characterized by a downregulation of pathogenic microbes and an upregulation of beneficial microbes including a higher abundance of the butyrate producer Anaerostipes hadrus (P = 0.046). Microbial functional genes enriched in remission were predominantly associated with metabolic pathways including vitamin and cofactor biosynthesis, as well as carbohydrate, amino acid, and lipid metabolism. CONCLUSION: The transition from flare to remission in Singaporean children with IBD is characterized by functional remodeling of the gut microbiome, which may contribute to recovery processes related to intestinal barrier integrity, cellular maintenance, and tissue repair. Targeted modulation of the gut microbiome may help sustain remission in paediatric IBD.

Functional shift↗

PubMed2026

Metagenomic analysis of the midgut microbiome in Dermacentor abaensis ticks at different feeding states.

Ticks are blood-sucking ectoparasites of humans and animals, ranking second only to mosquitoes as vectors of diseases. Dermacentor abaensis is distributed in Sichuan, Qinghai, and Gansu, China. Because D. abaensis harbors several pathogens, it poses a threat to public health and livestock production. However, the midgut microbiota of D. abaensis at distinct feeding states remains poorly characterized. Adult D. abaensis ticks at various feeding states were collected from yaks in Gansu Province, China. Genomic DNA was extracted from midguts and midgut contents of unfed, partially fed, and fully engorged female D. abaensis. A metagenomic sequencing approach was employed to profile the midgut microflora among three groups. A total of 83 phyla, 908 genera, and 1857 species were annotated across the three groups. At the phylum level, Pseudomonadota, Mucoromycota, and Ascomycota were the most abundant. At the species level, common bacterial species such as Klebsiella pneumoniae and Anaplasma phagocytophilum, alongside viruses and eukaryotes, were detected in all three groups. Unique microorganisms were also observed in each group: unfed (n = 305), partially fed (n = 59), and fully engorged (n = 20). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the D. abaensis microbiome contains a relatively high abundance of functional genes involved in lipid and amino acid metabolism across the three different feeding states. These findings indicate that while core microbial taxa are shared in the midgut of female D. abaensis, observable trends suggest variations in microbial diversity and composition as blood-feeding progresses. The present study provides a descriptive baseline of the midgut microbial composition of D. abaensis, which may inform future studies on tick biology and the ecology of tick-borne pathogens.

Animals↗

PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗

PubMed2026

Lactobacillus iners at the nexus of microbiota, immunity, and pregnancy.

Pregnancy induces a dynamic reconfiguration of the vaginal microbiome, typically marked by increased dominance of Lactobacillus species and reduced microbial diversity. Among these bacteria, Lactobacillus iners stands out for its unique genomic traits, controversial associations with vaginal health, and frequent presence across all stages of gestation. This review synthesizes current literature on the maternal microbiome with a focus on L. iners, exploring its strain-level diversity, metabolic idiosyncrasies, and inflammatory potential. We discuss how host factors such as ethnicity, sexual activity, maternal age, and especially obesity, influence microbial composition, and evaluate conflicting data surrounding L. iners in contexts like in vitro fertilization, preterm birth, and postpartum recovery. Emerging evidence suggests that L. iners may act as a transitional species, whose effect on pregnancy outcomes depends on its abundance, genetic features, and interactions with the host immune system. We also assess limitations of current animal models and propose future directions for understanding this enigmatic bacterium. Unraveling the role of L. iners will be essential to predicting, preventing, and managing adverse pregnancy outcomes in diverse populations.

Humans↗

PubMed2026

Soil management practices shape the abundance, diversity, and spread of antimicrobial resistance.

Agricultural soils are critical hotspots of antimicrobial resistance genes (ARGs). Yet, the environmental factors shaping these reservoirs and the hazards they pose to humans and livestock remain poorly understood. Because management practices introduce antibiotics, heavy metals, and nonantibiotic biocides, they can rapidly select for resistance. Most studies have examined components of management practices in isolation, overlooking the multiple stressors of modern industrial agriculture. Here, we used a large-scale field experiment to examine how multiple stressors from soil and crop management interact to shape antimicrobial resistance. We combined shotgun metagenomics, phylogenomics, and risk-score analyses to quantify the diversity of ARGs, mobile genetic elements (MGEs), and the transmission potential of drug-resistant pathogens. Relative to other management systems, intensive, chemically reliant monoculture systems, typical of the US Corn Belt, create strong selective pressures promoting more abundant and diverse ARGs and MGEs. These systems therefore carry greater potential to transmit ARGs, including those with relevance to both livestock and public health such as tetA and blaPAM, likely mediated by integration and excision. In contrast, less-intensive, lower-input systems with diverse crop rotations maintained resistomes with lower abundance, diversity, and transmission potential. Our results suggest that these patterns could arise due to the divergent effects of management practices on overall soil microbial diversity, an ecological barrier that can suppress ARGs. This study highlights the need to understand the combined stressors of agricultural practices, beyond antimicrobial use, to design effective strategies to mitigate antimicrobial resistance.

Soil Microbiology↗

PubMed2026

Multi-omics analysis reveals stage-associated differences in gut immunity and microbiota between juvenile and adult common carp (Cyprinus carpio).

In vertebrates, the development of intestinal immunity is closely associated with dynamic changes in the gut microbiota. However, stage-associated differences in intestinal immunity and gut microbial communities remain poorly characterized in teleost fish. In this study, transcriptomic analysis combined with 16S rRNA gene sequencing was employed to characterize intestinal immunity and gut microbial communities in juvenile and adult common carp (Cyprinus carpio). Transcriptomic profiling revealed marked developmental differences in intestinal immune function. Juvenile carp exhibited a predominantly innate immune phenotype, characterized by elevated expression of pro-inflammatory cytokines, antimicrobial peptides, and lysozyme-related genes. This immune profile was accompanied by enhanced mucosal barrier function and a relatively pro-inflammatory intestinal environment. In contrast, adult carp displayed increased expression of genes associated with adaptive immunity, suggesting that adult common carp exhibit relatively stronger adaptive immune characteristics than juvenile fish. Gut microbiota analysis demonstrated significant stage-dependent differences in microbial diversity and community composition. Juvenile fish were enriched with bacterial taxa potentially associated with innate immune activation, whereas adult fish harbored distinct microbial communities linked to intestinal homeostasis and barrier maintenance. Furthermore, correlation analyses identified significant associations between specific microbial taxa and innate immune-related gene expression, suggesting a close association between gut microbiota composition and intestinal immune characteristics in juvenile and adult common carp. Collectively, these findings reveal stage-associated differences in intestinal immunity and gut microbial communities between juvenile and adult common carp, thereby providing insights into intestinal immune characteristics at different developmental stages in teleost fish.

Animals↗

PubMed2026

Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.

UNLABELLED: Metagenomics enables comprehensive exploration of microbial communities but is influenced by library preparation and sequencing technologies, affecting recovery of microbial genomes and proteins. Here, we benchmarked six Illumina-compatible short-read library preparation conditions in triplicate at 2 × 150 bp and 2 × 250 bp read lengths alongside PacBio HiFi long-read sequencing using a composite environmental sample of marine mangrove sediment and terrestrial palm tree soil. Longer short reads (2 × 250 bp) combined with optimal library preparation approaches improved assembly quality, protein detection, and metagenome-assembled genome (MAG) recovery, achieving results approaching those of long-read sequencing. TruSeq libraries at 2 × 250 bp recovered more than sevenfold more unique proteins than the same kit at 2 × 150 bp (811,701 vs 110,108) using the same number of sequencing reads, while recovering a comparable number of high-quality MAGs to PacBio HiFi long-read sequencing (11 vs 18) and surpassing it in protein discovery by almost 10-fold (811,701 vs 87,745) at less than half of the sequencing cost. Furthermore, biosynthetic gene cluster analysis identified 46 biosynthetic gene clusters in TruSeq-250PE assemblies compared to 38 in PacBio HiFi, with several showing no close match in the MIBiG database. Although long reads yield more contiguity and complete genomes, longer short reads offer a cost-effective, scalable alternative for uncovering microbial and functional diversity. These findings provide critical guidance for metagenomic experimental design, demonstrating that strategic selection of library preparation chemistry and sequencing parameters can reveal more unknown microbial information in complex biomes without requiring additional sequencing depth. IMPORTANCE: Metagenomic outcomes are strongly influenced by library preparation and sequencing strategies, yet their combined effects in complex environmental samples remain poorly defined. Here, we provide the first direct comparison of Illumina NovaSeq short-read metagenomic sequencing at 2 × 150 bp and 2 × 250 bp across multiple library preparation kits, alongside PacBio HiFi long-read sequencing. We show that sequencing read length and library preparation critically shape assembly quality, protein recovery, and metagenome-assembled genome (MAG) reconstruction. These findings demonstrate that short-read sequencing at 2 × 250 bp, with appropriate library preparation, can match long-read technologies in MAG recovery while substantially surpassing them in protein discovery. With less than half of the sequencing price and a 3.5-fold reduction in cost per gigabase of usable data, this method facilitates more accessible large-scale metagenomic analysis within complex environmental systems.

Metagenomics↗

PubMed2025

A global survey of taxa-metabolic associations across mouse microbiome communities.

Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.

Animals↗

PubMed2026

Bioplastic biodegradability shapes microbial communities in a coastal brackish environment.

Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterized the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss as CO2 after 4 weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting that bioplastic biodegradation is constrained by and coupled to the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term 'bioplastisphere' to denote the distinctive microbial communities associated with biodegradable plastics.

Seawater↗

PubMed2026

Metagenomic-based quantification of Pseudomonas aeruginosa burden links microbiome collapse to mortality in severe community-acquired pneumonia.

BACKGROUND: Severe community-acquired pneumonia (sCAP) remains a major cause of mortality in critically ill patients, Pseudomonas aeruginosa (P. aeruginosa) is a frequent pathogen associated with poor prognosis in this population. While metagenomic next-generation sequencing (mNGS) is widely used for pathogen detection, its value in quantifying pathogen abundance and linking it to lung microbiome alterations remains unclear. OBJECTIVES: This study investigated the association between P. aeruginosa abundance quantified by mNGS and lung microbiome alterations and clinical outcomes in sCAP patients. METHODS: This multicenter retrospective study included 130 patients with sCAP caused by P. aeruginosa from five hospitals (September 2021-June 2025). Patients were stratified into low, medium, and high abundance groups according to mNGS-derived reads per ten million (RPTM) values of P. aeruginosa. Lung microbiome diversity and community structure were analyzed, and differences between groups were assessed using appropriate statistical methods. The association between P. aeruginosa abundance and clinical outcomes was evaluated using correlation analysis, sankey diagram, receiver operating characteristic curve, grey zone analysis and logistic regression. RESULTS: A total of 130 patients with sCAP due to P. aeruginosa were stratified into low, medium, and high abundance groups based on mNGS-derived RPTM value. Microbial diversity decreased progressively with increasing abundance, and community structures differed significantly among groups (all P < 0.05). P. aeruginosa became increasingly dominant, accounting for up to 95.99% of the microbiota in the high abundance group. Higher P. aeruginosa abundance was associated with increased disease severity, including longer mechanical ventilation, prolonged hospital stay, and higher 28-day mortality. Sankey diagram showed a progressive decline in treatment effectiveness and an increase in mortality with increasing P. aeruginosa abundance. P. aeruginosa_RPTM showed moderate predictive value for mortality (AUC = 0.761, Sens = 69.40%, Spec = 75.30%, cutoff: 41122, grey zone: 2287-220339) and remained independently associated with 28-day mortality in multivariable analysis [2.219 (1.509 to 3.262), P < 0.001]. CONCLUSION: In patients with sCAP, higher P. aeruginosa_RPTM measured by mNGS was associated with reduced lung microbiome diversity and unfavorable clinical outcomes. RPTM-based risk stratification may help identify patients at increased risk of poor prognosis.

Humans↗

PubMed2026

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.

BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear. RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles. CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.

Flavobacteriaceae↗

PubMed2025

Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.

Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.

Microbiome↗