Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver

Despite extensive investigations into the microbiome and metabolome changes associated with colon polyps and colorectal cancer (CRC), the microbiome and metabolome profiles of individuals with colonic polyposis, including those with (Gene-pos) and without (Gene-neg) a known genetic driver, remain comparatively unexplored. Using colon biopsies, polyps, and stool from patients with Gene-pos adenomatous polyposis (N = 9), Gene-neg adenomatous polyposis (N = 18), and serrated polyposis syndrome (SPS, N = 11), we demonstrated through 16S rRNA sequencing that the mucosa-associated microbiota in individuals with colonic polyposis is representative of the microbiota associated with small polyps, and that both Gene-pos and SPS cohorts exhibit differential microbiota populations relative to Gene-neg polyposis cohorts. Furthermore, we used these differential microbiota taxa to perform linear discriminant analysis to differentiate Gene-neg subjects from Gene-pos and from SPS subjects with an accuracy of 89% and 93% respectively. Stool metabolites were quantified via 1H NMR, revealing an increase in alanine in SPS subjects relative to non-polyposis subjects, and Partial Least Squares Discriminant Analysis (PLS-DA) analysis indicated that the proportion of leucine to tyrosine in fecal samples may be predictive of SPS. Use of these microbial and metabolomic signatures may allow for better diagnostric and risk-stratification tools for colonic polyposis patients and their families as well as promote development of microbiome-targeted approaches for polyp prevention.

Gut microbiome-driven regulation of sex hormone homeostasis: a potential neuroendocrine connection

The gut microbiome is known to have a bidirectional relationship with sex hormone homeostasis; however, its role in mediating interactions between the primary regulatory axes of sex hormones and their productions is yet to be fully understood. We utilized both conventionally raised and gnotobiotic mouse models to investigate the regulatory role of the gut microbiome on the hypothalamic-pituitary-gonadal (HPG) axis. Male and female conventionally raised mice underwent surgical modifications as follows: (1) hormonally intact controls; (2) gonadectomized males and females; (3) gonadectomized males and females supplemented with testosterone and estrogen, respectively. Fecal samples from these mice were used to colonize sex-matched, intact, germ-free recipient mice through fecal microbiota transplant (FMT). Serum gonadotropins, gonadal sex hormones, cecal microbiota, and the serum global metabolome were assessed. FMT recipients of gonadectomized-associated microbiota showed lower circulating gonadotropin levels than recipients of intact-associated microbiota, opposite to that of FMT donors. FMT recipients of gonadectomized-associated microbiota also had greater testicular weights compared to recipients of intact-associated microbiota. The gut microbiota composition of recipient mice differed significantly based on the FMT received, with the male microbiota having a more concerted impact in response to changes in the HPG axis. Network analyses showed that multiple metabolically unrelated pathways may be involved in driving differences in serum metabolites due to sex and microbiome received in the recipient mice. In sum, our findings indicate that the gut microbiome responds to the HPG axis and subsequently modulates its feedback mechanisms. A deeper understanding of interactions between the gut microbiota and the neuroendocrine-gonadal system may contribute to the development of therapies for sexually dimorphic diseases.

Vertical exchange versus horizontal dispersal in structuring local planktonic and sedimentary bacterial communities in polluted lotic ecosystems

Elucidating the mechanisms underlying community assembly remains a central question in community ecology, especially in aquatic ecosystems disrupted by human activities. Understanding the causes and consequences of community responses to changing environment is essential for revealing the ecological effects of anthropogenic disturbances and proposing practical strategies for ecological restoration. While stochastic dispersal and species sorting are known to influence local biological communities, most studies have focused on horizontal dispersal, often neglecting the vertical exchange of organisms between planktonic and sedimentary communities when studying stochastic dispersal. We used a highly disturbed urban river in Beijing as a model system to investigate the relative roles of stochastic dispersal versus species sorting driven by local pollution, as well as two components of stochastic dispersal, vertical exchange and horizontal dispersal, in structuring local bacterial communities. Our integrated analyses of planktonic and sedimentary bacterial communities revealed that, despite different spatial patterns along the river, both types of bacterial communities were primarily shaped by stochastic dispersal processes rather than species sorting influenced by the environmental gradient. Notably, in addition to the effect of horizontal dispersal along the river, the vertical exchange between planktonic and sedimentary bacterial communities significantly contributed to the formation of local communities. These findings suggest that both vertical exchange and horizontal dispersal should be considered when assessing the role of stochastic dispersal in shaping local community structure in microbial communities.

Animal farming and the oral microbiome in the Agricultural Health Study

BACKGROUND

Raising farm animals imparts various exposures that may shape the human microbiome. The oral microbiome has been increasingly implicated in disease development. Animal farming has also been associated with certain chronic diseases such as cancer; however, underlying biological mechanisms are unclear. We investigated associations between raising farm animals and the oral microbiome in the Agricultural Health Study.

METHODS

This analysis included 1,245 participants (865 farmers and 380 spouses) who provided oral wash specimens and information on types and numbers of specific animals raised on their farms within 2 years before sample collection. The oral microbiome was measured by sequencing the V4 region of the 16S ribosomal RNA gene. We evaluated associations of farm animal exposures with alpha and beta diversity metrics (within- and between-sample diversity, respectively), as well as presence and relative abundance of specific bacterial genera. All analyses adjusted for potential confounders (e.g., age, sex, smoking, alcohol consumption).

RESULTS

Overall, 63 % of participants raised farm animals, most commonly cattle (46 %) and hogs (20 %). Those who raised a large number of hogs (≥2,000 vs. no hogs) had higher alpha diversity. Conversely, raising sheep/goats and raising larger numbers of poultry were associated with lower alpha diversity. Beta diversity was not significantly different between participants with and without any farm animals. Participants raising any farm animals had higher relative abundance of Porphyromonas and lower relative abundances of Prevotella and Ruminococcaceae UCG-014. Several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium, Dialister, Stomatobaculum, and Solobacterium for sheep/goats and poultry).

CONCLUSIONS

This was the largest study of farm animal exposures and the human microbiome to date. Findings suggest that raising specific farm animals may influence the oral microbiome, supporting the need to further investigate the potential role of animal farming in disease etiology.

Investigating the role of primary fungi in Huangjiu fermentation: Insights from flavor orientation and synthetic microbiomes

Huangjiu, a traditional alcoholic beverage, presents a complex fermentation ecosystem primarily influenced by specific fungal species. This study utilized a culture-dependent approach and amplicon sequencing to explore fungal community succession during Huangjiu fermentation. Key fungi identified include Saccharomyces cerevisiae, Aspergillus species (flavus, oryzae, niger), Saccharomycopsis fibuligera, Thermomyces lanuginosus, Rhizopus arrhizus, Issatchenkia orientalis, Wickerhamomyces anomalus, and Diutina rugosa. Employing a synthetic microbiome, we developed a dual-strain fermentation system to evaluate the impact of these fungi on Huangjiu's organoleptic properties. Introduction of these fungi significantly altered the flavor profile, enhancing 23 volatile organic compounds (VOCs), with S. fibuligera notably increasing nine distinct VOCs. While molds contributed to bitterness by increasing bitter amino acids, S. fibuligera effectively mitigated these components, enhancing the beverage's alcohol body, smoothness, and balance. These findings provide crucial insights for optimizing Huangjiu fermentation to improve its quality and appeal.

Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer

Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.

Microbiomes of coastal sediments and plastispheres shaped by microplastics and decabrominated diphenyl ether

Deciphering the impact of microplastic and persistent organic pollutants (POPs) co-contamination on coastal sediment is critical for developing effective remediation strategies for polluted sites yet remains underexplored. This study investigated the interactions between microplastics, decabrominated diphenyl ether (deca-BDE), and their co-contamination effects on the evolvement of coastal sediment and plastisphere microbiomes for over 2 years. Results showed that deca-BDE was naturally debrominated in sediments via diverse pathways, with microplastic polystyrene stimulating the debromination rate by up to 78.7 ± 10.0 %. The putative OHRB Dehalobacter and uncultured Dehalococcoidia populations were identified responsible for the complete debromination. Co-exposure to microplastics and deca-BDE induced significant shifts in community composition, diversity, and function in the sediment microbiomes, while plastisphere microbiomes exhibited distinct compositions and functional profiles, specializing in pathogenicity, pollutant degradation, and biogeochemical cycling. The type of plastics and the presence of deca-BDE influenced the plastisphere composition. Changes in sediment properties and debromination activity profoundly shaped microbial communities, with deterministic assembly dominating the plastisphere. Co-contamination increased the complexity, modularity, and stability of the plastisphere networks, creating unique niches for OHRB. These findings highlight the intricate interplay between microplastics, deca-BDE, and microbiomes, with significant implications for ecosystem health and remediation efforts.

Black soldier fly larvae mediate Zinc and Chromium transformation through the ZnuCBA and citric acid cycle system

Intestinal microbiota and metal regulatory proteins (MRPs) underlie the transformation of heavy metals (HMs) by the black soldier fly larvae (BSFL), but the mechanisms involved are still not fully defined. Here, using 16S rRNA and metagenomics-assisted tracing, we found that zinc (Zn) and chromium (Cr) stress led to enrichment of Proteobacteria in the BSFL intestine. Support of Proteobacteria also led to increased levels of the Zn transporter proteins ZnuC/B/A and the Zn efflux proteins zntR/A. Meanwhile, the genes MltE, CitT, and SLT, which mediate the citric acid cycle, were also significantly up-regulated and involved in the cellular uptake of Cr. Although Zn and Cr stress affected the expression of antibiotic resistance genes and pathogenic genes, the BSFL intestine tended to form stable microbial communities (MCs) to transform HMs through a mechanism driven by ZupT and chrA. In addition, the expression of SCARB1 and LdcA was significantly down-regulated by acute HMs stimulation, but BSFL were still able to complete the life cycle. Therefore, we determined the protective role of MCs and MRPs on BSFL during the transformation of HMs.

Unveiling gut microbiota and metabolic functions contributed to polyvinyl chloride degradation in Spodoptera frugiperda larvae

The accumulation of synthetic plastic waste, particularly polyvinyl chloride (PVC), threatens ecosystems globally. While microbial biodegradation represents a sustainable solution, limited effective PVC-degrading microbial bioresources have been identified. Here, we investigated the gut microbiota of Spodoptera frugiperda larvae, revealing a consistent microbial profile dominated by Enterococcus in both gut contents and tissues. PVC film feeding induced significant microbiota shifts, with functional parallels to PVC powder-fed Tenebrio molitor larvae despite taxonomic divergence. Through enzyme-centric analysis, we found an Enterococcus casseliflavus strain from the gut of S. frugiperda larvae could encode a NAD-dependent oxidoreductase that directly dechlorinates additive-free PVC, representing the first case of enzymatic polymer dechlorination. This enzyme reduced PVC molecular weight (Mn: 12.02 %; Mw: 14.07 %) and notably liberated chloride ions (6.48 mg/L with NADH as a co-factor). Our findings demonstrate the PVC-degrading capacity of S. frugiperda gut microbiota and reveal its dechlorination mechanism, offering an enzymatic candidate for developing novel biocatalysts and engineered microbial strains for enhanced biodegradation. By unravelling insect-associated microbes and enzymes, this work lays a theoretical foundation for their application potentials in sustainable PVC wastes upcycling and microplastic remediation.

Dissolved organic matter (DOM) - Driven variations of cadmium mobility and bioavailability in waterlogged paddy soil

Cadmium (Cd) mobility and bioavailability in paddy soils are strongly influenced by dissolved organic matter (DOM), yet the mechanisms remain unclear. This study conducted a 90-day waterlogged soil incubation with DOM / sulfate amendments under varying Cd levels. Key parameters, including dissolved organic carbon (DOC), pe+pH, Fe/S - related parameters, alongside indicators of Cd mobility and bioavailability, were monitored. Results revealed that DOM addition increased Cd mobility on the 3rd day of incubation (DOI), irrespective of sulfate application, due to Cd desorption from iron oxides and DOM-Cd complexation. After the 10th DOI, DOM addition reduced Cd mobility and bioavailability mainly due to facilitation of sulfide-mediated Cd sequestration driven by Fe-S related reducing bacteria. The combined application with sulfate strengthened this effect. However, in low-Cd soils, DOM addition increased Cd bioavailability since the 45th DOI, likely due to the low Cd/DOM ratio, which limited sulfide immobilization. Nevertheless, sulfate application mitigated this effect. Furthermore, DOM supplementation generally decreased Cd mobility, but increased Cd availability at the 45th DOI in high-Cd soils due to competitive adsorption and Fe transformation. This study demonstrates the dual role of DOM in regulating Cd dynamics and its interaction with sulfate, offering insights for Cd contamination management in paddy soils.

Metabolite-mediated responses of phyllosphere microbiota to powdery mildew infection in resistant and susceptible black currant cultivars

Plant-metabolite-microbe interactions play essential roles in disease suppression. Most studies focus on the root exudates and rhizosphere microbiota to fight soil-borne pathogens, but it is poorly understood whether the changes in phyllosphere metabolites can actively recruit beneficial microbes to enhance disease resistance. In this study, the differences of phyllosphere microbial communities and key leaf metabolites were systematically explored in resistant and susceptible black currant cultivars related to powdery mildew (PM) by integrating microbiome and metabolomic analyses. The results showed that the diversity and composition of microbiome changed, as highlighted by a reduction in microbial alpha-diversity and beta-diversity of susceptible cultivars. An increasing fungal network complexity and a decreasing bacterial network complexity occurred in resistant cultivar. Bacillus, Burkholderia (bacteria), and Penicillium (fungi) were identified as keystone microorganisms and resistance effectors in resistant cultivar. Metabolites such as salicylic acid, trans-zeatin, and griseofulvin were more abundant in resistant cultivar, which had a positive regulatory effect on the abundance of bacterial and fungal keystones. These findings unravel that resistant cultivar can enrich beneficial microorganisms by adjusting leaf metabolites, thus showing the external disease-resistant response. Moreover, the reduced stomatal number and increased tissue thickness were observed in resistant cultivar, suggesting inherent physical structure also provides a basic defense against PM pathogens. Therefore, resistant black currant cultivar displayed multilevel defense responses of physical structures, metabolites, and microorganisms to PM pathogens. Collectively, our study highlights the potential for utilizing phyllosphere microbiome dynamics and metabolomic adjustments in agricultural practices, plant breeding, and microbiome engineering to develop disease-resistant crops.

Pseudomonas syringae exacerbates apple replant disease caused by Fusarium

Apple replant disease (ARD) causes significant economic losses globally, including in China. Analyzing the causes of this replant disease from the perspective of rhizosphere microecology is therefore essential. In this study, we examined rhizosphere soils from apple trees subjected to continuous cropping. The mechanisms underlying ARD were elucidated through high-throughput sequencing of the soil microbiome, co-occurrence network analysis using NetShift, and correlation analyses. Core bacterial microbes were isolated, and their roles in altering the microecological environment were verified through reinoculation experiments. The results indicated that the disease indices for apple seedlings cultivated increased in continuously cropped soils. Bacterial diversity decreased in continuously cropped apple orchards for 10 years (R10) and 15 years (R15), but the relative abundance of Pseudomonas increased. In contrast, fungal diversity increased, with the relative abundance of Fusarium also increasing. As a dominant genus, Pseudomonas exhibited significant network variation after 10 years of consecutive cultivation, suggesting that this microorganism may play a key role in the occurrence of ARD. Moreover, the correlation analysis revealed, for the first time, that Pseudomonas is negatively correlated with bacterial diversity but positively correlated with the relative abundance of Fusarium, indicating a close relationship between Pseudomonas and Fusarium in continuously cropped soil. Four key Pseudomonas amplicon sequence variants (ASVs) strains were isolated from the continuously cropped rhizosphere soil of apple trees, and reinoculation experiments verified that introducing Pseudomonas exacerbated the occurrence of replant diseases in both strawberry and apple, with significantly higher disease indices compared to single Fusarium inoculation. The findings of this study provide new and timely insights into the mechanism underlying the occurrence of ARD.

Lactate production from lactose-rich wastewater: A comparative study on reactor configurations to maximize conversion rates and efficiencies

About 90 % of global lactate production is derived from bacterial fermentation of sugars via pure homofermentative cultures in batch mode. Acid whey, which is a lactose-rich wastewater from the yogurt industry, can be used as an alternative substrate for commercial lactate production. Operating reactor microbiomes reduces the lactate production costs by circumventing sterilization, while continuous operation with biomass retention achieves higher productivity at shorter production times. To find the best reactor configuration with biomass retention for lactate production from acid whey, we operated three different reactor configurations: (1) an upflow anaerobic sludge blanket (UASB) reactor; (2) an anaerobic filter reactor (AFR); and (3) an anaerobic continuously stirred tank reactor (CSTR) with a hollow-fiber membrane module. We operated at different hydraulic retention times (HRTs) to find the optimum production parameters at a temperature of 50 °C and a pH of 5.0. We did not use an inoculum but enriched the endogenous D-lactate-producing Lactobacillus spp. that later dominated the reactor microbiomes (> 90 % relative abundance). Undissociated lactic acid concentrations of more than 60 mmol C L-1 inhibited the microbiomes. We alleviated the inhibition effect by shortening the HRT to 0.6 days and using diluted acid-whey substrate (1.67-fold dilution) to achieve almost complete conversion of the acid-whey sugars to lactate. At the 0.6-day HRT, the AFR and CSTR performed better than the UASB reactor due to their better cell retention abilities. During the period between Day 365-384, we experienced an error in the pH control of the CSTR system during which the pH value dropped to 4.3. After this pH-error period, the lactose and galactose-into-lactate (LG-into-LA) conversion efficiency for the CSTR considerably improved and surpassed the AFR. We achieved the highest lactate conversion rate of 1256 ± 46.3 mmol C L-1 d-1 (1.57 ± 0.06 g L-1 h-1) at a LG-into-LA conversion efficiency of 82.2 ± 3.4 % (in mmol C), with a yield of 0.85 ± 0.02 mmol C mmol C-1 (product per consumed substrate) for the CSTR.

Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies

Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.

Dual-mycorrhizal colonization is determined by plant age and host identity in two species of Populus

Plants have evolved symbioses with mycorrhizal and endophytic fungi that are essential for their growth and survival. While most plants associate with a single guild of mycorrhizal fungi, a select group termed "dual-mycorrhizal plants" associate with both arbuscular mycorrhizal and ectomycorrhizal fungi. Although a shift from predominance of arbuscular mycorrhizal to ectomycorrhizal colonization with plant development has been demonstrated on other dual-mycorrhizal hosts, it is not known how mycorrhizal colonization shifts with plant age in Populus species. We performed a controlled growth experiment with natural field-sourced inocula to test for age-dependent shifts in fungal colonization rates and for host-specific patterns of colonization in two species of Populus (P. tremuloides and P. trichocarpa). We found that only P. trichocarpa displayed dual-mycorrhizal colonization, while P. tremuloides associated with ectomycorrhizal fungi, but not arbuscular mycorrhizal fungi. Both guilds of mycorrhizal fungi increased in abundance with plant age, while root endophytic fungal colonization decreased. Many of the early-colonizing endophytic fungi that we documented have strong saprotrophic capabilities, which may be an important trait for fast colonization. Dark septate endophytes were more abundant than either guild of mycorrhizal fungi, and are likely to be functionally important members of the Populus root fungal community. Our findings represent a novel pattern in the development of dual-mycorrhizal colonization and illustrate that Populus species vary in their association with arbuscular mycorrhizal fungi. Our results also highlight the importance of dark septate endophyte colonization dynamics on dual-mycorrhizal plants.

Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L

Objectives

The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).

Data description

The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).

Depth-dependent response of soil microbial community and greenhouse gas efflux to polylactic acid microplastics and tidal cycles in a mangrove ecosystem

The impacts of microplastics (MPs) on greenhouse gas emissions from mangrove soil remain poorly understood. Previous studies mostly focused on the topsoil in stable inundation state, ignoring the effects of natural tidal cycle and deep soil under different soil oxygen conditions. In this study, we analyzed soil microbial communities and greenhouse gas emissions from mangrove soils across various depths and tidal conditions (by adding seawater to create different inundation durations) in response to polylactic acid (PLA) MP exposure. Results indicated that PLA MPs addition enhances CO2 and CH4 release from the continuously anaerobic subsoil (100-120 cm). With increasing submersion duration, PLA MPs facilitate the emission of CH4 from the topsoil (0-5 cm). An elevated C:N ratio may promote microbial nitrogen mining and organic carbon mineralization, indicating the threat of PLA MPs to soil carbon and nitrogen pools. PLA MPs addition significantly altered the bacterial community structure and reduced bacterial diversity in the subsoil. Increases in the abundance and functioning of communities associated with methanogenesis and sulfate reduction contributed to the release of CO2 and CH4. The duration of inundation had no significant impact on the microbial community structure in the topsoil. These findings demonstrate the accelerating effect of PLA MPs on organic carbon mineralization and carbon release, which was critically regulated by the soil depth and tidal inundation.

Spatial patterns of soil bacterial communities in grazing areas of Southwest Spain

The spatial distribution of soil bacterial communities in agrosilvopastoral systems remains understudied, despite its fundamental role in ecosystem functioning. This study investigates the spatial dynamics of dominant copiotrophic and oligotrophic bacterial phyla in grazing areas of Southwest Spain, focusing on their interactions with land management, soil properties, and environmental covariates. Five management systems; occasional grazing (OG), holistic management (HM), organic farming (OF), conventional rangeland (CR), and conventional grassland (CG) were analyzed across three topographic positions (hilltop, mid-slope, valley bottom), representing a gradient of grazing intensity. A total of 71 soil samples were collected and analyzed using 16S rRNA metabarcoding. Alpha and beta diversity metrics revealed significant shifts in community composition driven by both management and topography, with HM showing higher richness compared to CR and CG. Among dominant phyla, copiotrophic groups such as Proteobacteria and Actinobacteriota were more abundant in upper slope areas and under higher grazing intensity, whereas oligotrophic Verrucomicrobiota was enriched in valley bottoms and under lower grazing pressure. Spatial prediction models based on Random Forest and recursive feature elimination (RFE) identified key environmental drivers, with vegetation indices being more relevant for Proteobacteria and Verrucomicrobiota, and topographic features for Actinobacteriota. RDA and SEM confirmed that animal stocking rate and soil organic matter were major predictors of β-diversity. This study provides novel insights into microbial spatial heterogeneity in Mediterranean grazing systems, highlighting the interplay of management practices, soil characteristics, and topography. The findings underscore the ecological benefits of holistic management in enhancing bacterial diversity and inform strategies for sustainable land use in agrosilvopastoral ecosystems.

Targeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces

Cellulolytic bacteria with probiotic functions play a crucial role in promoting the intestinal health in herbivores. In this study, we aimed to correlate the 16S rRNA gene amplicon sequencing and fiber-degrading enzyme activity data from six different herbivore feces samples. By utilizing the separation and screening steps of probiotics, we targeted and screened high-efficiency fiber-degrading bacteria with probiotic functions. The animals included Maiwa Yak (MY), Holstein cow (CC), Tibetan sheep (TS), Southern Sichuan black goat (SG), Sichuan white rex rabbit (CR), and New Zealand white rabbit (ZR). The results showed that the enzymes associated with fiber degradation were higher in goat and sheep feces compared to cattle and rabbit's feces. Correlation analysis revealed that Bacillus and Fibrobacter were positively correlated with five types of fiber-degrading related enzymes. Notably, the relative abundance of Bacillus in the feces of Tibetan sheep was significantly higher than that of other five herbivores. A strain TS5 with good cellulose decomposition ability from the feces of Tibetan sheep by Congored staining, filter paper decomposition test, and enzyme activity determination was isolated. The strain was identified as Bacillus velezensis by biological characteristics, biochemical analysis, and 16S rRNA gene sequencing. To test the probiotic properties of Bacillus velezensis TS5, we evaluated its tolerance to acid and bile salt, production of digestive enzymes, antioxidants, antibacterial activity, and adhesion ability. The results showed that the strain had good tolerance to pH 2.0 and 0.3% bile salts, as well as good potential to produce cellulase, protease, amylase, and lipase. This strain also had good antioxidant capacity and the ability to antagonistic Staphylococcus aureus BJ216, Salmonella SC06, Enterotoxigenic Escherichia coli CVCC196, and Escherichia coli ATCC25922. More importantly, the strain had good self-aggregation and Caco-2 cell adhesion rate. In addition, we tested the safety of Bacillus velezensis TS5 by hemolysis test, antimicrobial susceptibility test, and acute toxicity test in mice. The results showed that the strain had no hemolytic phenotype, did not develop resistance to 19 commonly used antibiotics, had no cytotoxicity to Caco-2, and did not have acute toxic harm to mice. In summary, this study targeted isolated and screened a strain of Bacillus velezensis TS5 with high fiber-degrading ability and probiotic potency. This strain can be used as a potential probiotic for feeding microbial preparations for ruminants.

Invasive apple snails with their core microbes are underestimated hotspots for disseminating antibiotic resistance genes and virulence factors in aquatic habitats

Antibiotic resistance in pathogens is a threat to human health. The invasive apple snail (Pomacea canaliculata), widely distributed and linked to human activities, is a potential vector for human pathogens. However, its role in spreading antibiotic resistance genes (ARGs) is poorly understood. This study assessed the microbiological risk of this snail by sampling from five interconnected habitats: feces of invasive apple snails and native snails, ditch water, sediment, and soil. Using metagenomic and 16S rRNA sequencing, we analyzed the microbial communities and quantified the ARGs and virulence factors (VFs). Results showed that invasive apple snails carried significantly higher levels of ARGs and VFs compared with the native snails and environmental samples. ARGs and VFs were primarily found co-occurring in Aeromonas and Citrobacter freundii, with Aeromonas identified as the core microbe selected by invasive apple snails. Furthermore, the abundance and community dissimilarity of Aeromonas positively correlated with those of ARGs and VFs, both directly and indirectly through mobile genetic elements. This suggests Aeromonas may play a key role in disseminating ARGs and VFs across habitats. Overall, this study highlights the invasive apple snail as a significant vector for ARGs and virulent pathogens, providing critical insights for risk assessment and targeted management within the One Health framework.

Urbanisation Affects Millipede Gut Microbiota Communities by Impeding Host Gene Flow

Urbanisation leads to the alteration of the living environment of soil fauna and isolates them, significantly influencing the evolutionary processes of soil fauna. Faunal gut microbiota serves to bridge hosts with changing environments; thus, they are viable indicators of host adaptation. For this study, we investigated how urbanisation affects the gut microbiota and population genetics of Spirobolus bungii. The results revealed that urbanisation did not affect the genetic diversity of S. bungii populations but acted as a barrier, which hindered its gene flow. Genetic differentiation was associated with the compositional similarity of gut microbiota among populations; however, environmental distinctions had no impact. Our findings highlighted that gene flow between populations was a critical factor, which supported the premise that urbanisation influences the gut microbiota compositions of species. This study contributes to a deeper understanding of the mechanisms that underlie changes in faunal gut microbiota driven by gene flow in the context of urbanisation.

Insight into endophytic microbiota-driven geographical and bioactive signatures toward a novel quality assessment model for Codonopsis Radix

Codonopsis Radix, a medicinal and dietary herb in traditional Chinese medicine, largely owes its pharmacological efficacy to both intrinsic phytochemistry and symbiotic interactions with plant-associated microbes. Here, we deciphered the geo-environmental regulation of Codonopsis Radix's endophytic microbiota across four major production regions using 16S rRNA/ITS sequencing and bioactive compound profiling. Results demonstrated that the planting environment significantly shaped the endophytic community of Codonopsis Radix, where Bifidobacteriaceae and Muribaculaceae exhibited the strongest correlations with its bioactive components. Monolobus and Bradyrhizobium not only exhibit distinct associations with Lobetyolin and Atractylenolide III respectively, but also demonstrate significant correlations with the key biosynthetic pathways of these compounds. Leveraging machine learning, we developed the first microbiota-driven quality assessment model, achieving 100.0% and 85.7% prediction accuracies for Lobetyolin and Atractylenolide III respectively, using Random Forest algorithms. This dual-metric framework-integrating microbial signatures with chemical profiles-establishes a novel paradigm for Codonopsis Radix quality control, bridging ecological insights with precision agriculture. Our findings illuminate the microbiota's role as a biosynthetic orchestrator in geoherbalism, offering actionable strategies for sustainable cultivation and standardized production of Codonopsis Radix.

Intestinal microbiome profile of the brown rock sea cucumber (Holothuria glaberrima) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction

Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber's intestinal biology.

Grape polyphenols reduce fasting glucose and increase hyocholic acid in healthy humans: a meta-omics study

Grape polyphenols (GPs) are rich in B-type proanthocyanidins, which promote metabolic resilience. Longitudinal metabolomic, metagenomic, and metaproteomic changes were measured in 27 healthy subjects supplemented with soy protein isolate (SPI, 40 g per day) for 5 days followed by GPs complexed to SPI (GP-SPI standardized to 5% GPs, 40 g per day) for 10 days. Fecal, urine, and/or fasting blood samples were collected before supplementation (day -5), after 5 days of SPI (day 0), and after 2, 4 and 10 days of GP-SPI. Most multi-omic changes observed after 2 and/or 4 days of GP-SPI intake were temporary, returning to pre-supplementation profiles by day 10. Shotgun metagenomics sequencing provided insights that could not be captured with 16S rRNA amplicon sequencing. Notably, 10 days of GP-SPI decreased fasting blood glucose and increased serum hyocholic acid (HCA), a glucoregulatory bile acid, which negatively correlated with one gut bacterial guild. In conclusion, GP-induced suppression of a bacterial guild may lead to higher HCA and lower fasting blood glucose.

Host-specific microbiome-rumination interactions shape methane-yield phenotypes in dairy cattle

Enteric methane emissions (EMEs) negatively impact both the environment and livestock efficiency. Given the proposed link between CH4 yield and the rumination time (RT) phenotype, we hypothesize that this connection is mediated by the gut microbiome. This study investigated the RT-microbiome-EME connection using rumination-bolus, fecal, and rumen microbiomes as non-invasive proxies for identifying low-EME cows. High-RT cows ruminated 94 minutes longer per day (20%) and exhibited 26% lower EME than low-RT cows, confirming a strong RT-CH4-yield association. Microbial analysis revealed conserved methanogen diversity across the rumen, bolus, and fecal microbiomes, though functional differences were evident. High-RT cows had a greater abundance of Methanosphaera stadtmanae, suggesting an increased potential for methylotrophic methanogenesis, whereas low-RT cows exhibited higher Methanobrevibacter YE315 abundance, indicative of CO2-utilizing methanogenesis. Additionally, high-RT cows showed increased alternative hydrogen sinks, supported by upregulated genes encoding fumarate reductase, sulfate reductase, nitrate reductase, and ammonia-forming nitrite reductase, thereby reducing hydrogen availability for methanogenesis. Metabolically, high-RT cows had higher propionate concentrations and were enriched with rapid-fermenting bacteria (Prevotella, Sharpea, Veillonellaceae, and Succinivibrionaceae), whereas low-RT cows exhibited higher acetate concentrations with elevated acetate-producing pathways, reflecting differences in energy partitioning mechanisms. This study establishes RT as a microbiome-linked, non-invasive screening tool for identifying low-EME cows. The observed microbial and metabolic shifts in high-RT cows suggest that RT-based selection could enhance methane mitigation, rumen efficiency, and climate-smart livestock production. Leveraging RT-associated microbial profiles offers a scalable and cost-effective approach to reducing EME in cattle.

IMPORTANCE

Methane emissions from livestock contribute to climate change and reduce animal efficiency. This study reveals that cows with longer rumination times (chewing cud for an extra 94 minutes daily) produce 26% less methane than cows with shorter rumination times. The gut microbiome plays a key role-low-methane cows host microbial communities that produce less methane while efficiently utilizing hydrogen for energy conservation in the rumen. By analyzing rumination sensor data and/or in combination with microbial profiles from rumen or fecal samples, farmers can non-invasively identify and select cows that naturally emit less methane. This scalable, cost-effective strategy offers a practical solution for reducing livestock's environmental footprint while enhancing efficiency and advancing climate-smart agriculture.

Unlocking the agro-physiological potential of wheat rhizoplane fungi under low P conditions using a niche-conserved consortium approach

Plant growth-promoting fungi (PGPF) hold promise for enhancing crop yield. This study delves into the fungal diversity of the wheat rhizoplane across seven Moroccan agricultural regions, employing a niche-conserved strategy to construct fungal consortia (FC) exhibiting higher phosphorus (P) acquisition and plant growth promotion. This study combined culture-independent and culture-dependent methods exploring taxonomic and functional diversity in the rhizoplane of wheat plants obtained from 28 zones. Twenty fungal species from eight genera were isolated and confirmed through internal transcribed spacer (ITS) Sanger sequencing. P solubilization (PS) capacity was assessed for individual species, with Talaromyces sp. (F11) and Rhizopus arrhizus CMRC 585 (F12) exhibiting notable PS rates, potentially due to production of organic acids such as gluconic acid. PGPF traits and antagonism activities were considered when constructing 28 niche-conserved FC (using isolates from the same zone), seven intra-region FC (different zones within a region), and one inter-region FC. Under low P conditions, in planta inoculation with niche-conserved FC (notably FC14 and FC17) enhanced growth, physiological parameters, and P uptake of wheat, in both vegetative and reproductive stages. FC14 and FC17, composed of potent fungi such as F11 and F12, demonstrated superior plant growth benefits compared with intra- and inter-region constructed FC. Our study underscores the efficacy of the niche-conserved strategy in designing synthetic fungal community from isolates within the same niche, proving significant agro-physiological potential to enhance P uptake and plant growth of wheat.

Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora

Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the community dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition, while the location of the tree in the orchard and the flower's location on the tree had a marginal effect. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted toward E. amylovora dominating the community as time and phenological stages progressed, leading to a decreased community diversity. The E. amylovora population was represented almost exclusively by six amplicon sequence variants (ASVs) with similar proportions throughout the entire collection period. Other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of ASVs, and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Taxon-specific succession patterns under E. amylovora spread should be considered when choosing candidates for antagonist-based treatments for fire blight.IMPORTANCEThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the Rosaceae flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, the study design enabled us to evaluate the contribution of five important environmental parameters to community composition. We identified different ASV succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help improve biological treatments for fire blight.

Navigating complexities of polymorphic microbiomes in endometrial cancer

The microbiome is key to understanding endometrial cancer (EC) etiology and prevention strategies, implicated in the regulation of estrogen in estrogen-driven cancers. Utilizing robust methodologies in the QIIME 2 platform, we examined 16S rRNA vaginal and rectal microbiome data from an EC cohort: 192 women with benign gynecologic conditions, endometrial hyperplasia, or endometrial cancer. Distinct microbial compositions and community networks specific to EC were identified and related to histological grade with adjustments for EC risk factors. Vaginal health-associated Lactobacillus and Limosilactobacillus, and rectal Prevotella and Peptoniphilus, were depleted in EC, while detrimental vaginal Anaerococcus, Porphyromonas, Prevotella, Peptoniphilus, and rectal Buttiaxella were enriched. Significant bacterial features were shared between rectal and vaginal sites in EC, such as Prevotella timonensis and Peptoniphilus A. Vaginal Lactobacillus abundance contributed to less feature sharing from the rectum. Putative microbial metabolic analysis identified dysregulation of amino acid, complex carbohydrate, and hormone metabolism amongst patients with EC.

Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing

Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.

Plant microbiome responses to bioinoculants and volatiles

BACKGROUND

There is an increase in the adoption of biological solutions for plant production as a means of attaining sustainable agriculture. A detailed understanding of the influence of specific bioinoculants and their volatile metabolites on native soil and plant microbiomes can improve future microbiome management practices.

RESULTS

Here, we examined the effect of bacterial inoculants and volatile compounds as individual and combined treatments on apple plant and soil microbiome. The study used specially designed microcosms that facilitated the separation of the different plant compartments. A compartment- and soil-specific effect of treatments on the native soil and plant microbiome was observed. The live bacterial inoculants as compared to their volatiles had a stronger effect on the plant and soil microbiome, particularly the root microbial community. The combined effect of bacterial inoculants was higher compared to volatiles (R2 = 5% vs. 3%). Treatment-specific effects were observed, like the influence of 2-butanone on the phyllosphere bacterial diversity, and an increase in fungal richness in Serratia-treated soils.

CONCLUSIONS

Among the examined treatments, inoculation with bacteria compared to volatile metabolites induced more significant shifts within the plant and soil microbiome. This observation has implications regarding the merits of applying living microorganisms. The findings highlight the potential of microbiome management approaches for enhancing microbiota functions.

Stronger together: harnessing natural algal communities as potential probiotics for inhibition of aquaculture pathogens

Intensive fish rearing in aquaculture is challenged by infectious diseases, and although vaccines have been successfully developed for mature fish, alternative disease control measures are needed for fish larvae and juveniles. Probiotics offer a promising alternative to antibiotics, with the potential to reduce the risk of antibiotic resistance. Probiotics are typically isolated and used as pure cultures; however, in natural environments, it is the concerted effort of the complex microbiome that keeps pathogens at bay. Here, we developed an in vitro assay to evaluate the anti-pathogen efficacy of mixed algal microbiomes from the live feed microalgae Tetraselmis suecica and Isochrysis galbana. The inhibition of a green fluorescent protein (GFP)-tagged Vibrio anguillarum, a key fish pathogen, by microbial communities was measured and quantified as reduction in fluorescence. The Isochrysis galbana microbiome was more inhibitory to V. anguillarum than the Tetraselmis suecica microbiome. During co-culture with the pathogen, the bacterial density of the Isochrysis microbiomes increased, while the diversity was reduced as determined by metataxonomic analyses. Bacteria isolated from the fully inhibitory microbiomes were members of Alteromonadaceae, Halomonadaceae, Rhodobacteraceae, Vibrionaceae, Flavobacteriaceae, and Erythrobacteraceae. Although some strains individually inhibited the pathogen, these were not the key members of the microbiome, and enhanced inhibition was observed when Sulfitobacter pontiacus D3 and Vreelandella alkaliphila D2 were co-cultured, even though neither was inhibitory as monocultures. Thus, this study demonstrates that microbial communities derived from natural algal microbiomes can have anti-pathogen effects, and that bacterial co-cultures may offer synergistic advantages over monocultures as probiotics, highlighting their promise for aquaculture health strategies.IMPORTANCEAquaculture is the fastest-growing food protein-producing sector, and sustainable disease control measures are required. Probiotics have gained interest as a promising solution for combating fish pathogens, and using mixtures of microorganisms rather than pure cultures may represent a more stable pathogen control. We developed an assay using green fluorescent protein (GFP) tagging of a fish pathogen, enabling the quantitative assessment of the anti-pathogen effects of complex microbiomes. We show that the efficiency of pathogen suppression can be increased with co-cultures compared to monocultures, thus emphasizing the potential in using mixtures of bacteria as probiotics.

Plastic degradation in Lake Geneva: Influence of depth, seasonal shifts, and bacterial community dynamics

Aquatic ecosystems suffer disproportionately from plastic pollution given that they integrate material from terrestrial watersheds. Most studies on microbial colonisation and degradation of plastics have focused on marine environments, leaving a knowledge gap for freshwaters. Our study explores the possible degradation and the role of bacterial community composition of plastics in Lake Geneva. We exposed polyethylene terephthalate (PET) and low-density polyethylene (LDPE) for 45 weeks to environmental lake gradients that change with depth and season. The substrates were suspended at 2 and 30 m depth, resulting in strikingly different environmental conditions for biofilm development, including light (PAR), temperature, and nutrient availability. We monitored the bacterial colonisation using 16S rRNA sequencing and assessed the abundance of the alkane hydrolase gene (alkB) to evaluate the potential ability of the biofilm to degrade PET and LDPE. Additionally, we analysed plastic surface modifications through spectroscopy, contact angle measurements and microscopy. We found that the PET surface showed no degradation after 45 weeks in the lake, at either depth. The LDPE surface at 2 m exhibited a decrease in hydrophobicity, but no evidence of oxidation or degradation was found. In contrast, the LDPE surface at 30 m displayed oxidation, a decrease in hydrophobicity, and porous cavities. In addition, we observed an increase in the alkane alkB gene abundance in the biofilm, with the development of plastic-degrading taxa in the community. Our results underline the complexity of plastic degradation in aquatic ecosystems; not only does the type of plastic have an effect, so do the spatio-temporal variable environmental lake conditions and the biofilm community. The multifactorial nature of these processes complicates predictions on the fate of plastics in the environment.

Custom-made medium approach for effective enrichment and isolation of chemolithotrophic iron-oxidizing bacteria

Chemolithotrophic neutrophilic iron (Fe)-oxidizing bacteria, which mainly belong to the family Gallionellaceae, universally prevail in terrestrial environments changing Fe cycling. However, they are typically recognized as difficult-to-culture microbes. Despite efforts, there are few Fe(II)-oxidizing lithotroph isolates; hence, their physiological and ecological knowledge remains limited. This limitation is largely owing to difficulties in their cultivation, and we hypothesize that the difficulty exists because substrate and mineral concentrations in the cultivation medium are not tuned to a specific environmental condition under which these organisms live. To address this hypothesis, this study proposes a novel custom-made medium approach for chemolithotrophic Fe(II)-oxidizing bacteria; a method that manipulates medium components through diligent analysis of field environment. A new custom-made medium simulating energy substrates and nutrients under the field condition was prepared by modifying both chemical composition and physical setup in the glass-tube medium. In particular, the modification of the physical setup in the tube had a significant effect on adjusting dissolved Fe(II) and O2 concentrations to the field environment. Using the medium, Gallionellaceae members were successfully enriched and a new Gallionellaceae species was isolated from a natural hot spring site. Compared with conventional medium, the custom-made medium has significantly higher ability in enriching Gallionellaceae members.

Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments

Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria, and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from tetrachloroethene respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 medium-quality bins with over 75% completeness and less than 5% contamination. Sixteen bins harbored RDase genes and were affiliated taxonomically to the class of Bacilli and phyla of Bacteroidota, Synergistota, and Spirochaetota, which have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically close to the genus Vulcanibacillus (phylum Firmicutes), contained an unprecedented 97 reductive dehalogenase (RDase) genes. Of these, 84 RDase genes of bin.26 were transcribed during tetrachloroethene dechlorination in addition to RDase genes from the members of Synergistales (bin.5 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested that the RDase genes were likely under the regulation of transcriptional regulators not previously associated with organohalide respiration, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to add to the current knowledge of the diversity, activity, and regulation of RDase genes.IMPORTANCEPristine marine environment is the major reservoir for naturally produced organohalides, in which reductive dehalogenation underneath plays an important role in the overall cycling of these compounds. Here, we obtain some novel OHRB genomes from Aarhus Bay marine sediments, which are phylogenetically distant to the well-documented OHRB and widely distributed across the bacterial phyla, such as Bacteroidota, Synergistota, and Spirochaetota. Furthermore, transcriptional profiles unravel that these RDase genes are induced differently, and their activity is controlled by diverse regulatory systems. Accordingly, elucidating the reductive dehalogenation of pristine marine environments substantially advances our understanding of the diversity, phylogeny, and regulatory variety of dehalogenating bacteria contributing to the global halogen cycle.

Biodegradation of Benzo(a)pyrene in Contaminated Soil: Plant and Microorganism Contributions from Isotope Tracing

Biological degradation effectively removes benzo(a)pyrene (BaP) from contaminated soil; however, knowledge regarding the contributions of plant absorption, microbial degradation, and volatilization to BaP removal remains limited. In this study, the BaP removal pathway in contaminated soil was investigated. The structural evolution of the microbial community in contaminated soil was revealed using a comparative experimental study. BaP, as a representative of high-molecular-weight polycyclic aromatic hydrocarbons, was removed from freshly contaminated soil by microbial degradation, plant absorption, and volatilization in proportions of 20.955%, 12.771%, and 0.005%, respectively. The proportions of BaP removed by microbial degradation, plant absorption, and volatilization in aged contaminated soil were 29.471%, 16.453%, and 0.004%. Microbial degradation was the most responsible mechanism for BaP removal. Moreover, a higher number of BaP degrading bacteria occurred in the aged contaminated soil. At the genus level, Pseudomonas and Sphingomonas were detected in both types of soils, being the key bacterial species involved in BaP degradation.

Serratia marcescens Sm85 produces dimethyl disulfide defense against rice sheath blight and effects on phyllosphere bacterial community

BACKGROUND

Rice sheath blight (RSB), caused by Rhizoctonia solani Kuhn, significantly impacts rice yield and quality. The extensive use of chemical pesticides, while often effective, requires high application rates, causes environmental damage, is expensive, and contributes to the development of pesticide resistance. The lack of reliability and robustness of these conventional techniques necessitates the development of sustainable and environmentally friendly agricultural practices. Identifying novel biological control agents is crucial for developing effective and eco-friendly strategies to manage RSB.

RESULTS

This study identifies S. marcescens 85 (Sm85), isolated from rice stems, as a potential biocontrol agent against RSB. Sm85 produces the volatile chemical dimethyl disulfide (DMDS), which has antagonistic activity both in vivo (67.4% effective) and in vitro (97.7% effective). DMDS disrupts pathogen cell membrane integrity by increasing reactive oxygen species (ROS) production and reducing ergosterol content. The pot experiments demonstrated that DMDS treatment significantly reduces RSB lesion length, with a control effect comparable to commercial fungicides. The high-throughput data revealed that DMDS application alters the phyllosphere microbial community structure, increasing its richness and diversity. Notably, DMDS treatment enriches potentially beneficial bacteria such as Stenotrophomonas and Burkholderia, known for their roles in plant stress tolerance and pesticide degradation. Functional gene analysis reveals an upregulation of sulfur metabolism-related genes in the phyllosphere microbiome, suggesting adaptive responses to DMDS.

CONCLUSION

This study highlights the potential of Sm85 and its volatile metabolite DMDS as eco-friendly alternatives for RSB management, while also emphasizing the importance of considering microbial community dynamics in biocontrol strategies. © 2025 Society of Chemical Industry.

Deciphering the Language of Intestinal Microbiota Associated with Sepsis, Organ Failure, and Mortality in Patients with Alcohol-Related Acute-on-Chronic Liver Failure (ACLF): A Pioneer Study in Latin America

ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico.

Exploring the relationship between APOEε4 allele and gut microbiota composition and function in healthy adults

The APOE ε4 allele (APOE4) is a known risk factor for neurodegenerative and cardiovascular diseases, but its link to body composition and metabolism remains debated. The gut microbiota influences host metabolism and immunity, yet its relationship with APOE genotype in healthy individuals is not well understood. The objective of this work was to examine associations between APOE genotype and gut microbiota composition and function in healthy adults, focusing on microbial and metabolic differences related to the APOE4 allele. Seventy-seven healthy Spanish adults were genotyped for APOE. Fecal microbiota profiles were assessed by 16 S rRNA gene sequencing, and predicted functions were inferred using PICRUSt2. Body composition (DEXA) and physical activity (accelerometry) were also measured. APOE4 carriers exhibited subtle shifts in microbiota composition, including a five-fold reduction in Megamonas and lower abundance of the Eubacterium brachy group-both linked to energy harvest and adiposity-compared to APOE3 homozygotes. An uncharacterized Puniceicoccaceae genus was enriched in APOE4 carriers. Although E. brachy group abundance correlated with adiposity, no significant differences in body composition were observed. Functional predictions showed APOE4-associated microbiota enriched in pathways for carotenoid biosynthesis and trehalose metabolism, and depleted in tryptophan biosynthesis, propionate production, and multidrug resistance mechanisms. APOE4 carriers harbor gut microbiota with distinct taxonomic and functional features, potentially reflecting adaptations to metabolic and oxidative challenges. These findings underscore the relevance of the gut microbiome in shaping APOE4-associated phenotypes and warrant further investigation into its mechanistic contributions to health and disease.

Shell bacterial community dynamics suggest that American lobster (Homarus americanus) impoundment shell disease is caused by a dysbiosis

Impoundment shell disease (ISD) in the American lobster (Homarus americanus) is a distinct pathological condition from the more well-known epizootic shell disease. It is commonly observed at low prevalences in live American lobsters held overwinter in tidal pounds and significantly reduces their economic value. Impoundment shell disease was originally described in 1937; however, its etiology remains unclear. The main goal of this study was to characterize the bacterial community associated with ISD in Canadian lobsters. Lobsters were collected from a pound in southwest Nova Scotia, Canada, and the full 16S rRNA gene of bacterial communities from lesion and healthy shell areas of asymptomatic (As), moderately symptomatic (MS) and severely symptomatic (SS) animals was sequenced. Pielou evenness and Shannon diversity indexes of alpha-diversity were higher in healthy areas compared to lesion areas. Beta-diversity metrics indicate that the bacterial diversity differences are driven mainly by the relative abundance of a small number of bacteria, rather than the specific taxa present in the samples. Taxa were designated as being potentially involved with ISD based on their relative frequency, relative abundance or being core bacteriome in the lesion shell area. Among those found in this study, Tenacibaculum and Vibrio were previously described in ISD lesions; but others, such as Cellvibrionaceae, Polaribacter, Maribacter and Sulfitobacter were not. Altogether, the findings of this study indicate that ISD is driven by dysbiosis. Moreover, the inconsistency of taxa with previous studies may indicate that ISD consists of a combination of specific functional groups of bacteria, rather specific taxa.

Microbial diversity of high-elevated fumarole fields, low-biomass communities on the boundary between ice and fire

Fumarole fields on active volcanoes are habitats that host unique microbial ecosystems. However, DNA extraction from them for further analysis is rather challenging. In this study, we compared two different ways of sample homogenization for DNA extraction to further profile the microbial communities of active fumarolic fields from Elbrus and Ushkovsky volcanoes and the frozen fumarole deposits of Fujiyama. Vertical homogenizer gave significantly higher DNA concentrations for the Elbrus samples, and more archaeal amplicon sequence variants for Elbrus and Ushkovsky samples compared to the horizontal one. This suggests that vertical homogenizer might be preferable for DNA extraction from sandy and rocky soils. Independent of the homogenizer type, the dominant phyla for Elbrus were Acidobacteriota and Pseudomonadota, and Crenarchaeota for Ushkovsky. The bacterial community of Fuji was less diverse, with Actinomycetota, Pseudomonadota and Bacillota being the dominant phyla. Thus, the studied fumaroles showed distinct microbial profiles, revealing unique adaptations to their respective extreme environments. Within the fungal community, Ascomycota, Basidiomycota and Chytridiomycota were the most dominant phyla for all three volcanoes, but their abundance varied. This study offers the first comprehensive analysis of microbial and fungal communities of active and frozen fumarolic fields, and demonstrates that the choice of methodology can significantly influence the understanding of microbial diversity in extreme environments.

Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis

Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.

Temporal microbial colonization on different forages is driven by the rumen environmental conditions

The rumen is one of the four compartments of the ruminant stomach and houses a diverse array of anaerobic microbes that play a crucial role in feed digestion and volatile fatty acid (VFA) production. The aim of this study was to explore how two different in vivo rumen environmental conditions, AHR (created from sheep-fed alfalfa hay) and CSR (created from sheep-fed corn stover), affect fiber digestion and rumen bacterial colonization in relation to two types of forage, alfalfa hay (AH) and corn stover (CS). Both AH and CS forages were subjected to in-sacco incubation in AHR and CSR conditions for a period of 48 h. The results revealed that CSR exhibited a less variant pH, lower total VFA concentration, and higher acetate-to-propionate ratio than AHR. CSR significantly enhanced the degradation of neutral detergent fiber and acid detergent fiber in both incubated forages (AH and CS). Although CSR did not improve the degradation of dry matter (DM) or crude protein (CP) on AH, it improved the degradation of DM and CP on CS. Both CS and AH incubated under CSR were found to have a greater abundance of fibrolytic bacteria (e.g., Fibrobacter and Butyrivibrio 2) compared to the same forage incubated under AHR, especially during the initial stages of incubation. However, CS and AH incubated under AHR were colonized by bacteria specialized in breaking down soluble carbohydrates (e.g., Prevotella and Succinivibrio). Compared with AHR, CSR enhanced the degradation rates of both incubated forages (CS and AH). These findings underscore the role of the rumen microenvironment in affecting the composition of adherent microbial communities and enhancing the breakdown of forages. Therefore, optimizing the rumen microenvironment to promote the attachment of fibrolytic bacteria during the early fermentation stages while minimizing hydrogen accumulation to stabilize the pH could lead to improved forage fermentation and animal performance.

Endophytic fungal community composition and function response to strawberry genotype and disease resistance

Background

Utilizating the plant endophytic microbiomes to enhance pathogen resistance in crop production is an emerging alternative method to chemical pesticides. However, research on the composition and role of microbial communities related to perennial fruit plants, such as the strawberry, is still limited.

Methods

We provide a comprehensive description of the composition and diversity of fungal communities in three niches (root, stem, and leaf) of three strawberry cultivars ('White Elves', 'Tokun', and 'Akihime') using internal transcribed spacer (ITS) rRNA amplicon sequencing and isolation culture methods. In addition, we also evaluated the disease tolerance ability of three strawberry cultivars to Colletotrichum gloeosporioides and Alternaria alternata through pathogenicity testing.

Results

'White Elves' has stronger resistance to Colletotrichum gloeosporioides, and Alternaria alternata, followed by 'Tokun', while 'Akihime' has relatively weaker resistance to these pathogens. A total of 258 fungal strains were isolated from healthy strawberry plants and assigned to 34 fungal genera based on morphological and molecular characteristics analysis. Beneficial fungal genera such as Trichoderma and Talaromyces were more prevalent in 'White Elves', whereas common pathogenic fungi in strawberry, such as Colletotrichum, Alternaria, and Fusarium, were more prevalent in 'Akihime'. The composition and diversity of microbial communities vary among genotypes, and resistance to pathogens may play dominant roles in determining the microbial community structure. This study's results aid the biological control of strawberry fungal diseases and are useful for plant microbiome engineering in strawberry cultivation.

Tetracycline has no long-term effects on gut physiology and microbiome of the new world screwworm, Cochliomyia hominivorax, which has positive implications for transgenic male-only rearing systems

Tetracycline repressible (Tet-Off) male-only sexing systems have great potential for improving the efficacy of sterile insect control programs in addition to reducing rearing cost. The relationship between insects and their microbial symbionts, as well as potential physiological stress caused by tetracycline class antibiotics, pose concerns that Tet-Off strains could have reduced fitness in nature. Here, we evaluated the biological performance, midgut microbiome, and midgut transcriptomes of wild-type screwworm, Cochliomyia hominivorax, reared in diet without Tc (control), with Tc (on-Tc), or a pseudo "male-only" condition where offspring of the Tc fed line were reared without Tc (post-Tc), like Tet-Off strains previously developed for this species. Biological performance was not significantly changed by the inclusion of Tc in the diet, and in most cases the flies reared with Tc were generally more fit than lines reared without Tc. The gut microbiome and transcriptome revealed interesting and similar patterns. In both surveys, the greatest changes were between both control and post-Tc treatments and the on-Tc treatment. Very few differences were observed between control and post-Tc treatments, suggesting that there are few negative persistent effects of Tc exposure to fly colonies, and flies revert to their natural state rapidly after the removal of Tc. These results suggest there are limited negative impacts of Tet-Off regulatory systems for use by the C. hominivorax eradication program, and differences observed in Tet-Off strain performance are likely not related to Tc exposure.

Characterisation and comparison of semen microbiota and bacterial load in men with infertility, recurrent miscarriage, or proven fertility

Several studies have associated seminal microbiota abnormalities with male infertility but have yielded differing results owing to their limited sizes or depths of analyses. The semen microbiota during recurrent pregnancy loss (RPL) has not been investigated. Comprehensively assessing the seminal microbiota in men with reproductive disorders could elucidate its potential role in clinical management. We used semen analysis, terminal-deoxynucleotidyl-transferase-mediated-deoxyuridine-triphosphate-nick-end-labelling, Comet DNA fragmentation, luminol reactive oxidative species (ROS) chemiluminescence, and metataxonomic profiling of semen microbiota by 16S rRNA amplicon sequencing in this prospective, cross-sectional study to investigate composition and bacterial load of seminal bacterial genera and species, semen parameters, ROS, and sperm DNA fragmentation in men with reproductive disorders and proven fathers. 223 men were enrolled, including healthy men with proven paternity (n=63), the male partners in a couple encountering RPL (n=46), men with male factor infertility (n=58), and the male partners of couples with unexplained infertility (n=56). Rates of high sperm DNA fragmentation, elevated ROS, and oligospermia were more prevalent in the study group compared with control. In all groups, semen microbiota clustered into three major genera-dominant groups (1, Streptococcus; 2, Prevotella; 3, Lactobacillus and Gardnerella); no species clusters were identified. Group 2 had the highest microbial richness (p<0.001), alpha-diversity (p<0.001), and bacterial load (p<0.0001). Overall bacterial composition or load has not been found to associate with semen analysis, ROS, or DNA fragmentation. Whilst global perturbation of the seminal microbiota is not associated with male reproductive disorders, men with unidentified seminal Flavobacterium are more likely to have abnormal seminal analysis. Future studies may elucidate if Flavobacterium reduction has therapeutic potential.

Improvement of antioxidant capacity and gut microbiota balance in adult zebrafish (Danio rerio) by addition of fermented distillers' dried grains with solubles (DDGS)

The continuous high price of fishmeal has prompted the aquaculture industry to seek alternative protein sources. Distillers' dried grains with solubles (DDGS) possess significant utilization value as a plant-based protein, yet its substitution ratio is limited due to the anti-nutritional factors. This study aimed to assess the potential of compound bacteria-fermented DDGS as a protein source for aquatic feed. DDGS was fermented using complex bacteria, and the treatment group with the highest crude protein content after fermentation was used as the raw material for the experimental diets. Based on different replacement levels of hatching brine shrimp with DDGS, four dietary groups were established: D0, D10, D20, and D30. Each tank was stocked with 30 zebrafish, with three replicates per treatment group. Fish were fed twice daily, and the experiment lasted for 30 days. The main results are as follows: the inclusion of 10% fermented DDGS in the diet significantly enhanced superoxide dismutase and glutathione activities in both the gut and muscle tissue of zebrafish compared to the control group (D0). The relative abundance of the probiotic Cetobacterium exhibited a significant increase of 38% in the D10 group compared to the D0 group. A PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) study unveiled a substantial augmentation in the abundance of metabolic pathways, encompassing cofactor and vitamin metabolism as well as carbohydrate metabolism. In conclusion, the findings demonstrated that incorporating fermented DDGS into the diet significantly augmented the antioxidant capacity and disease resistance of zebrafish.

Gut microbiota mediates SREBP-1c-driven hepatic lipogenesis and steatosis in response to zero-fat high-sucrose diet

OBJECTIVES

Sucrose-rich diets promote hepatic de novo lipogenesis (DNL) and steatosis through interactions with the gut microbiota. However, the role of sugar-microbiota dynamics in the absence of dietary fat remains unclear. This study aimed to investigate the effects of a high-sucrose, zero-fat diet (ZFD) on hepatic steatosis and host metabolism in conventionally raised (CONVR) and germ-free (GF) mice.

METHODS

CONVR and GF mice were fed a ZFD, and hepatic lipid accumulation, gene expression, and metabolite levels were analyzed. DNL activity was assessed by measuring malonyl-CoA levels, expression of key DNL enzymes, and activation of the transcription factor SREBP-1c. Metabolomic analyses of portal vein plasma identified microbiota-derived metabolites linked to hepatic steatosis. To further examine the role of SREBP-1c, its hepatic expression was knocked down using antisense oligonucleotides in CONVR ZFD-fed mice.

RESULTS

The gut microbiota was essential for sucrose-induced DNL and hepatic steatosis. In CONVR ZFD-fed mice, hepatic fat accumulation increased alongside elevated expression of genes encoding DNL enzymes, higher malonyl-CoA levels, and upregulation of SREBP-1c. Regardless of microbiota status, ZFD induced fatty acid elongase and desaturase gene expression and increased hepatic monounsaturated fatty acids. Metabolomic analyses identified microbiota-derived metabolites associated with hepatic steatosis. SREBP-1c knockdown in CONVR ZFD-fed mice reduced hepatic steatosis and suppressed fatty acid synthase expression.

CONCLUSIONS

Sucrose-microbiota interactions and SREBP-1c are required for DNL and hepatic steatosis in the absence of dietary fat. These findings provide new insights into the complex interplay between diet, gut microbiota, and metabolic regulation.

Host-Microbial Cometabolite Ursodeoxycholic Acid Protects Against Poststroke Cognitive Impairment

BACKGROUND

Poststroke cognitive impairment (PSCI) is a common residual disability after stroke, often underestimated and underdiagnosed. We previously found that ursodeoxycholic acid (UDCA), a host-microbiota cometabolite, ameliorates brain damage in stroke mice. Based on these findings, we aimed to evaluate the predictive value of UDCA for PSCI risk in a prospective cohort study.

METHODS AND RESULTS

We recruited 202 patients with mild acute ischemic stroke and 63 patients with symptomatic large-artery atherosclerotic stenosis as the modeling and external validation cohorts, respectively. Mice were subjected to transient middle cerebral artery occlusion, and cognitive function was assessed using the Morris water maze test. Patients with mild acute ischemic stroke who developed PSCI exhibited significant alterations in gut microbiota and plasma bile acid profiles during the acute stroke phase, including a notable reduction in UDCA level. Through feature selection and machine learning, we constructed a predictive model for PSCI incorporating plasma UDCA level, the relative abundance of Clostridia, Bacilli, and Bacteroides, as well as age, educational level, and the presence of moderate to severe white matter lesions. This model exhibited robust predictive performance in both internal (area under the curve, 0.904 [95% CI, 0.808-1.000]) and external (area under the curve, 0.838 [95% CI, 0.742-0.934]) validations. Animal studies in mice also showed reduced UDCA levels in plasma and brain tissue following stroke. UDCA administration improved cognitive function in stroke mice by reducing hippocampal microglial activation and neuronal apoptosis.

CONCLUSIONS

Our findings indicate that UDCA has potential as a biomarker for predicting PSCI risk and plays a neuroprotective role in the progression of PSCI. This suggests that early identification and intervention targeting UDCA could represent a promising strategy for the prevention and treatment of PSCI.

Probiotic Administration Modulates Gut Microbiota and Suppresses Tumor Growth in Murine Models of Colorectal Cancer

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide with limited treatment options for advanced disease stages. Growing evidence implicates the gut microbiota in CRC pathogenesis, prompting interest in probiotics as a potential therapeutic strategy. In this study, we evaluated the effects of two probiotic compositions, CI (a mix of lactobacilli and bifidobacteria) and CII (bifidobacteria alone), in two murine CRC models: the orthotopic MC-38 cecum injection model and the inflammation-driven azoxymethane/dextran sodium sulfate (AOM/DSS) model. CI showed significant anti-tumor effects in the orthotopic model, reducing tumor weight and volume, which was, however, not associated with robust immune activation, suggesting microbiota-driven mechanisms. In contrast, CII was more effective in the AOM/DSS model, reducing colonic inflammation and completely preventing tumor development. Our study demonstrates that probiotics might have great therapeutic potential via modulation of the gut microbiota, and they can exert anti-tumor effects in murine models of CRC with distinct compositions showing differential efficacy depending on the model. CI stabilized the gut microbiome and inhibited pro-tumorigenic taxa in the MC-38 cecum injection model, while CII exhibited anti-inflammatory properties in the AOM/DSS model, highlighting the potential of probiotics as context-specific interventions for CRC. These findings contribute to the growing body of evidence supporting microbiota-targeted strategies in oncology and their relevance for therapeutic applications.

Parity-Associated Differences in the Antioxidants and Fecal Microbiota of Bactrian Camels

Camels survive in deserts through unique, adapted metabolic and immunological processes that are normally lethal to other species. Antioxidants and the gastrointestinal microbiota play major roles in redox homeostasis, yet they remain unexplored in camels to date. The objectives of this study were to characterize the dynamics of milk antioxidants, serum antioxidants, and the fecal microbiome of lactating Bactrian camels with different parities. In total, 30 lactating camels were selected and categorized into the following 3 groups: 10 were assigned to the first parity group (P_1), 10 were classified into the third parity group (P_3), and 10 belonged to the fifth parity group (P_5). The antioxidant parameters of the lactating camels were determined in milk and serum. The fecal microbial community of lactating camels was assessed using 16S rRNA amplicon sequencing, and the resulting library was sequenced on an Illumina NovaSeq platform. The amount of total antioxidant capacity (T-AOC) and antioxidant activity for polypepetides (DPPH) in the third parity was the highest among the groups both in the camel milk and its serum. In the case of hydroxyl radical (OH) and SOD, the amounts were 9.62 U/mL (SEM = 0.4950) and 13.64 U/mL (SEM = 0.5144), respectively, for P_1 in the serum, which were extremely significantly greater than those of the other groups. The Shannon index was significantly different between the P_1 group and either the P_3 or P_5 group. Additionally, Simpson's diversity index significantly differed between the P_1 group and the P_5 group. Furthermore, the number of OH in camels is positively associated with the metabolic pathway of non-oxidative pentose phosphate pathway and ANAGLYCOLYSIS-PWY. In conclusion, this study revealed that different parities were associated with distinct levels of antioxidant parameters and fecal microbial ecologies in lactating Bactrian camels, where parity affects metabolic and microbial health. Understanding these dynamics in camels could optimize their nutritional management, enhancing their welfare in challenging environments.