DADA2: High-resolution sample inference from Illumina amplicon data

Microbial shifts and VFA production in the optimization of anaerobic digestion by thermal hydrolysis coupled with vacuum fermentation

This study investigated a novel thermal-hydrolysis combined with a vacuum fermentation system for high-grade volatile fatty acids (VFA) recovery, and the corresponding changes in the microbial community. Four systems with and without hydrothermal pre-treatment (HTP) and vacuum were mobilized; results revealed that integration of HTP with vacuum has the highest potential in terms of VFA recovery, sludge disintegration, and solid reduction. HTP and vacuum fermentation systems were associated with the highest COD solubilization (45 %), and VFA yield (0.32 g COD/g VSS added). Vacuum fermenters with and without pre-treatment have the highest specific denitrification rates of 7.6 and 7.2 mg NO3-N/g VSS.h, respectively, compared to all other samples and control (acetate). Changes brought about by vacuum fermentation included a shift in the microbial community toward enriching fermenters, mainly Caprothermobacteria and Thermotagea, responsible for VFA production.

Sophocarpine suppresses MAPK-mediated inflammation by restoring gut microbiota in colorectal cancer

BACKGROUND

Colorectal cancer (CRC), as one of the most common cancers globally, poses a significant challenge to public health due to its high incidence and mortality rates. This underscores the need for continuous exploration of new therapeutic targets and effective drugs. Sophocarpine (SC), a natural compound derived from traditional Chinese medicine, holds considerable therapeutic potential in the treatment of CRC, however, the relevant mechanisms remains unclear.

PURPOSE

This study aims to explore the anti-tumor effects of SC against CRC by modulating gut microbiota, and uncover potential mechanisms linking SC's therapeutic effects to gut microbiota regulation by analyzing the impact of SC on microbiota composition and CRC progression.

MATERIAL

This study explores the impact of SC on the gut microbiota in CRC by constructing subcutaneous xenograft tumors of CRC and integrating 16S rRNA sequencing and RNA transcriptomic sequencing. The fecal microbiota transplantation (FMT) mouse model was used to validate the biological function of SC in correcting gut microbiota dysbiosis to treat CRC. Subsequently, we conducted in vitro studies on the molecular mechanisms by which SC regulates the gut microbiota as an effective hallmark of CRC treatment, using lipopolysaccharide (LPS) to simulate an inflammatory gut microbiota environment and P38 MAPK knockdown cell line.

RESULTS

SC significantly inhibited CRC cell proliferation with IC50 values of 2.547±0.256 μM for HCT116 and 2.851±0.332 μM for LoVo cells. In vivo experiments demonstrated that SC effectively suppressed tumor growth in xenograft models. 16S rRNA sequencing revealed that SC modulated gut microbiota composition, particularly affecting Bacteroides and Alistipes populations. SC significantly reduced the levels of inflammatory factors and inhibited the MAPK signaling pathway, as evidenced by decreased p-JNK, p-p38 MAPK, and p-NF-κB p65 expression.

CONCLUSIONS

Current clinical practice still lacks effective therapeutic agents targeting CRC through gut microbiota modulation. This study presents the first evidence that SC, a natural compound, exhibits dual-action therapeutic efficacy against CRC progression by simultaneously modulating gut microbial composition and suppressing MAPK pathway-mediated inflammatory responses. These findings highlight SC's novel therapeutic potential as a promising microbiota-regulating candidate for CRC intervention, offering an innovative approach that bridges microbial ecology with cancer signaling pathways.

Microbial community development in an oil sands pit lake

Surface mining and extraction of oil sands in Canada produces fluid tailings that contain several compounds of concern for the environment. One option for mine reclamation is the construction of Pit Lakes (PLs) to contain and remediate these tailings. Ultimately, PLs should support food webs typical of boreal lakes. From 2015 to 2021, we applied 16S/18S rRNA gene amplicon sequencing and metagenomics to monitor prokaryotic and eukaryotic microbes in the only full-scale PL of the oil sands industry (Base Mine Lake or BML), and compared it to two control environments: a freshwater reservoir unaffected by tailings, and active tailings ponds receiving regular industrial input. Microbial communities in BML were always intermediate to the two control environments based on alpha and beta diversity analyses. BML communities were highly variable with year, season, and water depth, and contained fewer core species than the freshwater reservoir. Several hydrocarbon degraders and sulfur cycling bacteria were identified as indicator species of tailings ponds, while several phototrophs were indicative of freshwater. However, all of these species were abundant in BML, suggesting that the PL supports food webs characteristic of each control environment. Over the 6-year study, the relative abundances of some common freshwater phytoplankton (Cryptomonas, Mychonastes, Trebouxiophyceae, Cyanobium) and heterotrophic bacteria (Sporichthyaceae, Ca. Fonsibacter, Ilumatobacteraceae, Microbacteriaceae, Ca. Planktophila) increased in BML. The results suggest that microbial communities and processes in BML represent an intermediate state between a tailings pond and a natural freshwater system, and did not stabilize within 10 years of its creation.

Shift in activated sludge microbiomes associated with nitrite accumulation and high nitrous oxide emissions

Nitrous oxide (N2O) emissions can constitute over half of the carbon footprint of a wastewater treatment plant (WWTP), and emission peaks frequently correlate with nitrite (NO2-) concentrations. However, connections between the microbiome and high N2O and NO2- levels are not well-documented. Here, we characterize the microbiomes in several parallel lines of a WWTP during massive N2O emissions (20 % of influent nitrogen load) with prolonged NO2- accumulation in most lines, aiming to identify key differences between communities in lines with high and low NO2- concentrations. The abundance of nitrite-oxidizing bacteria (NOB) was extremely low in the lines with NO2- accumulation, which also had slightly lower abundances of ammonia-oxidizing bacteria (AOB). Some incomplete denitrifiers were more abundant in the lines with NO2- accumulation. Lines without NO2- had a higher relative abundance of filamentous bacteria and better floc formation. These findings confirmed our hypothesis that loss of NOB caused NO2- accumulation, inducing increased N2O emissions. AOB are suspected to be the main source of N2O during the studied period, with a likely contribution from heterotrophic denitrifiers. A few species were identified as interesting candidates for further study regarding their potential role in increased N2O emission from WWTPs. Long-term microbiome monitoring is necessary to understand the changes in the microbiome that might initiate NO2- accumulation and high N2O emissions.

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.

Relationships between soil health and dynamics of soil potential pathogenic microbiota in functional domains of Xi'an urban greenspaces, China

Soil potential pathogenic microbiota exacerbate the environment and human health through invading normal tissues of the human body, but their distributions and interactions across functional domains in urban greenspaces are poorly understood. Herein, we collected soil samples from parkland and residential land to explore the relationships between soil health and the dynamics of soil potential pathogenic microbiota. Soil organic matter-associated properties, soil multifunctionality and health were significantly about 30 % higher in parkland, but soil stoichiometry including C/N, C/P, and C/N/P were lower in parkland. Alpha diversity of soil pathogenic bacterial communities was higher than for fungal communities in residential land. The relative abundances of the dominant genera Mycobacterium, Metarhizium, and Cladosporium that may cause chronic lung and gastrointestinal diseases in humans were greater for residential land. Potential connected networks including soil pathogenic bacterial and fungal phylotypes were more complicated and stable in residential land, based on higher total and positive connections and higher robustness. Meanwhile, bacterial phylotypes belonging to the genus Shigella were identified as keystone species in parkland network, all of which were chronic pathogens. Soil total nitrogen and phosphorus as dominant properties had greater total effects on soil health in parkland and residential land, respectively. In general, soil health was mostly affected by soil multifunctionality in parkland, but was subject to higher explanation in residential land. These findings underscore intimate relationships between soil health and the dynamics of soil potential pathogenic microbiota in urban greenspaces, which has implications for human daily outdoor routines and urban habitability.

Long-term NPK fertilization enhances microbial carbon use efficiency in Andosols by alleviating P limitation and shifting microbial strategies

Microbial carbon use efficiency (CUE) is an essential indicator of soil organic carbon (SOC) dynamics. The high yield (Y)-resource acquisition (A)-stress tolerance (S) life strategy framework was used to assess microbial adaptation and its impact on CUE in response to soil environment and nutrient availability. Topsoil (0-15 cm) was collected from a 36-year experimental field of Andosol in Japan with six fertilizer treatments: no application, inorganic PK, NK, NPK, compost, and NPK with compost (NPKCM) to elucidate the effects of nutrient availability and environmental changes caused by fertilization on CUE. Soil chemical properties, microbial biomass and community structure, and extracellular enzyme activities (EEAs) were measured. Microbial nutrient limitation and CUE were assessed using enzyme stoichiometry (CUEst), and structural equation modeling (SEM) tested the conjecture that microbial nutrient limitation, mainly P-limitation, reduces CUEst through changes in bacterial community structures and EEAs. Results showed higher CUEst in NPK-treated soils (NPK: 0.37, NPKCM: 0.32) compared to P-deficient soils (Ctrl: 0.19, NK: 0.22). Increased P availability and reduced DOC:AP and IN:AP ratios in NPK-treated soils favored a shift of dominant bacterial strategies from A-strategists (including Alphaproteobacteria, Vicinamibacterales, and AD3) to Y-strategists (including Bacteroidota, Verrucomicrobiota, Blastocatellales, Bryobacterales, and Ktedonobacterales). SEM revealed that increased soil C and P availability alleviated microbial P limitation, enhancing CUEst directly and via reducing C-acquiring EEAs and altering microbial strategies. Overall, NPK fertilization may be an optimal strategy for enhancing SOC sequestration by improving microbial CUE in Andosols, emphasizing the trade-off between nutrient acquisition and energy conservation.

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.

Development of a device to trap soil bacteria capable of degrading organic contaminants such as alkanes and polycyclic aromatic hydrocarbons

The microbial biodegradation potential of contaminated sites is critical for efficient bioremediation, particularly through bioaugmentation with microorganisms that degrade organic pollutants. The BactoTrapS tool was developed to select and enrich bacteria tolerant to contaminants and capable of biodegradation directly from soils. It comprises a nylon mesh filled with activated carbon or vermiculite spiked with PAHs (phenanthrene, pyrene, dibenzo-a,h-anthracene) or alkanes (n-hexadecane, cyclohexane), while control traps remained unspiked. After five weeks of soil incubation, spiked traps showed significantly higher mineralisation. Bacterial colonisation was evaluated via CFU counts and 16S rDNA qPCR, revealing increased densities in spiked conditions. Alpha diversity analysis showed reduced diversity in spiked traps, while beta diversity confirmed selective enrichment of genera such as Mycobacterium and Polaromonas under PAHs, and Nocardioides and Nocardia under alkanes. These genera were identified as indicator species for the respective contaminants. qPCR of key biodegradation genes (PAH-RHDα, AlkB, CYP153) revealed elevated gene copy numbers in spiked traps. Most isolates from spiked conditions metabolised phenanthrene and hexadecane as sole carbon sources. BactoTrapS offers a rapid, efficient method to enrich biodegrading bacteria for hydrocarbons and other organic contaminants, promising broad applicability for future remediation efforts.

Multi-omics signature profiles of cold-smoked salmon from different processing plants: Insights into spoilage dynamics

Cold-smoked salmon (CSS) is highly susceptible to spoilage due to its processing and storage requirements. This study leverages a multi-omics approach to unravel the complex interactions between microbiota, biochemical changes, and sensory characteristics during the storage of CSS produced in three distinct processing plants. By integrating high-throughput metabarcoding, volatile organic compound (VOC) profiling, biochemical assays, and sensory evaluations, plant-specific spoilage trajectories and molecular signatures that influence product quality were identified. Initial storage phases revealed a shared unspoiled profile across all samples marked by high levels of phenolic VOCs. However, as storage progressed, spoilage pathways diverged depending on the processing plant, driven by variations in microbiota composition and metabolic activity. Distinct bacterial communities, including genera such as Photobacterium, Aliivibrio, Carnobacterium, and Brochothrix, shaped the production of spoilage-related VOCs. Statistical analyses using the DIABLO framework uncovered strong correlations between bacterial taxa, volatile organic compounds (VOCs), and sensory attributes, emphasizing the distinct spoilage signatures associated with each processing plant. This study provides new insights into the spoilage mechanisms of cold-smoked salmon by integrating multi-omics data to identify plant-specific microbiota and their metabolic contributions. Beyond identifying distinct spoilage signatures, this study highlights the potential of multi-omics approaches to develop targeted interventions for maintaining product quality.

Effect of laparoscopic niche resection on vaginal microbiota and its relation to pregnancy rate

OBJECTIVE

To study the impact of a laparoscopic niche resection on vaginal microbiota in relation to pregnancy rate.

METHODS

A explorative prospective cohort study that included women with a large niche (residual myometrium ≤ 3 mm), actual wish to conceive who were scheduled for laparoscopic niche resection. Pre- and three months post-operatively, a vaginal swab was collected during the mid-luteal phase (cycle day 19 to 24). The microbiota composition was determined using 16S rDNA sequencing. Microbiota profiles were assigned to community state types (CST) based on the dominant bacterial species.

RESULTS

In total, 55 women completed sequential sampling. In all women, laparoscopic niche resection significantly reduced niche volume, withmean paireddifference of 1766.6 mm3 (95 % CI: 640.4 - 2892.8). CST-IV was the dominant type both pre- and post-operatively (38.2 % vs 36.4 %, respectively). In ten (18.2 %) women the dominant CST changed after surgery. Three (5.5 %) women experienced a favourable change linked to fertility, while two (3.6 %) had unfavourable change and five (9.1 %) showed neutral shift. Women with favourable change had a greater reduction in niche volume (median reduction 1067.4 mm3 (p = 0.014)). Within a year, 23 (54.8 %) women became pregnant. The highest pregnancy rate (90.0 %, n = 9) was observed in women with post-operative CST-I, while the lowest rate (38.5 %, n = 5) was seen in those with CST-III.

CONCLUSION

Laparoscopic niche resection resulted in a more than 10-fold reduction in niche volume. However, no significant changes in vaginal microbiota were observed postoperatively. Notably, women who experienced the largest reduction in niche volume also demonstrated a favourable shift in their microbiome profile, which is associated with improved fertility.Postoperatively, the highest pregnancy rate (90 %) was observed in women with Lactobacillus crispatus-dominant microbiota (p = 0.78). These results provide valuable insights into the pathophysiology of uterine niches and suggest potential therapeutic approaches for women experiencing niche-related infertility, however lager studies are needed to confirm these findings.

Biological methane removal by groundwater trickling biofiltration for emissions reduction

Methane removal is an essential step in drinking water production from methane-rich groundwaters. Conventional aeration-based stripping results in significant direct methane emissions, contributing up to one-third of a treatment plant's total carbon footprint. To address this, a full-scale trickling filter was operated for biological methane oxidation upstream of a submerged sand filter, and its performance was compared to a conventional aeration-submerged sand filtration set-up. Full-scale data were combined with ex-situ batch assays and metagenome-resolved metaproteomics to quantify the individual contribution of the main (a)biotic processes and characterize the enriched microbial communities. Both treatment setups fully removed methane, iron, ammonium, and manganese, yet the underlying mechanisms differed significantly. Methane was completely removed from the effluent after trickling filtration, with stripping and biological oxidation each accounting for half of the removal, thereby halving overall methane emissions. Methane-oxidizing bacteria not only outcompeted nitrifiers in the trickling filter, but also likely contributed directly to ammonia oxidation. In contrast to the submerged filter preceded by methane stripping, signatures of biological iron oxidation were almost completely absent in the trickling filter, suggesting that the presence of methane directly or indirectly promotes chemical iron oxidation. All systems had similar ex-situ manganese oxidation capacities, yet removal occurred only in the submerged filters but not the trickling filter. Ultimately, our results demonstrate that trickling filtration is effective in promoting biological methane oxidation at comparable produced drinking water quality, highlighting its potential for advancing sustainable drinking water production.

Rice grain quality alteration through manipulation of parboiling procedures to affect the concentration of macro- and micro- nutrient elements, B-vitamins, inorganic toxicants, and bacterial contamination

A Bangladesh village rice parboiling plant was used to investigate how to improve essential elements and B-vitamin content of rice, while reducing the toxicants arsenic and cadmium, and potential bacterial pathogens. A 25 -factorial experiment was conducted where husked and de-husked rice was parboiled at different pre-parboiling soaking times, pre-parboiling soaking temperatures, parboiled through either boiling or steaming, and parboiled for 2 different times. Three rice cultivars were used. Using wholegrain, rather than rough rice, with 15 mins of parboiling, gave the optimal reduction in inorganic arsenic (25 %), as compared to widely used rough rice parboiling procedures. This combination of treatments also enhanced calcium (circa. 200 %) and iron (circa. 50 %), but lost circa. 50 % of potassium. The wholegrain parboiling procedures reduced vitamin B1 and B6 compared to rough rice parboiling, but made no difference for B2 and B3. Bacillus and Enterobacter related sequences showed highest levels of abundance, and were identified in 100 % and 77 % of non-parboiled rice samples, respectively. The overall implications of this study was that wholegrain, as compared to rough rice, parboiling should be adopted, but the B-vitamin and potassium intakes of the receiving populace need to be considered.

A red lentils-based synbiotic cookie exerts neuroprotective effects in a mouse model of Alzheimer's disease

Gut microbiota preservation or rational manipulation is a key condition for healthy longevity and a promising strategy to prevent neurodegenerations exploiting the gut-brain axis, with a key role of prebiotics and probiotics. Whether their combination in a functional food can provide a synergistic effect to the host remains controversial. To fill this gap, we supplemented the diet of 3xTg-AD Alzheimer's disease mice with a red lentils (prebiotic)-based cookie enriched with neuroprotective probiotics and we performed behavioural, biochemical and molecular tests. Chronic consumption of this synbiotic preparation (functional cookie) preserved cognition, reduced amyloid load, improved glucose and lipid homeostasis and diminished oxidation and inflammation related damages compared to animals receiving a classic cookie (standard recipe). The synergistic effect was indicated by significantly higher glucose insulinotropic polypeptide concentrations in the functional cookie group compared to probiotic group. Moreover, Ruminoclostridium sp KB18 and Ruminicoccus decreased in the gut of mice supplemented with the functional cookie, partially explaining the improved short-term memory upon treatments and substantiating the combined use over individual components. This synbiotic innovative snack represents a prototype of a simple and affordable dietary approach to promote healthy aging and prevent or delay the onset of neurodegenerations.

Vegetation succession enhances microbial diversity, network complexity, and stability in coastal wetlands, underscoring the pivotal role of soil salinity and key microbial species

In coastal wetlands, vegetation succession is primarily driven by changes in hydrology, sedimentation, and soil salinity. This ecological process is known to significantly influence microbial communities. However, its specific effect on microbial interactions and network dynamics in coastal wetlands remains insufficiently understood. This study adopted a spatial ecological sequence approach instead of a temporal succession method to comprehensively analyze the effects of vegetation succession on microbial communities in the Yellow River Delta. The results demonstrated that soil salinity, rather than nutrient levels, was the primary driver of microbial community shifts during succession. Succession increased the relative abundance of dominant phyla, such as Acidobacteria, Actinobacteria, Chloroflexi, and Planctomycetota, whereas key taxa, including salt-tolerant species, functioned as pivotal nodes regulating community interactions. Co-occurrence network analysis revealed that vegetation succession significantly enhanced the complexity and stability of microbial networks by reducing soil salinity and thereby altering the composition of key microbial taxa. These findings reveal the salinity-mediated mechanisms underlying microbial network assembly during vegetation succession in coastal wetlands and identify environmentally responsive microbial taxa that act as critical connectors within microbial communities, providing a mechanistic basis for the ecological restoration and sustainable management of salinized coastal ecosystems.

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.

Coupling of sulfate reduction and dissolved organic carbon degradation accelerated by microplastics in blue carbon ecosystems

Microplastics have increasingly accumulated in sulfate- and organic matter-rich mangrove ecosystems, yet their effects on microbially mediated carbon and sulfur cycling in sediments remains poorly understood. In this study, we performed a 70-day anaerobic microcosm experiment to examine the effects of polylactic acid (PLA) microplastics with different sizes on sulfate reduction and dissolved organic carbon (DOC) degradation in mangrove sediments. Our results demonstrated that millimeter-scale PLA (mm-PLA) more effectively enhanced sulfate reduction, sulfur isotope fractionation, reduced sulfide production, and carbon dioxide (CO2) emission compared to micrometer-scale PLA (m-PLA). These results suggested that mm-PLA had a more pronounced impact on the carbon and sulfur cycles. Integrated 16S rRNA gene amplicon sequencing and metagenomic analyses revealed that mm-PLA preferentially enriched key functional microorganisms, including acetate-producing bacteria (e.g., Acetobacteroides), completely oxidizing sulfate-reducing bacteria (e.g., Desulfobacter), and incompletely oxidizing sulfate-reducing bacteria (e.g., Desulfobulbus). These microorganisms exhibited higher abundances and greater genetic potential for carbon metabolism and sulfate reduction under mm-PLA treatment. Their relative abundances showed positive correlations with sulfate reduction rates, sulfur isotope fractionation, and CO2 emission, identifying them as crucial drivers of coupled carbon-sulfur cycling. Furthermore, the synergistic interactions among Acetobacteroides, Desulfobacter, and Desulfobulbus facilitated the oxidation of sediment-derived DOC, highlighting significant implications for carbon sequestration in blue carbon ecosystems.

Uncharacterized members of the phylum Rozellomycota dominate the fungal community of a full-scale slow sand filter for drinking water production

Slow sand filters (SSFs) for drinking water production are habitats for diverse microbes from multiple domains of life, which are integral to the ability of SSFs to purify water. While cultivation-independent analyses of the prokaryotic communities of SSFs have provided valuable insights, little attention has been paid to fungi inhabiting SSFs. This study characterized the fungal communities in the sand biofilm of one established, one inoculated and one non-inoculated SSF. The removal of the top-layer of sand ("scraping") allowed fungal communities in the top and subsurface layers of sand to be analyzed using amplicon sequencing of the ITS2 region of fungal rRNA genes. The top layers of SSF sand contained fungal communities dominated by phylum Ascomycota (43.5-75.6 %). After scraping, high abundances (>70 %) of phylum Rozellomycota were revealed in the established filter. These fungi were also detected in an inoculated filter, but not in a non-inoculated filter, suggesting potential dispersal to new filters by inoculation. The diverse Rozellomycota sequences potentially represented 6 different order-level clades, with most being related to previously observed Branch03 Rozellomycota. Their roles in SSF function are unknown but may be related to the removal of indicator bacteria as this phylum includes potential parasites of grazing eukaryotes. Fungi known to constitute microbial risk or contribute to micropollutant biodegradation were in low abundance and only sporadically detected. Lifestyle traits could be predicted for 61.8 % of fungi in the SSF biofilm; most of these were saprotrophic microfungi or yeasts. This study presents an overview of the composition of fungal communities in full-scale SSF, and their potential interactions with water quality. It also highlights the need for more knowledge regarding the ecology of "dark matter"-fungi, such as Rozellomycota, and presents an accessible and societally relevant environment for future research of these microbes.

Prebiotic potential of wheat and dark rye: modulation of gut microbiota and short-chain fatty acid-producing bacteria

The consumption of whole grains supports metabolic health in the gut and reduces the risk of chronic diseases. Dietary fiber derived from whole grains is one of the key factors contributing to these benefits. These fibers act as prebiotics, promoting the growth of beneficial bacteria and shaping microbial composition in the gut. This study examined the effects of wheat and dark rye, two fiber-rich whole grains, on the gut microbiota using an in vitro fecal incubation system. Following whole grain treatment, the gut microbiota showed an increase in the relative abundances of Bifidobacterium, Faecalibacterium, Blautia, and Lachnospiraceae. These bacteria are known short-chain fatty acid producers, suggesting a potential role in supporting host health. Additionally, functional pathway analysis predicted the upregulation of metabolic pathways related to specific carbohydrate metabolism. Taken together, these findings enhance our understanding of how wheat and dark rye consumption influences gut microbiota composition.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-025-01889-w.

Seasonally recurring patterns of dominant Crenothrix spp. in a European alluvial drinking water well: Significance and potential indicator role

Iron and manganese (Fe/Mn) often lead to aesthetic quality issues in water supply. Strong and problematic black-brown particle formation was persistently observed in an alluvial drinking water well, even though oxygen enrichment probes, intended for in situ i.e., subsurface iron/manganese removal, were installed. To investigate the cause of the problem, a comparative and multiparametric approach was undertaken at the problematic well, seven additional wells (with 0.3 to 70 km distance to the affected well) and all the adjacent surface waters. Via a time-series investigation of up to 2.5 years, microbiological analysis (high-throughput 16S rRNA gene amplicon sequencing, total cell count) and chemical analysis (high-resolution elemental analysis using inductively coupled mass spectrometry and others) of the water samples were performed. Results revealed previously unreported, extremely dynamic, and seasonally recurring patterns of genus Crenothrix (a sheathed, filamentous bacterial population) in water samples obtained from the particle-affected well. Crenothrix spp. dominated the microbial community in summer months (up to 82 % relative abundance), being virtually absent in winter. Explanatory models for the high dynamics and association with bio-geochemical processes were established. These included methane formation and manganese mobilization in relation to riverbank filtration in the summer months, as well as changing aerobic and anaerobic conditions in the aquifer. Dominance of Crenothrix spp. in the affected well, low abundance in weak particle-affected wells, and total absence in non-affected wells was observed. This led to the suggestion of Crenothrix spp. as a technical indicator for Fe/Mn treatment failure for alluvial groundwater (e.g., genetic marker quantification by q/dPCR), to be evaluated in future studies regarding their applicability across a broader geographic context. Despite being first described in association with drinking water deterioration 150 years ago, this is the first study reporting seasonally recurring dominant patterns of Crenothrix spp. in association with operational/aesthetic issues for drinking water production.

Assessment of ship hull-attached marine diatoms: species composition and reattachment

Ship biofouling is a primary pathway for the introduction and global spread of non-indigenous species, posing significant risks to marine ecosystems. However, the extent to which ship hull-attached diatoms survive and disperse following in-water hull cleaning (IwHC) remains poorly understood. Here, we analyzed the attached diatoms compositions in the in-water hull cleaning water (IwHCW) from three international ships entering Korea as well as benthic diatoms at nearby stations, using both morphological and molecular methods. In addition, we assessed the survival of ship hull-attached diatoms using reattachment analysis. Water temperature and salinity varied during sampling of the IwHCW of the ships, while the conditions at the four nearby stations were more consistent. The diatom Halamphora spp. was most abundant in the IwHCW of the ships, whereas Achnanthes species dominated at the nearby stations. Non-metric Multidimensional Scaling (NMDS) revealed significant variation in species composition between the IwHCW and the stations, suggesting limited dispersal of ship-associated diatoms or spatiotemporal influences. Survival and reattachment analyses revealed that Halamphora oceanica survived for over 21 days in unfiltered IwHCW, with no attached diatoms observed in IwHCW filtered through 5 and 32 μm filters. These findings indicate that diatoms in an unfiltered IwHCW may survive and reattach to substrates, highlighting the need for IwHC risk assessment and biofouling management in coastal waters.

Anaerobic digestion of cyanobacterial biomass for plant fertilizer production on Mars

BACKGROUND

A sustained presence on Mars requires the production of food on site, but farming is limited by the local availability of suitable nutrients. Cyanobacteria can feed on Martian resources, and we hypothesized that the nutrients they mobilize could be extracted through anaerobic digestion and used as crop fertilizer.

METHODS

We therefore tested the abilities of three microbial communities to digest the biomass of Anabaena sp. in minimal medium, 200 g L-1 Mars regolith simulant (MGS-1), and water.

RESULTS

All communities produced ammonium and removed organic carbon in all media, especially in minimal medium and 200 g L-1 MGS-1. However, MGS-1 also adsorbed organics and reduced the phosphate and ammonium recovery efficiency. A taxonomic analysis revealed a syntrophic fermentative community and hydrogenotrophic methanogens in minimal medium, but methanogens were outcompeted in MGS-1 by sulfate-reducing bacteria.

IMPACT

Overall, this study suggests the viability of a bioprocess which could support crop production from Martian resources.

Community stability of free-living and particle-attached prokaryotes in coastal waters across four seasons: insights from 9.5 years of weekly sampling

Free-living (FL) and particle-attached (PA) prokaryotes, having distinct ecological niches, play significant roles in marine ecosystems. These communities respond rapidly to environmental changes and exhibit seasonal patterns. However, their temporal stability, crucial for maintaining microbial community structure and function, remains poorly understood. This study assessed community stability, particularly in terms of resistance to environmental perturbations, and inferred regulatory mechanisms using weekly collected samples over 9.5 years from FL and PA communities in coastal water. Short-read amplicon sequencing revealed habitat-specific microbial compositions, with Actinobacteria and Euryarchaeota dominating FL community, while Planctomycetes and Verrucomicrobia prevailed in PA community. Network analysis, constructed based on relative abundance, uncovered seasonal co-occurrence patterns and highlighted keystone taxa, such as Nitrosopumilus in FL and Synechococcus in PA community, as critical for maintaining stability within specific seasons and niches. Seasonal variations in community stability indices suggest that higher network complexity can enhance resistance; however, excessive interactions with greater complexity may also undermine it. Furthermore, it was found that FL community stability was primarily affected by abiotic factors, likely due to direct exposure to environmental changes, whereas PA community stability was more influenced by biotic factors, as their association with particles fosters localized interactions and biological processes. These findings reveal the intricate balance between network complexity and stability and the importance of niche-specific approaches in ecological research. Our results contribute to a deeper understanding of marine microbial niche partitioning and provide insights into ecosystem management and conservation strategies, particularly regarding keystone taxa.

The control of physical and biological drivers on pelagic methane fluxes in a Patagonian fjord (Golfo Almirante Montt, Chile)

Methane fluxes from coastal waters such as fjords and the underlying control mechanisms are poorly understood. During the austral summer, we investigated a fjord in the Chilean part of Patagonia, the Golfo Almirante Montt. The study is based on measurements of methane concentration, stable carbon isotopes and the distribution and activity of methane-oxidizing bacteria in the water column, as well as oceanographic and geological observations. Our results indicate that methane is of biogenic origin and released from gas-rich sediments at the entrance of the fjord, characterized by pockmarks and gas flares. Tidal currents and turbulent mixing at the sill cause a near-surface methane plume to spread into the main fjord basin and mix with the methane- and oxygen-depleted deep water. Wind-induced mixing at the sea surface controls the methane flux from the plume into the atmosphere. The methane plume is consumed by methanotrophic bacteria of the Methylomonadaceae and Ga0077536 families, which are differently distributed along the water column. An enrichment of the characteristic gene methane monooxygenase (pmoA) in the methane-poor deep water, and a conspicuously high δ13C-CH4 signature suggest that methane-rich intrusions regularly enter the deep water, where the methane is microbially oxidized. Our interdisciplinary study offers a comprehensive insight into the complex physical and biological processes that modulate methane dynamics in fjords and thus help to better assess how methane emissions from these systems will change under anthropogenic influence.

Removal of antibiotic and disinfectant compounds from digested pig manure by an aerobic hybrid biofilm process

Using nutrient-rich manure as fertiliser on agricultural land improves crop yield, biodiversity, soil structure, water and nutrient availability. However, manure often contains high levels of antibiotics, as only 10-30 % are metabolised by the animal, thus, soil application contributes to the spread of antibiotics and antibiotic-resistant genes (ARGs). As anaerobic digestion fails to remove the antibiotics and ARGs completely, this study investigates aerobic moving bed biofilm reactors (MBBRs) as post-treatment. The dissipation of sulfadiazine, sulfamethoxazole, ofloxacin, ciprofloxacin, roxithromycin, erythromycin, tylosin, tetracycline, chlortetracycline, benzalkonium chloride C12 and -C14 (BAC-12 and -14) was observed in small laboratory batch MBBRs with digested pig manure. Proficiency testing resulted in an overall removal of 92 %. Sulfamethoxazole and erythromycin were removed by >99 % within 12 and 23 days, respectively. The digestate exhibited high concentrations of benzalkonium biocides, i.e., BAC-12 and -14 (800 μg/L and 172 μg/L, respectively), highlighting the necessity for post-treatment before application to agricultural soil. Within 23 days, the aerobic MBBRs achieved 89 % and 93 % degradation of BAC-12 and -14, respectively. The biofilms improved the total removal by 19 % and BAC degradation by 61-68 % while increasing bacterial diversity. The MBBR-operation increased the abundance of the genera Paracoccus, Parvibaculum, and Clostridium sensu stricto 1. The sulfonamide-resistance genes were the most abundant ARGs (96 % and 98 % in the sludge and carrier biofilm, respectively). The ARG-abundance increased after antibiotic spiking and declined during incubation, reducing direct ARG spread to the environment by degrading antimicrobial concentrations. We, therefore, propose to treat anaerobically digested manure by aerobic biofilm treatment for antibiotic removal.

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.

Linking Chitin Degradation to Arsenic Methylation under Oxic Conditions: A Critical Driver of Arsenic Cycling in Paddy Soils

Aerobic microbial arsenic (As) methylation exhibits significant efficiency, potentially influencing As fluxes and their biogeochemistry in paddy soils. However, the role of primary degraders initiating decomposition of complex biopolymers in As methylation and the underlying driving mechanisms remain largely unexplored. This study uncovers a direct metabolic connection between chitin, a major component of particulate organic matter in the soil, and As methylation facilitated by specialized aerobic chitin-degrading bacteria. Chitin markedly enhanced As methylation and its volatilization in paddy soils under aerobic conditions, resulting in 2.9- and 25-fold higher increases compared with the treatments with lignocellulosic residue and components, respectively. Chitinophagaceae members were enriched in the presence of chitin, with bacteria related to Chitinophaga likely serving as the key contributors. The direct coupling between As methylation and chitin hydrolysis was further confirmed using a representative Chitinophaga strain isolated from a paddy soil, which produced dimethylarsenate and trimethylarsenate as the major MeAs products. Comparative genomic analysis revealed that a considerable proportion of Chitinophaga found diverse soil environments possess complete functional genes for As methylation and chitin utilization, highlighting their potential for regulating As cycling broadly. These findings emphasize the chitin degradation-associated As methylation as a previously overlooked contributor to MeAs fluxes, enhancing our understanding of the interconnected biogeochemistry of As and carbon in soils.

Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest

Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.

IMPORTANCE

The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.

Biodegradation of Arsenosugars from Red Alga Pyropia haitanensis

Arsenic accumulates in eukaryotic algae mostly in the form of arsenosugars and arsenosugar phospholipids, and those organoarsenicals are eventually released and biodegraded to maintain the dynamic balance of arsenic species in the environment. However, the specific bacteria involved in the biodegradation of arsenosugars released from the marine algae remains unknown. Our current work aims to identify bacteria linked to organoarsenical degradation under both anaerobic and aerobic conditions. In this study, red alga Pyropia haitanensis was degraded under anaerobic and aerobic conditions for 28 days after being incubated in seawater with or without 1 μM arsenite under aerobic conditions for 5 days. The compositions of the bacterial community, total arsenic, and arsenic species were analyzed. Both total arsenic and arsenolipids were released from the algae more rapidly under anaerobic conditions than under aerobic conditions. After 28 days of aerobic incubation, the predominant arsenic species inside the algae were phosphate arsenosugars (89.1%), while dimethylarsonic acid (83.8%) was the major species under anaerobic conditions. Moreover, the analysis of the bacterial community structure revealed that different bacteria were enriched under anaerobic (Pseudoalteromonas) and aerobic conditions (Pir4_lineage). Pseudoalteromonas sp. C71 isolated from seawater was used to degrade arsenosugars. The results showed that Pseudoalteromonas sp. C71 efficiently transformed phosphate arsenosugar to glycerol arsenosugar extracellularly and intracellularly. This study offers new insights into the interaction between bacteria and organoarsenical degradation, contributing to our understanding of arsenic biogeochemical cycles in marine systems.

Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics

Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the α-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.

IMPORTANCE

We explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.

Environmental diversity of Candidatus Babelota and their relationships with protists

Ca. Babelota is a phylum of strictly intracellular bacteria whose representatives are commonly detected in various environments through metagenomics, though their presence, ecology, and biology have never been addressed so far. As a group of strict intracellular, we hypothesize that their presence, occurrence, and abundance heavily depend on their hosts, which are known as heterotrophic protists, based on few described isolates. Here, we conducted a sampling campaign allowing to characterize protists and associated bacterial communities, using high-throughput sequencing. In parallel, a systematic enrichment of protists from samples was performed to attempt characterization and isolation of new Ca. Babelota within native hosts. We found that Ca. Babelota are among the most widespread phylum among the rare ones. Protist enrichments are allowed in certain cases to enrich as well for Ca. Babelota, which could be visualized in vivo infecting protist cells. Though cosmopolitan, Ca. Babelota diversity was highly site-specific. Cooccurrence analyses allowed to retrieve well-known as well as new putative associations involving numerous protists of various trophic regimes. The combination of approaches developed in this study enhances our understanding of Ca. Babelota ecology and biology, while paving the way for future isolation of new members of this elusive phylum, which could have huge impact on protists-and ecosystems-functioning.IMPORTANCEOur understanding of microbial diversity surrounding us and colonizing the environment has been dramatically impacted by the advent of DNA-based analyses. Such progress helped shine a new light on numerous lineages of yet-to-be-characterized microbes, whose ecology and biology are basically unknown. Among those uncharacterized clades is the Candidatus Babelota, a bacterial phylum for which parasitism seems to be an ancestral trait. All known Ca. Babelota thrive by infecting phagotrophic protist hosts, thereby impacting this basal link of the trophic chain. The Ca. Babelota constitutes a model that stands out, as phylum-wide conserved parasitism has only been described in one previous occurrence for Bacteria, with the Chlamydiota. Thus, exploring the intricate interplay between Ca. Babelota and their protist hosts will advance our knowledge of bacterial diversity, their ecology, and global impact on ecosystem functioning.

The microbiome of the human facial skin is unique compared to that of other hominids

The human facial skin microbiome is remarkably similar across all people sampled to date, dominated by facultative anaerobe Cutibacterium. The origin of this genus is unknown, with no close relatives currently described from samples of primate skin. This apparent human-specific bacterial taxon could reflect the unique nature of human skin, which is significantly more oily than that of our closest primate relatives. However, previous studies have not sampled the facial skin microbiome of our closest primates. Here, we profiled the skin microbiome of zoo-housed chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla gorilla), alongside their human care staff, using both 16S and shotgun sequencing. We showed that facial skin microbiomes differ significantly across host species, with humans having the lowest diversity and the most unique community among the three species. We were unable to find a close relative of Cutibacterium on either chimpanzee or gorilla facial skin, consistent with human specificity. Hominid skin microbiome functional profiles were more functionally similar compared to their taxonomic profiles. However, we still found notable functional differences, including lower proportions of fatty acid biosynthesis in humans, consistent with microbes' reliance on host-derived lipids. Our study highlights the uniqueness of the human facial skin microbiome and supports a horizontal acquisition of its dominant resident from a yet unknown source.IMPORTANCEUnderstanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts distinct bacteria-particularly Cutibacterium acnes-we did not know if these bacteria and their associated genes were also present on the faces of our closest relatives, chimpanzees and gorillas. Our study shows that human facial skin hosts markedly different bacteria than other primates, with C. acnes being uniquely abundant on human faces. This finding suggests that this key bacterial species may have adapted specifically to human skin, which produces more oils than other primates.

Transcriptional Difference of Deep-Sea Microorganisms under Different Sampling Methods

The metabolic potential and activity of deep-sea microbes have not been fully explored by meta-transcriptomics using the samples obtained by different sampling methods. Here, we report active deep-sea microbes obtained by the methods of multiple in situ nucleic acid collection (MISNAC), in situ microbial filtration and fixation (ISMIFF), in situ microbial filtration without fixation (ISMIFU), and the Niskin bottle at a 1038 m depth in the South China Sea. Higher biodiversity and different dominant active microbial taxa in the metatranscriptomes were detected in the MISNAC and ISMIFF samples compared with the other two approaches. The transcriptional profiles of 40 conserved genes were similar between the MISNAC and ISMIFF samples, while the expression of a quarter of these genes was not detected in the ISMIFU sample. Genes related to the CO oxidation and nitrification processes were highly transcribed in the MISNAC and ISMIFF transcriptomes, whereas those for chemotaxis and low-oxygen adaptation were highly transcribed in the Niskin samples. Overall, our result highlights the importance of in situ sampling and preservation for more precise quantification of the ecological function of active deep-sea microbiomes.

Study on the growth and decline patterns and environmental drivers of pathogens during the stabilization process of simulated landfilling municipal solid waste

Waste and leachate in landfills are substantial reservoirs of pathogens, however information about the risk of pathogen contamination during the stabilization process under different landfill conditions is very limited. In this study, dynamic changes of culturable pathogens, bacteria community, and human bacterial pathogens (HBPs) during the stabilization process under different landfill conditions were investigated, and the environmental drivers were explored. Results showed that total coliforms, Enterococcus, and Staphylococcus aureus were the dominant pathogens detected in waste and leachate samples. During the landfill stabilization process, the concentration of culturable pathogens peaked at the hydrolysis-acidification stage (3.6 × 105 CFU·g-1) in the anaerobic condition, fluctuated from 4.18 × 104 to 5.35 × 105 CFU·g-1 in the anaerobic leachate-recirculation condition, and kept rising (from 4.18 × 104 to 2.12 × 106 CFU·g-1) in the micro-aerobic condition. Moreover, HBPs abundance and diversity in the waste and leachate under micro-aerobic conditions were higher than those under the other two conditions, suggesting a higher risk of pathogen contamination. Sulfate and pH were significantly (p < 0.05) correlated with the composition of bacterial communities and HBPs, likely serving as the major environmental driving factors. Additionally, the interactions between HBPs and functional bacterial groups tended towards cooperative symbiotic relationships, with hydrolytic-acidogenic bacteria promoting the growth and proliferation of most pathogens. These findings will help to understand the changes and environmental drivers of pathogens during landfill stabilization, which will provide a theoretical basis for the risk prevention and control of pathogens in waste disposal.

The bridging role of soil organic carbon in regulating bacterial community by microplastic pollution: Evidence from different microplastic additions

The serious threat posed by microplastics pollution to soil ecosystems and human health has attracted worldwide attention. Microplastics of different types are present in the soil environment, whereas research about the effects of different microplastics on soil ecology are limited. This study sought to determine how three common microplastics (polyethylene (PE), polystyrene (PS), and polyvinyl chloride (PVC)) affect soil physicochemical characteristics, enzyme activities, bacterial community, and their metabolic pathways at a 1 % w/w concentration. All three microplastic treatments significantly increased soil organic carbon (SOC), labile organic C fractions, and enhanced soil carbon to nitrogen ratio. PE, PS, and PVC microplastics exhibited promotion of α-glucosidase (α-GC), sucrase (SC), and alkaline phosphatase (AKP) activities. PS microplastics caused a significant increase in N-acetyl-β-D-glucosidase (NAG) and leucine aminopeptidase (LAP) activities, while PVC microplastics significantly decreased β-glucosidase (β-GC) activity. Microplastic treatments increased the bacterial community diversity while altering its composition. Proteobacteria and Chloroflexi were the dominant bacterial phyla in the soil, with microplastic treatments increasing the relative abundance of Chloroflexi and decreasing that of Proteobacteria. Functional prediction analysis indicated that microplastic treatments enriched genes involved in carbohydrate and amino acid metabolism, while reducing the abundance of genes related to signal transduction and cell motility. Correlation and pathway analyses revealed that microplastics affect bacterial community diversity and composition through direct and indirect effects (by acting on SOC or its key labile fractions), thereby influencing soil enzyme activities. In conclusion, the work emphasizes the impacts of different microplastics on soil ecosystems in terms of commonalities and dissimilarities, with the innovative finding of indirect regulation of bacterial community by SOC under microplastics contamination. This provides new perspectives for subsequent studies.

Perinatal bisphenol A exposure impairs gut microbial colonization: Implications for offspring obesity and neurodevelopment

Exposure to plasticiser xenobiotics such as BPA has emerged as a significant health challenge due to globalised and industrial packaged food production. Toxicological approaches in animal models have revealed complex effects, using variable doses of BPA, on reproduction, development, obesity, immune function, metabolic and systemic toxicity. Besides, gut microbiota has emerged as a key player in regulating the impact of xenobiotic exposure on host metabolism. The effect that BPA may exert on the gut microbiota and its consequences for the host's health remains unclear. Exposure to BPA during the perinatal period requires special attention and prevention approaches since it is a particularly vulnerable period and highly implicated in the metabolic health of childhood and adulthood. The aim of this study was to assess the effects of the BPA administration during the perinatal period on promoting obesity phenotypes, altering the composition of the gut microbiota and neurocognitive development of the offspring in a murine model. In this study, pregnant mice and their offspring were administered BPA, and the increase in weight and fat accumulation, the gut microbiota composition, and the cognitive development of the offspring were analyzed. In addition, a high-fat diet (HFD) was given to the mice to test for the synergistic obesogenic effect of BPA. Our results demonstrated that BPA exposure impaired the natural remodelling of the gut microbiota during pregnancy. For instance, Akkermansia and Prevotellaceae decreased during natural remodelling of the gut microbiota during pregnancy, but they did not change in the BPA-exposed pregnant mice. Conversely, several members of the Dubosiella genus increased during normal pregnancy but not in BPA-exposed pregnant mice. Moreover, BPA exposure and HFD differentially affect gut microbial transfer from mothers to offspring and both synergistically impact the gut microbiota's establishment in the offspring. Perinatal BPA exposure imprinted changes during colonisation and maturation process of the offspring gut microbiota, identifying Lactobacillus, Eubacterium and Acetatifactor as signature genera enriched in BPA and BPA-exposed mice fed with HFD, taxa involved in a more efficient at energy harvesting from the diet. Moreover, perinatal BPA exposure seemed to alter fat and lean percentages and triggered Muribaculacea taxa imbalance that appears to be associated with disrupted activity, spatial learning, and memory, mimicking impulsivity and hyperactivity-like behavior in the offspring. In conclusion, BPA exposure and HFD exert an influence on the vertical transfer of gut microbiota from mothers to offspring and drive towards an altered establishment of gut microbiota taxa in early life, contributing to enhancing susceptibility to obesity and behavioural disorders.

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.

Response of abundant and rare microbial species to 40-year long-term fertilization practices irrespective of bulk and rhizosphere soils

Fertilization practices could exert significant influence on the diversity, interactions, and functions of soil microorganisms. However, little is known about how specific microbial groups and their interactions adapt or evolve in response to agricultural practices, especially long-term mineral fertilization. Here we explored the community assembly process shaping the microbial community and co-occurrence networks of abundant and rare groups based on a high-throughput sequencing approach in a field experiment with 40 years of mineral nitrogen (N) and phosphorus (P) fertilization. The results indicated that fertilization (25-51 %) had a strong impact on microbial community structure, while little difference were found between rhizosphere and bulk soils irrespective of abundant and rare microbial groups. Deterministic processes primarily govern the assembly of both abundant and rare bacterial and fungal taxa. Random forest analysis revealed that soil pH and N-related nutrients (i.e. nitrate nitrogen (NO3--N), dissolved organic nitrogen (DON) and ammonium nitrogen (NH4+-N)) were the key factors influencing microbial community structure. Structural equation modeling and mantel test further indicated that deterministic factors, particularly soil pH, influence co-occurrence network complexity by modulating the microbiome. Overall, these findings provide insights into factors shaping the microbial community assembly and co-occurrence network dynamics in agroecosystems subjected to long-term fertilization.

Synergistic effects of surfactant biostimulation and indigenous fungal bioaugmentation for enhanced bioremediation of PAH-contaminated soils

Surfactant biostimulation and autochthonous fungal bioaugmentation have emerged as promising strategies for the bioremediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). However, the mechanisms driving their combined effects remain poorly understood. This study investigates the degradation mechanisms associated with bioaugmentation using the indigenous fungus Aspergillus fumigatus LJD-29 and surfactant Tween 80. By employing stable-isotope probing and high-throughput sequencing, we comprehensively assessed these processes. In our study, the results demonstrate that both Aspergillus fumigatus LJD-29 and Tween 80 significantly enhanced the degradation efficiency of phenanthrene and modified the microbial community composition, particularly among active degraders. Extracellular enzymes were identified as key players in the phenanthrene transformation process. Tween 80 improved the bioavailability of phenanthrene, stimulating the growth of native PAH degraders, with Pseudonocardia emerging as a prominent genus. Although the combined surfactant-fungal treatment did not substantially increase terminal degradation efficiency due to limitations in phenanthrene bioavailability, it accelerated the degradation rate. Additionally, Tween 80 helped restore the microbial community structure disrupted by fungal bioaugmentation. These findings provide valuable insights into the mechanisms of surfactant biostimulation and indigenous fungal bioaugmentation, highlighting the potential of this integrated bioremediation strategy for managing PAH-contaminated soils.

Assessment of seasonal variations in antibiotic resistance genes and microbial communities in sewage treatment plants for public health monitoring

The spread of antimicrobial resistance (AMR) around the globe, especially in the urban cities with high population, is a major concern. Therefore, the current study aims at identifying antibiotic resistant bacteria, microbial community compositions and the quantification of antimicrobial resistant genes from six sewage treatment plants (STPs) across Pune city in Maharashtra, India. A total of 106 isolates obtained were tested against six antibiotics in which the highest resistance was observed against trimethoprim (24.53 %). The qPCR assays of seven antibiotic resistance genes revealed abundance of blaimp-1 and mecA genes in the summer and monsoon seasons followed by blaNDM-1 gene in the summer and winter seasons. The alpha diversity indices depicted highest microbial diversity of inlet samples during winter, followed by inlet samples during the summer and monsoon seasons. Comparative analysis revealed Bifidobacterium (51 %), Pseudomonas (28.7 %) and Zoogloea (17.6 %) as the most abundant genera in the inlet samples during the summer, monsoon and winter seasons respectively while Acinetobacter (31 %) and Flavobacterium (23 % in winter and 18.2 % in summer) dominated the outlet samples. The co-network analysis revealed positive and negative interactions in the winter and monsoon but only positive interactions in the summer season. Venn diagrams showed higher abundance of ASVs in the outlet samples than the inlet. The top genera correlated exactly opposite with the pH compared to BOD and COD. PICRUSt2-based functional prediction revealed a higher abundance of methicillin resistance, β-lactamase resistance and multidrug resistance genes in inlet samples while chloramphenicol resistance was found higher in outlet samples. Further, we observed that potential pathogens causing infectious disease such as pertussis, shigellosis and tuberculosis were present in all three seasons.

Microbial diversity, enzyme activity, metal contamination, and their responses to environmental drivers in an Indo-Burmese freshwater wetland

Seasonal fluctuations can influence many biotic and abiotic parameters in wetland environments. Present research on wetlands do not serve as a comprehensive model for understanding these seasonal influences, especially in Northeast India, where wetland ecosystems remain understudied. That being, our study investigated the seasonal, spatial, depth-wise variations of enzyme activity (xylanase, invertase, and cellulase), microbial community, and heavy metal concentrations [chromium (Cr), cadmium (Cd), lead (Pb), and iron (Fe)] in the sediments of Deepor Beel. Our results show, seasons rather than sediment layers influence all parameters. Enzyme activities peaked during post-monsoon (POM), with xylanase showing highest activity throughout (0.01-132.94 mmol/min/g). Culture independent bacterial diversity study based on next generation sequence (NGS) analysis revealed a steady decrease in unique amplicon sequence variants (ASVs) from pre-monsoon (PRM) (31), followed by POM (22) and finally monsoon (MON) (2). Bacteria consistently outnumbered archaea throughout the study. Heavy metals peaked during PRM, with Fe reaching 1416-1200 mg kg-1. Cr exceeded US EPA limit in all seasons, while Pb and Cd surpassed the limits during PRM and MON. Pearson's correlation showed that TC, TN, C/N ratio, and EC significantly influenced enzyme activity during PRM and POM. Correlations between microbial community and environmental parameters revealed enzyme activities, C/N ratio and TC to positively influence many microbial genera. In contrast, certain genera showed tolerance to elevated concentrations of Cd, Pb, and Fe. Our findings have considerable implications for predicting the dynamics of abiotic and biotic factors related to the carbon cycle as a consequence of seasonal change.

Marine plastic exposure triggers rapid recruitment of plastic-degrading bacteria and accelerates polymer-specific transformations

Plastic pollution in marine ecosystems is a growing concern, yet the degradation behavior of different plastic types and their interactions with microbial communities remain poorly understood. This study investigated the degradation kinetics and microbial colonization of four widely used plastic materials, surgical masks (most made of PP), PET bottles, PS foam, and PP cups, over 40 days of seawater exposure in the Central Atlantic of Morocco. Mass loss measurement revealed distinct degradation patterns, with PS foam showing the highest mass loss (13 %), followed by PET bottles (5 %), likely due to environmental stressors that promote mechanical fragmentation. Surgical masks and PP cups exhibited minimal degradation, retaining nearly all their original mass, as well as limited extent of biodegradation. Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Diffraction (XRD) analyses showed the formation of oxidative functional groups on PP cups and significant structural changes in PS foam and PET, particularly in their crystalline structures, correlating with their higher mass reduction rates. SEM/EDX biofilm imaging confirmed extensive microbial colonization, particularly on PS and PET surfaces. Using 16S rRNA metabarcoding, we identified a striking enrichment of Exiguobacterium, followed by Pseudomonas, Acinetobacter and Bacillus genera, containing reported plastic degrading strains, which were strongly correlated with the accelerated breakdown of plastics. However, its role in accelerating plastic breakdown in this study remains unclear and may warrant further investigation. Co-occurrence network analysis revealed a progressive shift in microbial community structure, evolving from highly interconnected networks at day 0 to more specialized, modular clusters by day 40, dominated by Proteobacteria and Firmicutes. Atomic Absorption Spectrometry (AAS) demonstrated significant heavy metal accumulation on plastic surfaces, potentially influencing microbial colonization and activity. While the observed fragmentation of PS foam and PET highlights the susceptibility of certain plastics to environmental stressors, this study also positions microbial colonization as a potential contributor to plastic surface changes, providing novel insights into the interplay between microbial communities and plastic degradation in marine environments.

Skyglow increases cyanobacteria abundance and organic matter cycling in lakes

Artificial light propagating towards the night sky can be scattered back to Earth and reach ecosystems tens of kilometres away from the original light source. This phenomenon is known as artificial skyglow. Its consequences on freshwaters are largely unknown. In a large-scale lake enclosure experiment, we found that skyglow at levels of 0.06 and 6 lux increased the abundance of anoxygenic aerobic phototrophs and cyanobacteria by 32 (±22) times. An ecosystem metabolome analysis revealed that skyglow increased the production of algal-derived metabolites, which appeared to stimulate heterotrophic activities as well. Furthermore, we found evidence that skyglow decreased the number of bacteria-bacteria interactions. Effects of skyglow were more pronounced at night, suggesting that responses to skyglow can occur on short time scales. Overall, our results call for considering skyglow as a reality of increasing importance for microbial communities and carbon cycling in lake ecosystems.

Composition and rhythmic variations in the microbiome of Southwestern Atlantic corals

BACKGROUND

Diel and tidal rhythms can regulate the metabolism, physiology, behavior, and gene expression patterns of different organisms, with evidence of an integration on the circadian behavior of host species and their microbial community. Corals host a diverse and dynamic microbial community, with variable diversity and abundance across geographic and temporal scales. Within scleractinian corals, those that host endosymbiotic algae (i.e., zooxanthellate) display a diel variation in the oxygen levels, an oscillation in their internal environment that has the potential to influence its microbiome abundance and/or composition. Here we investigate in situ daily fluctuations on the microbial community of two zooxanthellate (Madracis decactis and Mussismilia hispida) and two azooxanthellate coral species (Tubastraea coccinea and T. tagusensis) along a 72-hour period.

RESULTS

Day and night alpha diversity values were similar for all species, with Ma. decactis hosting a significantly more diverse community. Similarly, there was no fluctuation in the microbiome composition at the Amplicon Sequence Variants (ASV) level between day and night within species, but all species were significantly different from each other. Interestingly, Mu. hispida, an endemic species to the Southwestern Atlantic, had a high proportion of unidentified microbial taxa at genus level, suggesting a species-specific microbiome community composed by unidentified taxa. Significant rhythmicity in the abundance of individual ASVs was observed for one ASV (genus Pseudoalteromonas) in T. tagusensis and one (genus Woeseia) in Ma. decactis, with 24 and 12-hour fluctuations, respectively. In addition, DESeq2 recovered 13 ASVs (four in Ma. decactis, two in Mu. hispida, six in T. coccinea, and one in T. tagusensis) with different abundances between day and night.

CONCLUSIONS

Results show divergent microbial communities when comparing zooxanthellate and azooxanthellate species, with few significant changes within a 24-hour period. Future studies should focus on metabolic pathways to better understand how the microbiome community can adjust to environmental changes within the coral host in short time scales.

Beneficial bacteria-based bioformulations as potential biocontrol and biocleaning solutions for stone heritage conservation

Indigenous bacterial community of the deteriorated Rožanec Mithraeum monument (Slovenia) was analyzed as a basis for development of a synergistic bacterial consortium with potential to be re-introduced for biocontrol and biocleaning treatment of infested limestone monument. Core community constituents, based on the 16S rRNA gene sequences metabarcoding analysis, were representatives of Proteobacteria, Actinobacteriota, and Cyanobacteria phyla. Bacteria of Bacillus and Paenibacillus genera dominated in the culturable bacterial community. The most extensive enzymatic potential, as a foundation of biocleaning process, was observed for Bacillus mycoides MIT8.7 and Paenibacillus amylolyticus/taichungensis/tylopili/tundrae MIT8.18. In general, representatives of Bacillus genus demonstrated excellent amylase and protease potential, with small lipase, cellulase, mannanase, and xylanase activity. The highest PGI% values, against 7 autochthonous biodeteriogenic fungi, were measured for Bacillus velezensis MIT7.8 and Pseudomonas chlororaphis subsp. aurantiaca MIT4.11 highlighting them as the most promising bacterial antagonist for the consortium. Compared to commercial biocides 0.3% Preventol RI80, 100% Keim, and 100% BFA, recommended for application in stone conservation, Streptomyces anulatus 1-3 TSA and Streptomyces sp. 11-11MM full cultures also proved efficient and lacked any corrosive effect as reflected in unaltered surface roughness parameters Rq and Ra, over the 3 months application period on laboratory models made of limestone obtained in the proximity of the Rožanec Mithraeum relief. Characterized bacterial candidates possess potential to be used for development of a bacterial consortium that can be utilized in situ as a natural, environment friendly, and safe alternative effective in the conservation of stone heritage via joint activity making an important step towards desired widespread exclusion of biocide application.

Prospecting microbiota of Adriatic fish: Bacillus velezensis as a potential probiotic candidate

BACKGROUND

Aquaculture is one of the fastest growing sectors of food production and covers more than half of the market demand for fish and fishery products. However, aquaculture itself faces numerous challenges, such as infectious disease outbreaks, which are one of the limiting factors for the growth and environmental sustainability of modern aquaculture. Understanding the composition and diversity of the gut microbiota of fish is important to elucidate its role in host health and aquaculture management. In addition, the gut microbiota represents a valuable source of bacteria with probiotic potential for farmed fish.

RESULTS

In this study, we analysed the intestinal microbiota of two economically important fish species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), using 16S rRNA gene amplicon sequencing. The taxonomic analysis identified 462 amplicon sequence variants at a similarity level of 99 and showed similar alpha diversity indices between seabass and gilthead seabream. Beta diversity analysis showed no significant differentiation in gut microbiota between fish species or aquaculture sites. Among the culturable isolates, a high proportion of Photobacterium damselae and Bacillus spp. was detected. We selected a single Bacillus velezensis isolate and further characterised its biosynthetic potential by performing whole genome sequencing. Its genome contains biosynthetic gene clusters for most of the common secondary metabolites typical of B. velezensis. Antibiotic susceptibility testing showed the sensitivity of the selected isolates to several antibiotics according to EFSA recommendations. Furthermore, stimulation of peripheral blood leukocytes (PBL) with B. velezensis resulted in a strong pro-inflammatory response, with a pronounced upregulation of cytokines il1b, il6, tnfa and il10 observed over time.

CONCLUSIONS

Overall, this study provides an insight into the composition of the intestinal microbiota and the diversity of culturable intestinal bacteria of two economically most important fish species from Adriatic cage culture and sheds light on the autochthonous intestinal B. velezensis as a promising probiotic candidate for Mediterranean aquaculture.

Murine maternal microbiome modifies adverse effects of protein undernutrition on offspring neurobehaviour

Protein undernutrition results in impaired growth and neurobehavioural development in children. However, the impact of timing, environmental factors and maternal versus neonatal influences are unclear. Here, using a mouse model of fetal growth restriction where maternal protein intake is limited during pregnancy, we show that adult offspring exhibit cognitive and anxiety-like behavioural abnormalities. Cross-fostering newborn mice to dams previously exposed to either low protein or standard diet reveals that behavioural impairments in adult offspring require diet-induced conditioning of both fetal development and maternal peripartum physiology. Maternal gut microbiome diversity is reduced, maternal immune, milk, and serum metabolomic profiles are altered, and widespread changes in fetal brain transcriptomic and metabolomic profiles are observed, including subsets of microbiome-dependent metabolites. Finally, we show that dam treatment with a cocktail of ten diet- and microbiome-dependent metabolites results in differential effects on fetal development and postnatal behaviour. Our study highlights the impact of prenatal maternal protein undernutrition on offspring neurobehavioural trajectories and the role of the maternal microbiome.

Gut Microbial Signatures in Pediatric Crohn's Disease Vary According to Disease Activity Measures and Are Influenced by Proxies of Gastrointestinal Transit Time: An ImageKids Study

INTRODUCTION

We investigated relationships between disease activity measures and the gut microbiome in children with Crohn's disease (CD) and how these were confounded by gastrointestinal transit time.

METHODS

Microbiome was profiled (16S rRNA sequencing) in feces from 196 children with CD. Sixty participants also provided samples after 18 months. Mural inflammation (Pediatric Inflammatory Crohn's Magnetic Resonance Enterography Index, PICMI), the simple endoscopic score for CD, and the weighted pediatric Crohn's disease activity index (wPCDAI) were assessed. Fecal calprotectin, plasma C-reactive protein (CRP), and fecal water content (FWC), a proxy of gastrointestinal transit time, were measured too.

RESULTS

Microbiome α diversity, clustering, and differential taxa were related to disease status, but varied remarkably by disease activity measure used. The strongest relationships between microbiome and disease activity status were observed using wPCDAI; fewer or no relationships were seen using more objective measures like PICMI. Taxa predictive of disease activity status were dependent on the disease activity measure used with negligible overlap. Active disease was associated with more pathobionts (eg, Viellonella, Enterobacterales) and fewer fiber-fermenting organisms. The effect FWC had on microbiome superseded the effect of active disease for all disease activity measures, particularly with wPCDAI. Accounting for FWC, the differences in microbial signatures explained by disease activity status were attenuated or lost.

CONCLUSIONS

In CD, microbiome signatures fluctuate depending on the measure used to assess disease severity; several of these signals might be secondary disease effects linked with changes in gut motility in active disease. PICMI appears to be less influenced when studying relationships between microbiome and mural inflammation in CD.

Mitochondrial sirtuin 4 shapes the intestinal microbiota of Drosophila by controlling lysozyme expression

BACKGROUND

Sirtuins are deacetylases that are highly conserved throughout the animal kingdom. They act as metabolic sensors that coordinate cellular responses, allowing an adapted response to various stressors. Epithelial cells, especially those of the intestine, are directly exposed to a wide range of stressors. Together with the microbiota, they form a complex ecosystem with mutual influences. The significance of sirtuins in this complex system is still waiting to be clarified.

RESULTS

Here, we show that a protein-restricted diet strongly increases the intestinal expression of sirtuin 4 (dSirt4), the only mitochondrial sirtuin in Drosophila. To elucidate the effects of deregulated dSirt4 expression in the intestine, we analyzed dSirt4 knockout flies. These flies showed substantial changes in their intestinal proteome and physiological properties. One of the most striking effects was the strong induction of lysozymes in the intestine, with a corresponding increase in lysozyme activity. This effect was organ-autonomous, as it was also observed in flies with dSirt4 knocked out only in intestinal enterocytes. The significant increase in lysozyme abundance in response to tissue-specific dSirt4 knockdown did not reduce the total number of bacteria in the intestine. However, it did affect the microbiota composition by reducing the number of gram-positive bacteria. This effect on microbiota composition can be attributed to dSirt4-dependent lysozyme expression, which is absent in a lysozyme-deficient background. dSirt4 knockout in the enterocytes shortened the lifespan of the flies, as did ectopic lysozyme overexpression in the enterocytes.

CONCLUSIONS

The only mitochondrial sirtuin in Drosophila, dSirt4, is induced by dietary stress in intestinal epithelial cells, which directly regulates the lysozyme activity of these cells. We could associate this altered lysozyme activity with a shift in the microbiota composition, demonstrating a direct link between stress, nutrition, and the host's microbiota regulation.