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At least 19 recordsLinked to original sources
PubMed2026

Environmental coupling between metal resistance genes and bacterial communities in Beijing urban green-space soils.

Urban green spaces are intensively managed ecosystems exposed to chronic, multisource, low-intensity anthropogenic inputs. These inputs may alter soil microbial communities and influence the distribution of metal resistance genes (MRGs). However, MRG distributions and their relationships with environmental conditions and bacterial communities remain unclear under the complex, non-extreme pollution conditions typical of these ecosystems. We investigated Beijing urban green spaces as a representative system using metagenomic sequencing and metagenome-assembled genome (MAG) analysis. We characterized soil MRG composition, its environmental associations, and the distribution of potential hosts. MRG composition differed significantly among ecological conservation (EC), transitional urban (TU), and central urban (CU) zones. These differences were closely associated with soil physicochemical properties and bacterial community structure. Available phosphorus (AP) was significantly associated with variation in both bacterial community structure and MRG composition. MAG-based analysis identified distinct potential-host compositions across the three functional zones. Proteobacteria were more frequently represented among dereplicated MAGs from EC soils, whereas Actinobacteria were more frequent in TU and CU soils. Heavy metal concentrations correlated with MRG composition. However, variation partitioning analysis did not identify an independent contribution from heavy metals after accounting for soil physicochemical properties and bacterial community structure. These findings indicate that urban green-space soil monitoring should incorporate environmental conditions and microbial community characteristics rather than rely solely on total metal concentrations.

Soil Microbiology↗
PubMed2026

The COVID-19 pandemic influenced the temporal dynamics of antimicrobial resistance markers and bacterial community across urban wastewater treatment plants.

Urban wastewater systems represent important interfaces between human activity and the environmental occurrence of antimicrobial resistance (AMR) markers. We assessed the temporal dynamics of intI1, ermB, and the 16 S rRNA gene by quantitative PCR across three wastewater systems (EPC, CJC, and JW) in Fortaleza, Brazil, from November 2021 to November 2023. Bacterial communities were additionally characterized by 16 S rRNA gene metabarcoding in 18 samples collected in December 2021 and January 2022. A synchronized decline in 16 S rRNA gene and intI1 concentrations beginning in late 2022 was observed across all three wastewater systems, suggesting a shift toward lower microbial abundance. The ermB gene showed higher and more variable concentrations during part of the pandemic period, followed by convergence toward lower levels; however, the absence of antimicrobial-consumption data precluded attribution of this pattern to changes in macrolide selective pressure. Normalized antimicrobial resistance marker abundances were comparatively stable at EPC and JW but more variable at CJC. EPC exhibited the highest ASV richness, whereas CJC and JW showed greater diversity according to Shannon and inverse Simpson indices. Beta-diversity analyses identified wastewater system as the principal factor associated with bacterial community structure, while the effect of sampling period was smaller and metric-dependent. Neither ermB nor intI1 was individually associated with community composition, although intI1 showed a limited effect after adjustment for wastewater system in one model. Physicochemical parameters were not significantly associated with normalized marker abundances in the exploratory paired analysis. Arcobacter, Acinetobacter, and other potentially relevant genera were detected, but no direct associations between these taxa and the monitored AMR markers could be established. These findings highlight the value of integrating longitudinal qPCR, microbiome profiling, and environmental characterization to improve the interpretation of targeted AMR markers in One Health wastewater surveillance.

Wastewater↗
PubMed2025

Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Plants↗
PubMed2026

Species-specific structuring of gut bacterial and fungal communities in honey bees Apis cerana and Apis mellifera.

Honey bee gut microbiome studies have primarily emphasized bacteria, leaving fungal communities comparatively overlooked despite their ecological and functional importance. Whole-genome shotgun metagenomics of Apis cerana and Apis mellifera revealed fungal assemblages dominated by Ascomycota, with Basidiomycota and Microsporidia in minor proportions, alongside gut bacterial communities composed mainly of Pseudomonadota, Bacillota, and Actinomycetota. The bacterial diversity was markedly higher in A. mellifera (Shannon = 5.90; Simpson = 0.98) than in A. cerana (Shannon = 4.01; Simpson = 0.94; p > 0.05), while fungal diversity remained comparable between species (p > 0.05). Beta-diversity analyses revealed strong host-specific clustering for both bacterial (PERMANOVA R2 = 0.7989, p > 0.05) and fungal communities (R2 = 0.7218, p > 0.05), indicating distinct microbial organization driven by host species. Bacterial-fungal co-occurrence patterns exhibited host-specific structuring, suggesting differential inter-kingdom community organization between A. cerana and A. mellifera. Linear Discriminant Analysis Effect Size (LEfSe) identified 93 discriminatory fungal taxa (45 enriched in A. cerana, 48 in A. mellifera), highlighting yeast-dominated signatures in A. mellifera and Basidiomycota-affiliated enrichments in A. cerana. KEGG and CAZy profiling revealed host- and kingdom-specific functional differences, with bacterial communities of A. mellifera showing distinct representation of carbohydrate metabolism and nutrient-cycling functions, while fungal communities exhibited a comparatively narrower functional repertoire. Together, these findings provide a high-resolution view of honey bee bacterial and fungal microbiomes, highlighting strong host-driven divergence in taxonomy, function, and cross-kingdom interactions.

Animals↗
PubMed2026

Decoding microbial metabolic complementarity from individual traits to community structuring.

A fundamental challenge in microbiome research lies in elucidating the functional capacity of microbial communities through community membership and genomic data. As community structuring and emergent functional traits are determined by bacterial community metabolic networks, it is important to gain insights into the principles that govern bacteria-bacteria interactions. Here, we applied an integrative framework linking individual strain-level traits to community structuring in a simplified synthetic bacterial community (SSC8) that promotes the growth of ungrafted watermelon. By combining mono- and coculture assays with genome-scale metabolic modeling and metabolomic profiling of spent media, we characterized directional interactions and resource dependencies among community members. Our findings show that positive interactions dominated the community network, accounting for 55% of all pairwise combinations, indicating a high prevalence of growth-promoting effects among strains. Genome-scale metabolic modeling showed that functional divergence among strains enhanced the potential for metabolic complementarity as phylogenetic distance increased. Integrating metabolic modeling with metabolomics further suggested that Pseudomonas azotifigens Q6 not only benefited from all other community members, but also exhibited mutualistic interactions with the other three strains, with metabolite exchange involving compounds such as L-lysine and L-cysteine. Pseudomonas azotifigens Q6 acted as an important driver of community composition by affecting the abundance of several other consortium members in vitro. These findings highlight the role of metabolic complementarity in driving community structuring by promoting selective persistence of specific strains. Our work provides mechanistic insights into microbial interaction networks in vitro and offers a conceptual foundation for the rational design of functionally robust and plant-beneficial microbiomes.

Bacteria↗
PubMed2026

Recurrent and niche-specific functional bacteriome of maize hybrid revealed by integrated metabarcoding and culturomics.

The plant microbiome plays a pivotal role in plant survival in natural habitats by facilitating nutrient acquisition, stress adaptation, and disease suppression, while also offering opportunities to enhance crop productivity and climate resilience. However, the distribution of persistent and culturable bacteriome across maize-associated niches and their functional potential remain poorly resolved. This study integrated metagenomic next-generation sequencing (mNGS-based metabarcoding) and culturomics to characterise the maize-associated bacteriome of bulk soil, rhizoplane, phylloplane, and cob of the maize hybrid PHM-1 under contrasting cropping and tillage systems, and to identify recurrent and agriculturally promising bacteriome components. The bacteriome exhibited pronounced niche-specific structuring, whereas overall bacterial community composition did not differ significantly across cropping and tillage treatments (ANOSIM, R = 0.038, p = 0.306). Proteobacteria predominated in the culturable bacteriome (69-84%; mean, 76.2%) but accounted for only 1% of the total bacteriome, whereas Patescibacteria and Firmicutes were relatively enriched. Niche-specific dominance was evident, with Pantoea accounting for 40.79% of the total and 56.27% of the culturable phylloplane bacteriome under cereal monocropping, while Serratia represented 31.59% and 59.40% of the total and culturable cob bacteriomes, respectively. Across niches, mNGS captured substantially greater bacteriome diversity, particularly uncultured and unidentified taxa in soil-associated compartments, whereas culturomics recovered a narrower but functionally accessible fraction. Culturomics yielded 99 isolates representing 32 species across 12 genera, including six genera shared with the mNGS-derived recurrent bacteriome: Bacillus, Enterobacter, Pantoea, Pseudomonas, Serratia, and Stenotrophomonas. Functional screening identified strong biocontrol and plant-beneficial traits among core-associated isolates. Pseudomonas oryzihabitans ZM-DL-PA10 inhibited Rhizoctonia solani, Macrophomina phaseolina, and Bipolaris maydis by up to 40.6%, 43.9%, and 45.2%, respectively, through secreted and volatile metabolites; exhibited P, K, and Zn solubilisation; and produced IAA and siderophores. It also recorded the lowest B. maydis disease index (ADI) of 1.00. Pantoea ananatis ZM-BH-EA4 showed 52.4% and 68.5% inhibition of R. solani and B. maydis, respectively, through volatile metabolites. Collectively, the integration of mNGS and culturomics revealed a strongly compartmentalised maize bacteriome and identified recurrent, culturable, and functionally promising bacterial taxa, providing a targeted resource for microbiome-based crop protection and climate-resilient maize production.

Zea mays↗
PubMed2026

Long-term petroleum pollution alters soil microbial communities via electron transfer capacity: Evidence from a 35-year chronosequence.

Petroleum pollution poses a serious threat to soil ecosystems, especially in areas surrounding oil wells, where contamination should not be overlooked. Through a 35-year longitudinal study of soils surrounding oil wells, we demonstrate that petroleum hydrocarbons accumulate predominantly in the top 10 cm of soil, reducing the electron acceptor capacity (EAC) by 61.59 % (from 12.68 to 4.87 μmole-/gC) and decreasing the electron transfer capacity (ETC) by 43 %. Structural equation modeling identified ETC as the critical mediator of microbial community shifts, with EAC playing a pivotal role in sustaining redox processes. Notably, hydrocarbon accumulation triggered a microbial succession: The abundance of Actinomycetota (including genera Rhodococcus, Arthrobacter, and Rubrobacter) showed the most significant fluctuations within 2 years, while Pseudomonadota (genera Methylobacter, Thiobacillus, and Pseudomonas), which were dominant in uncontaminated soils, decreased markedly during this period. This transition coincided with peak microbial dysbiosis (microbial dysbiosis index in 2022 reached 31.41 times that of controls). Within two to four years following mild petroleum stress, the bacterial community established a new structural configuration, revealing a crucial window for ecological recovery. The coupling between ETC reduction and microbial succession highlights the pivotal role of electron flux in soil recovery. Our findings establish a mechanistic framework for ETC-targeted restoration strategies to enhance bioremediation in petroleum-contaminated soils.

Soil Microbiology↗
PubMed2026

DURABLE: A Workflow for Determining Corrosion-Driving and Protective Microbial Mechanisms.

Microbiologically influenced corrosion (MIC) threatens global infrastructure, causing billions of dollars in annual losses. Its persistence stems from unresolved mechanisms─particularly the metabolites produced by microorganisms that drive or inhibit corrosion─and the microbial community structures. Progress has been hindered by the absence of systematic workflows to rapidly and accurately identify MIC-relevant microorganisms and their functions. Here, we present DURABLE (Detection of Unique Corrosion Resistant or Accelerating Biologics in a Laboratory Environment), a pipeline that couples high-throughput microbial screening with genomic and metabolic workflows. We applied the DURABLE workflow to six diesel tank samples and revealed fuel-dependent microbial community structures, which showed greater diversity and evenness in bacterial communities than their fungal counterparts. The workflow used carbon steel beads to rapidly screen over 80 bacterial isolates for corrosive activity, reducing assay time to approximately 2 days compared with the conventional 30-day metal coupon test. More than 40 isolates were identified as corrosive. Further testing using mass spectrometry analysis revealed corrosion-associated metabolites, which were further validated using electrochemical assays. Thus, DURABLE achieved a ∼15-fold increase in screening speed and provided a scalable and mechanistic framework for dissecting MIC dynamics. We expect this advance will enable the development of precision mitigation strategies in hydrocarbon fuel infrastructure.

Bacteria↗
PubMed2026

Involvement of cross-genus phages in bacterial resistance to chlorine disinfection.

Chlorine disinfection resistance in pathogenic microorganisms poses severe environmental concerns and public health risks. While phages play critical roles in host adaptation to environmental stress, how poly-host phages contribute to bacterial resistance to chlorine disinfectants remains poorly understood. Here, we investigated shifts in the population dynamics, transcriptional profiles, and function potentials of cross-genus phage-bacterial communities under exposure to chlorine disinfectants in a continuously operated anaerobic-anoxic-oxic system over a 92-day period, using integrated metagenomic and metatranscriptomic approaches. In the presence and absence of chlorine disinfectants, the genomic abundance and diversity of phage and bacterial communities showed similar variation trends, and the community structures of both exhibited clear differences. A strong significant positive correlation was observed between phage and bacterial diversity under chlorine exposure (R&#x202f;=&#x202f;0.975, p&#x202f;=&#x202f;0.00,057), whereas no significant correlation was detected in the absence of chlorine disinfection (R&#x202f;=&#x202f;-0.314, p&#x202f;=&#x202f;0.613), suggesting that chlorine disinfectants may enhance phage-bacteria interactions. Host-associated phages exhibited high consistency with their corresponding putative hosts in terms of genomic abundance (M2&#x202f;=&#x202f;0.0945, p&#x202f;=&#x202f;0.001) and transcript abundance (M2&#x202f;=&#x202f;0.3668, p&#x202f;=&#x202f;0.001), and they were also significantly correlated with cross-genus phages in both genomic abundance (R&#x202f;=&#x202f;0.97, p&#x202f;<&#x202f;2.2e-16) and transcript abundance (R&#x202f;=&#x202f;0.83, p&#x202f;<&#x202f;2.2e-16), which collectively suggests the critical role of cross-genus phages in the resistance of microbial communities to chlorine disinfectants. Bipartite association network analysis shows that cross-genus phages carry highly homologous genes to their putative hosts and may be involved in the horizontal transfer of these genes among bacteria. These homologous genes are involved in DNA repair, redox balance regulation, environmental stress adaptation and efflux pump functions, suggesting a synergistic role between cross-genus phages and their putative hosts in chlorine resistance. Our findings reveal that cross-genus phages can contribute to the resistance of bacterial communities to chlorine disinfectants, providing the theoretical foundation for evaluating the role of poly-host phages in microbial communities.

Chlorine resistance↗
PubMed2026

Characteristics and assembly mechanisms of tobacco-associated bacteria in typical tobacco-planting regions across China.

INTRODUCTION: Plant-associated microbiota critically modulates host growth and environmental adaptation, yet assembly mechanisms, niche differentiation, and ecological strategies of bacterial communities inhabiting tobacco microhabitats remain poorly elucidated across geographical gradients. METHODS: Here, we systematically characterized bacterial microbiome assembly across five tobacco-associated niches (bulk soil, rhizosphere soil, root, stem, and leaf) from seven typical tobacco-planting regions using 16S rRNA amplicon sequencing, genome annotation, and niche breadth analysis. The independent and interactive effects of geographical location and host compartment on community structure, and further compared genomic traits, functional profiles, and life-history strategies between specialist and generalist bacterial populations were quantified. RESULTS: The results revealed a deterministic soil-plant continuum stratification of bacterial communities and diversity, with progressively simplified communities and decreasing alpha diversity from bulk soil to above-ground tissues, accompanied by progressive dominance of Proteobacteria. Geographical factors predominantly structured soil microbial communities via divergent edaphic properties, while host filtering acted as a universal dominant driver shaping endophytic microbiome assembly. Niche differentiation analysis demonstrated that niche-specialized bacterial ASVs overwhelmingly dominated all microhabitats and geographical sites, whereas generalist taxa only constituted auxiliary populations. Although specialist and generalist microbes exhibited highly conserved core genomic architectures and overall functional repertoires, they displayed distinct niche-specific functional divergence in metabolic pathways, stress resistance, and secondary metabolism across host compartments. Life-history strategy analysis further revealed that Y-strategist represented the core adaptive bacterial population, especially enriched in above-ground tobacco tissues. DISCUSSION: Our study establishes a hierarchical dual-filtering assembly model for tobacco microbiota, clarifies the ecological differentiation and functional adaptation of specialist and generalist bacteria, and provides fundamental insights into the assembly rules and adaptive mechanisms of crop-associated microbiomes for future microbial resource utilization and agricultural microbiome regulation.

biogeography↗
PubMed2025

Bacterial immune systems as causes and consequences of microbiome structure.

Attacks from molecular parasites such as mobile genetic elements (MGEs) have driven the evolution of defense systems in bacterial genomes. Yet, despite significant advances in understanding the molecular mechanisms of these bacterial immune systems, we have only a rudimentary understanding of their ecology and evolution. Bacteria exist as part of complex microbiomes, but community ecology and microbiome research has yet to characterize the impacts of interactions between MGEs and defense mechanisms upon the structure, dynamics and evolution of microbiomes. This Essay introduces and discusses the interplay between bacterial community dynamics and bacterial immune systems, speculating about how these reciprocal interactions may shape microbial community structure and function.

Bacteria↗
PubMed2025

From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.

Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.

Humans↗
PubMed2026

Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.

Though they jointly shape community responses to environmental perturbations, ecology and evolution are often examined separately, even in microorganisms where both occur over short timescales. Here we examine ecological and evolutionary responses to 33&#xa0;years of nitrogen fertilization using the legume-rhizobium mutualism. Pairing a manipulative inoculation study with full-length 16S rRNA gene amplicon sequencing and structural equation modeling allows us to synthesize across biological scales: whole bacterial community, genus Rhizobium, Rhizobium ASVs, and symbiosis plasmids. Clover's preferred partner decreases in N-addition soils, limiting host growth, while a diverse and largely uncharacterized Rhizobium community increases. This ecological change is compounded by a concurrent evolutionary degradation of symbiont partner quality via changing frequencies of symbiotic plasmids. Ecological (rarer symbionts) and evolutionary (inferior symbionts) processes each accounted for roughly half of this loss of host benefit, revealing that ecology and evolution jointly shape mutualism breakdown over the short timescales typical of microbial systems.

ecology↗
PubMed2026

Phenacetin inhibited but acetaminophen stabilized partial nitrification/anammox system: Studies on microbial metabolism and resistance genes in biofilm and plastisphere.

Partial nitrification (PN) inhibitors, such as phenacetin (PNCT) and acetaminophen (APAP), ensure a stable nitrite supply for anaerobic ammonium oxidation (anammox). But the unknown impact of inhibitors on anammox limit the application of inhibitors. In addition to the biofilm carriers used in biological nitrogen removal systems, microplastics (MPs) (a type of emerging contaminants) are the common substrate for microbial colonization, even enriched resistance genes (RGs). This research compared the effects of 0.5, 1 and 5&#xa0;mg/L PNCT or APAP on partial nitrification-anammox (PN/A) biofilm and plastisphere. 1&#xa0;mg/L PNCT inhibited the nitrogen removal functional bacteria (Nitrosomonas, Candidatus Kuenenia, Candidatus Brocadia and Nitrospira), resulting in the sharp deteriorated performance of PN/A system. 5&#xa0;mg/L PNCT inhibited multiple metabolism pathways, resulting in the absence of electrons and energy supply of microorganisms. 0.5-1&#xa0;mg/L APAP maintained the stable operation of PN/A system. Nitrospira abundances declined from 2.8% to 1.1% after 0.5&#xa0;mg/L APAP exposure. But 5&#xa0;mg/L APAP inhibited the abundance of amoA and the production of extracellular polymeric substances, which caused the slight fluctuation of PN/A performance. PN inhibitors did not cause the sharp increase of most RGs in biofilm and water. However, MPs exhibited the huge capacity of enriching RGs, which should be removed. This study proposed that 0.5&#xa0;mg/L of APAP was suitable for the PN/A system to control dosage for practical application.

Biofilms↗
PubMed2025

Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.

Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.

Humans↗
PubMed2026

Unlocking the unexplored AMPSphere in marine rare species.

BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action. RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (<&#x2009;0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems. CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.

Biofilms↗
PubMed2025

Landscape heterogeneity, forest structure, and mammalian host diversity shape tick density and prevalence of the causative agent of Lyme borreliosis.

Ticks, particularly Ixodes ricinus, and the associated Lyme borreliosis risk, represent key concerns within the One Health framework, prompting extensive research in this field. However, comprehensive studies that jointly consider landscape characteristics, local forest structure and management, climate, and host community composition-alongside direct measures of tick density and infection status with Borrelia spp., the bacterial agents causing Lyme borreliosis, are scarce. In this study, we test the hypothesis that habitat diversity exerts a dilution effect, primarily by supporting greater diversity of mammal hosts. Therefore, we examined I. ricinus tick density and Borrelia spp. prevalence in relation to a comprehensive set of habitat and host-related variables. Ticks were collected using the flagging method and mammal hosts were monitored using an innovative camera-trapping approach across 25 forest plots along a land-use gradient within the Schw&#xe4;bische Alb exploratory in Germany. Both tick density and Borrelia spp. prevalence are influenced by a complex combination of habitat factors across different spatial scales, as well as the mammal host community composition. Overall, our results provide novel support to the dilution effect hypothesis, suggesting that greater habitat and host diversity contribute to a reduced Lyme borreliosis risk in this region.

Animals↗
PubMed2026

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.

BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry. RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom&#xa0;3 improved the neutral detergent fiber degradation (NDFD) by 20.39%&#xa0;averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom&#xa0;3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF,&#xa0;+&#x2009;11.47%). Genomic analysis revealed that the SynCom&#xa0;3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes. CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.

Animals↗