DADA2: High-resolution sample inference from Illumina amplicon data

Western Diet and fecal microbiota transplantation alter phenotypic, liver fatty acids, and gut metagenomics and metabolomics in Mtarc2 knockout mice

Background

The mitochondrial amidoxime-reducing component-2 (Mtarc) enzyme complex is located on the outer mitochondrial membrane and may be involved in lipid metabolism regulation.

Aim

This study evaluated the impact of fecal microbiota transplantation (FMT) on phenotypic outcomes, liver accumulation of fatty acids (FAs), and modifications to the gut microbial community, as well as the abundance of short-chain fatty acids (SCFAs) and amino acids (AAs), in both sexes of Mtarc2 knockout (Mtarc2-KO) and C57BL/6 N mice fed a Western Diet (WD).

Methodology

Mice were fed a WD (study groups) or normal diet (control groups) and were subjected to intestinal flushing with either a polyethylene glycol (PEG) solution (study groups) or water (control groups); this was followed by intragastrical administration of a human feces suspension (study groups) or water (control groups). Liver FA composition and fecal SCFAs and AAs were measured by mass spectrometry. Metagenomic-based analysis was performed by sequencing the variable V3 and V4 regions of the bacterial 16 S rRNA gene.

Principal findings

Weight gain in C57BL/6 N mice fed a WD was significantly higher than in Mtarc2-KO mice. Compared with water only, intestinal cleansing with PEG resulted in significantly lower weight gain in C57BL/6 N mice but not in Mtarc2-KO mice. FMT did not affect body weight in C57BL/6 N mice, and decreased in Mtarc2-KO females and males fed a ND and a WD, respectively. No significant differences in liver FAs composition were found between mouse strains. While PEG treatment significantly affected liver FAs composition, FMT modulated FAs levels to a much smaller extent. However, neither intestinal cleansing nor FMT affected the microscopic findings of fatty liver. WD feeding affected bacterial diversity, taxonomy and SCFAs and AAs abundances in Mtarc2-KO and C57BL/6 N mice not subjected to PEG treatment. Both intestinal cleansing alone and FMT modulated gut bacterial composition, especially in C57BL/6 N mice, and metabolite abundances in Mtarc2-KO mice.

Conclusion

WD and FMT differentially modified phenotypic parameters, liver FA composition, and gut bacteria in comparisons between Mtarc2-KO and C57BL/6 N. This suggests the Mtarc complex plays a significant role in regulating energy metabolism in mice.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12263-025-00772-x.

Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions

BACKGROUND

Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.

METHODS

In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24 h, 48 h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.

RESULTS

The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+ PMA) were significantly lower than in untreated (-PMA) samples (p < 0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p < 0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48 h (p > 0.05). Of specific genera, only + PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p < 0.05) in comparison to + PMA fresh human milk samples.

CONCLUSIONS

The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4 °C for up to 48 h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.

Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples

High-throughput 16S rRNA metagenomic sequencing has advanced our understanding of the gut microbiome, but its reliability depends on upstream processes such as DNA extraction and bacterial library preparation. In this study, we evaluated the impact of three different DNA extraction methods (a manual method with an ad hoc-designed pre-extraction phase (PE-QIA), and two automated magnetic bead-based methods (T180H and TAT132H)) and two bacterial library preparation protocols (home brew and VeriFi) on the 16S rRNA-based metagenomic profiling of faecal samples. T180H and TAT132H produced significantly higher DNA concentrations than PE-QIA, whereas TAT132H yielded DNA of lower purity compared to the others. In the taxonomic analysis, PE-QIA provided a balanced recovery of Gram-positive and Gram-negative bacteria, TAT132H was enriched in Gram-positive taxa, and T180H was enriched in Gram-negative taxa. An analysis of Microbial Community Standard (MOCK) samples showed that PE-QIA and T180H were more accurate than TAT132H. Finally, the VeriFi method yielded higher amplicon concentrations and sequence counts than the home brew protocol, despite the high level of chimeras. In conclusion, a robust performance in terms of DNA yield, purity, and taxonomic representation was obtained by PE-QIA and T180H. Furthermore, it was found that the impact of PCR-based steps on gut microbiota profiling can be minimized by an accurate bioinformatic pipeline.

Microscale analyses of arginine's effect on oral biofilms

OBJECTIVES

Arginine is a caries-preventive agent that modulates the microbial composition of dental biofilms and raises pH via bacterial ammonia production. The effect of arginine on biofilm pH has only been measured in bulk, and it is unknown how treatment affects microscale pH developments inside dental biofilms. Moreover, little is known about arginine's impact on the biofilm matrix. This study investigated the effects of arginine on biofilm pH, matrix architecture and microbial composition in a saliva-derived biofilm model.

METHODS

72-h biofilms were grown with or without sucrose, and arginine was either supplemented during growth or provided as pulsed treatment. pH was measured in different locations at the biofilm base using confocal-microscopy-based pH ratiometry. Matrix carbohydrates and extracellular DNA (eDNA) were assessed via fluorescence-lectin-binding-analysis and eDNA mapping. Microbial composition was determined by 16S rRNA gene sequencing.

RESULTS

Arginine supplementation during growth considerably raised the biofilm pH, despite the presence of sucrose, and counteracted sucrose-induced shifts in microbial composition. Pulsed arginine treatment, in contrast, had little influence on microbial composition, but still a significant effect on biofilm pH. Importantly, arginine treatment increased the pH variance between different biofilm areas, suggesting that local factors in the biofilm microarchitecture modulate the treatment response. Lastly, arginine supplementation reduced the abundance of matrix carbohydrates, while increasing eDNA levels.

CONCLUSIONS

Arginine impacts biofilm pH at the microscale and changes the microbial and matrix composition in a saliva-derived biofilm model.

CLINICAL SIGNIFICANCE

Arginine exerts caries-preventive effects via multiple mechanisms, including modulations of biofilm pH and matrix microarchitecture.

Underwater drone-based eDNA metabarcoding reveals regional differences in fish communities and early detection of alien species around the Korean Peninsula

Coastal ecosystems surrounding the Korean Peninsula are undergoing rapid environmental changes driven by global climate warming, highlighting the need for efficient methods to monitor marine biodiversity. This study aimed to analyze fish communities across four coastal regions: the East Sea, South Sea, West Sea, and Jeju using environmental DNA (eDNA) metabarcoding. Underwater drones were employed to collect water samples. A total of 63 sampling sites were surveyed, detecting 167 fish species from 72 families, encompassing tropical, subtropical, temperate, boreal, polar, and deep-water taxa. The East Sea hosted a mix of cold- and warm-water species, while Jeju exhibited a relatively high proportion of tropical and subtropical fish. Additionally, 13 alien species were identified, underscoring the utility of eDNA for the early detection of non-native taxa expanding their ranges in response to ongoing warming trends. This study further validated that eDNA sampling using underwater drones offers a rapid, non-invasive approach to biodiversity assessments, effectively addressing many of the limitations associated with traditional survey techniques. Collectively, these findings highlight the potential of eDNA to generate critical and timely data on fish assemblages the emergence of alien species, providing valuable insights to inform proactive resource management, and climate change research in marine ecosystems.

Prebiotics Rescue Gut Microbiome Dysregulation and Enhance Cognitive and Gastrointestinal Function in a Mouse Model of Schizophrenia

BACKGROUND AND HYPOTHESIS

Schizophrenia is a devastating psychiatric disorder characterized by positive (eg, hallucinations) and negative (eg, reduced motivation) symptoms, and cognitive deficits. Chronic gastrointestinal tract issues exist as comorbid symptoms of schizophrenia. Recent findings indicate the involvement of the microorganisms that inhabit the gut, the microbiota (and the broader microbiome which also includes microbial genomes, etc.) in schizophrenia pathogenesis. In the present study, we hypothesized that chronic administration with prebiotics fructooligosaccharide and galactooligosaccharide (FOS and GOS; a combination used clinically for other disorders) would restore gut microbiome composition of the metabotropic glutamate receptor 5 (mGlu5) knockout (KO) mouse model of schizophrenia, which we previously demonstrated to exhibit gut dysbiosis.

STUDY DESIGN

We assessed the impact of prebiotics on gut microbiome composition and function, as well as the gastrointestinal function and schizophrenia-like phenotype of mGlu5 KO mice and wild-type littermates. We administered a combination of the prebiotics FOS and GOS, vs vehicle control administration, in both the mouse model of schizophrenia and wild-type littermates.

STUDY RESULTS

The present study firstly corroborated the altered gut microbiome composition in the mGlu5 KO mouse model of schizophrenia. Importantly, we have revealed an altered microbial metabolic profile. We have also shown that the prebiotics we administered were not only able to rescue these gut microbiome changes but also had additional beneficial effects including cognitive enhancement and improved gastrointestinal function.

CONCLUSION

These preclinical findings indicate that prebiotics, such as the combination of FOS and GOS used in the present study, may have therapeutic potential in schizophrenia as an add-on intervention with an exceptional safety profile.

Local tree cover predicts mosquito species richness and disease vector presence in a tropical countryside landscape

Context

Land use change and deforestation drive both biodiversity loss and zoonotic disease transmission in tropical countrysides. For mosquito communities that can include disease vectors, forest loss has been linked to reduced biodiversity and increased vector presence. The spatial scales at which land use and tree cover shape mosquito communities present a knowledge gap relevant to both biodiversity and public health.

Objectives

We investigated the responses of mosquito species richness and Aedes albopictus disease vector presence to land use and to tree cover surrounding survey sites at different spatial scales. We also investigated species compositional turnover across land uses and along environmental gradients.

Methods

We paired a field survey of mosquito communities in agricultural, residential, and forested lands in rural southern Costa Rica with remotely sensed tree cover data. We compared mosquito richness and vector presence responses to tree cover measured across scales from 30 to 1000 m, and across land uses. We analyzed mosquito community compositional turnover between land uses and along environmental gradients of tree cover, temperature, elevation, and geographic distance.

Results

Tree cover was both positively correlated with mosquito species richness and negatively correlated with the presence of the common invasive dengue vector Ae. albopictus at small spatial scales of 90-250 m. Land use predicted community composition and Ae. albopictus presence.

Conclusions

The results suggest that local tree cover preservation and expansion can support mosquito species richness and reduce disease vector presence. The identified spatial range at which tree cover shapes mosquito communities can inform the development of land management practices to protect both ecosystem and public health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10980-025-02105-0.

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

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

Are you my mother? When host genetics and gut microbiota tell different phylogenetic stories in the Africanized honey bee hybrid (Apis mellifera scutellata × sspp.)

Africanized honey bees (Apis mellifera scutellata × sspp.) originated in Brazil through the crossbreeding of African (A. mellifera scutellata) and European (A. mellifera sspp.) honey bee subspecies. African genes came to dominate in these hybrid honey bees over time. Gut microbiota co-evolve with their hosts and generally reflect host phylogeny. To examine if this was true in Africanized honey bee hybrids (also known as scutellata-European hybrids), we compared the gut microbiota (16S rRNA) of three honey bee subspecies: African, European, and Africanized bees. Publicly available sequencing data from five honey bee studies were downloaded from the National Center for Biotechnology Information (NCBI). European bee samples (n = 42) came from the United Kingdom, Switzerland, and the United States. African bee samples (n = 82) came from Kenya. Africanized bee samples (n = 10) came from Brazil. Unexpectedly, Africanized honey bee gut microbiota was far more similar to European bees than to African bees despite the closer host genetic relationship between African and Africanized bees. All three subspecies shared similar relative abundances of core taxa. We posit that the similarity in gut microbiota between Africanized and European honey bees arose from the nature of the crossbreeding and the social/environmental transmission of gut microbiota within hives. Namely, African queens took over European hives. However, the hybrid offspring acquired their gut microbiota from European nurse bees and European hive materials, resulting in the stable transmission of European gut microbiota across generations. Our results provide an intriguing insight into the potential ecological, social, and environmental factors that shape the gut microbiota of the Africanized honey bee hybrid.IMPORTANCEAfricanized honey bee hybrids originated in Brazil through the crossbreeding of African and European honey bee subspecies. In this study, we examined the gut microbiota of all three honey bee subspecies (African, European, Africanized). A few core microbiota were shared across all subspecies. Interestingly, while African honey bee genes dominated in the Africanized honey bee hybrids, their gut microbial composition was most similar to European bees. This is likely related to the way these bees were crossbred-with African queens taking over European hives, while gut microbial inoculation of hybrids came from European nurse bees and European hive materials. Gut microbiota are critical to honey bee health, and studying the gut microbiota of closely related honey bee subspecies helps understand the factors that influence gut microbial composition. This is important for our broader understanding of honey bee health, conservation, and evolution.

Abiotic stress destabilizes the bacterial community of sugar kelp, Saccharina latissima (Phaeophyceae)

As climate change progresses, the intensity and variability of freshwater outflow into the ocean are predicted to increase. The resulting increase in low-salinity events, paired with other abiotic stressors (including increasing temperatures), will be a source of stress for the kelp Saccharina latissima (Saccharina hereafter) and potentially Saccharina-associated bacteria. Bacteria influence host health and can facilitate or hinder host survival and acclimation to stressful abiotic conditions. Therefore, understanding how bacterial communities change under abiotic stress is critical for understanding how abiotic stress will affect kelp physiology. We investigated the effect of abiotic stress on Saccharina and associated bacteria by surveying the bacterial community associated with Saccharina across naturally occurring salinity and temperature gradients, coupled with salinity manipulation experiments. Overall, Saccharina harbored a stable core bacterial community, which decreased in relative abundance under abiotic stress. In the field, both salinity and temperature shaped the bacterial community, with temperature having higher explanatory power most of the time. In the lab, we confirmed that the patterns observed in the field could be replicated by manipulating salinity alone. Decreased relative abundance of core bacteria and increased community dissimilarity in low-salinity in the lab suggest that low-salinity alone can induce a stress response, detectable in the bacterial community of Saccharina.

Inoculation of apple plantlets with Rhodococcus pseudokoreensis R79T enhances diversity and modulates the structure of bacterial rhizosphere communities in soil affected by apple replant disease

BACKGROUND

Apple replant disease (ARD) represents a dysbiotic rhizosphere condition potentially driven by root exudates including phytoalexins at the root-soil interface. A promising mitigation strategy could be the application of bioinoculants that reduce these compounds and foster a diverse microbiome. This study investigated the effects of Rhodococcus pseudokoreensis R79T, a strain with benzoate-degrading capabilities and genetic potential to degrade biphenyls, on the rhizosphere microbiome of apple plantlets grown in ARD-affected soil in a greenhouse experiment.

RESULTS

We applied R79T at 10⁶ to 10⁹ CFU/ml, assessing its impact on bacterial 16S rRNA diversity and abundance, as well as the abundance of biphenyl dioxygenase (bphd) genes. Eight weeks post-inoculation reads of strain R79T persisted in the rhizosphere, particularly at higher inoculation levels. Inoculation enhanced bacterial diversity and bphd gene abundance, with significant shifts in community composition. Key responders included members of Gaiellales, which increased, and Streptomyces, which decreased. Co-occurrence network analysis revealed that inoculation promoted positive interactions, more homogeneous connectivity, and a higher degree of connections. Effects on bacterial community structure varied significantly with inoculation concentration.

CONCLUSIONS

The fact that R79T enhanced rhizosphere bacterial diversity and modulated community composition in ARD-affected soil highlights the potential of R79T to reshape microbial interactions. Further research is needed to elucidate the mechanisms underlying these effects, including studies on in situ degradation of phytoalexins and inoculation of R79T alongside bacteria for plant growth promotion (PGP) in synthetic communities for elevated efficiency against ARD.

Root-associated microbiota of decline-affected and asymptomatic Pinus sylvestris trees

Forest decline is a worldwide phenomenon affecting many species such as Pinus sylvestris. Although it is driven by multiple stressors, the role of tree associated microorganisms remains still unclear. To reduce this knowledge gap we obtained amplicon sequences of the microbiota inhabiting the rhizosphere soil and root endosphere (bacterial 16S rRNA and fungal ITS2) of decline-affected and asymptomatic P. sylvestris trees in spring and summer. The dataset comprised a total of 384 samples from three mountainous areas which yielded an average of 59,592.3 ± 7,371 and 56,894.3 ± 12,983.5 (spring and summer) bacterial and 74,827.9 ± 12,095.4 and 85,363.9 ± 14,199.3 (spring and summer) fungal raw reads, resulting in 23,982.4 ± 11,312.4 (spring) and 17,921.8 ± 10,802.7 (summer) bacterial and 50,571.1 ± 10,499.5 (spring) and 49,509.4 ± 12,673.8 (summer) fungal quality-filtered sequences. These data and the corresponding metadata could be used to identify pine decline bioindicators, to develop novel diagnosis tools of specific microorganisms and could serve as reference against which to compare other microbial communities.

A multi-strain, biofilm-forming cocktail of Bacillus spp. and Pediococcus spp. alters the microbial composition on polyethylene calf housing surfaces

Application of a beneficial microbial cocktail of Bacillus spp. and Pediococcus spp. was evaluated first for adherence to polyethylene calf hutch material, and second, to determine if application in situ to individual calf hutches post-cleaning influenced surface recolonization by enteric pathogens. Three treatments were utilized: (i) no application (NC), (ii) chlorine-free, distilled water (DW), or (iii) an application of a microbial inoculant containing Bacillus spp. and Pediococcus spp. at a concentration of 0.4 g/m2 of hutch space (LF). Thirty-six 15 × 15 cm pieces of naïve, sterile polyethylene calf hutch material received either NC or LF and were incubated at 28°C, and bacterial growth was evaluated by total aerobic plate counts at 24, 48, and 72 h post-application. Thirty polyethylene calf hutches (n = 10/treatment) were randomized to NC, DW, or LF 24 h after cleaning. Calves were placed in the hutches 24 h after treatment application and monitored daily for 28 d. In situ surface samples were randomized by time from five unique locations within the calf hutch interior: 24 h post-cleaning and then 24 h, 7 d, 14 d, and 21 d post-application. Total aerobic plate counts and culture-independent approaches RT-qPCR and 16S amplicon sequencing were used to detect and identify the composition of the bacterial community in situ. The bacteria in the inoculant were able to successfully colonize on polyethylene, and application to individual polyethylene calf housing in situ influenced microbial diversity and reduced the presence of some undesirable bacteria on high-contact interior surfaces.IMPORTANCEDue to its multifactorial nature, neonatal calf diarrhea can be difficult to manage on farms. Clean housing environments are a critical disease control point, especially for calves less than one month of age. Application of a beneficial biofilm-forming bacterial product after cleaning of neonatal calf housing may influence the microbial communities present on the surface, particularly those that may present disease risk to calves in early life.

Association between oral microbial diversity (only bacteria) and diabetes in U.S. adults: analysis of NHANES 2009-2012 data

OBJECTIVE

Studies on the relationship between oral microbial diversity and diabetes were limited. This study analyzed the oral microbial composition and diversity using NHANES data to explore its potential role in diabetes pathogenesis; Methods: A cross-sectional design was employed, utilizing NHANES data (2009-2012), including oral microbiota samples and diabetes-related indicators. Oral samples were collected via mouthwash and analyzed using 16 S rRNA gene sequencing. The Shannon-Wiener Index represented microbial diversity (Only bacteria). Multivariate logistic regression, restricted cubic splines, and subgroup analyses were employed to evaluate associations.

RESULTS

A significant association was found between oral microbial diversity and diabetes. According to the completely adjusted model, a one-unit increment in the Shannon-Wiener Index was associated with a 12.1% increase in the likelihood of developing diabetes (OR = 1.121, 95%CI: 1.120 ~ 1.122). Subgroup analyses showed divergent findings. In subgroups with lower body weight and BMI, increased microbial diversity correlated with a decreased likelihood of developing diabetes (OR = 0.68 (0.68-0.68)); Conclusions: Oral microbial diversity exhibits a complex relationship with diabetes risk. The increase and subsequent decrease of oral microbiota diversity in relation to diabetes risk. This suggests that certain specific microbes or interactions between microbes may influence the development of diabetes. However, due to the many limitations of this study, it cannot prove the causal relationship between oral microbial richness and diabetes. Further longitudinal and mechanistic studies are essential to elucidate the causal links and dynamic alterations between the oral microbiome and the progression of diabetes.

The effect of the administration form of antibiotic therapy on the gut microbiome in patients with infected diabetic foot ulcers - DFIATIM trial

BACKGROUND

Diabetic foot infections (DFIs) contribute to the global disability burden. Beta-lactams are the most commonly used antibiotics for treating DFIs. However, the use of antibiotics may lead to disruption of the healthy balance of the gut microbiota, causing dysbiosis.

METHODS

Patients with infected diabetic foot ulcers (iDFUs) were treated with two kinds of beta-lactams (amoxicillin/clavulanic acid or ceftazidime) according to microbial sensitivity of causative agents via bolus or continuous administration modes. Changes in the gut microbiome of patients were analyzed. Diabetic patients without iDFUs were used as a control group. 16 S ribosomal RNA gene amplicon sequencing was performed on stool samples collected from participants.

RESULTS

Alpha diversity and beta diversity of gut microbiota of treated patients did not show significant differences between bolus and continuous modes. However, significant differences were observed between gut microbiota diversity of treated patients and control group. PCoA plots showed individualized responses of the patient's gut microbiota to antibiotics at different times using both administration forms associated with the pre-treatment state of microbiota composition. Enterococcus, Sellimonas, and Lachnoclostridium were the common bacterial markers differentially abundant in the gut microbiota of antibiotic-treated patients with iDFUs while Roseburia, Dorea, and Monoglobus were mainly abundant in the gut microbiota of patients without iDFUs. Predicted pathways like "Transporters", "ABC transporters" and "Phosphotranspherase system (PTS)" were upregulated in the gut microbiome of patients treated with bolus regime which may lead to increased intestinal barrier permeability.

CONCLUSION

The present study reported alterations in gut microbiota composition and functionality and provided the bacterial markers as well as potential metabolic signatures associated with each administration mode in patients with iDFUs, which may be used as a reference set for future studies of the effect of antibiotics administration on the gut microbiome of patients with iDFUs. This study shed light on the importance of understanding the effect of antibiotic administration form on gut microbiome in patients with iDFUs.

TRIAL REGISTRATION

The DFIATIM Clinical Trial (Full title: "Rationalisation of ATB therapy in diabetic foot infection and its impact on the intestinal microbiota") is submitted to the European Union Clinical Trials Database under the EudraCT Number: 2019-001997-27. The date of registration is July 17th, 2020.

Cooked Bean (Phaseolus vulgaris L.) Consumption Alters Bile Acid Metabolism in a Mouse Model of Diet-Induced Metabolic Dysfunction: Proof-of-Concept Investigation

Background/Objectives: Metabolic dysregulation underlies a myriad of chronic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD) and obesity, and bile acids emerge as an important mediator in their etiology. Weight control by improving diet quality is the standard of care in prevention and control of these metabolic diseases. Inclusion of pulses, such as common bean, is an affordable yet neglected approach to improving diet quality and metabolic outcomes. Thus, this study evaluated the possibility that common bean alters bile acid metabolism in a health-beneficial manner. Methods: Using biospecimens from several similarly designed studies, cecal content, feces, liver tissue, and plasma samples from C57BL/6 mice fed an obesogenic diet lacking (control) or containing cooked common bean were subjected to total bile acid analysis and untargeted metabolomics. RNA-seq, qPCR, and Western blot assays of liver tissue complemented the bile acid analyses. Microbial composition and predicted function in the cecal contents were evaluated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Results: Bean-fed mice had increased cecal bile acid content and excreted more bile acids per gram of feces. Consistent with these effects, increased synthesis of bile acids in the liver was observed. Microbial composition and capacity to metabolize bile acids were markedly altered by bean, with greater prominence of secondary bile acid metabolites in bean-fed mice, i.e., microbial metabolites of chenodeoxycholate/lithocholate increased while metabolites of hyocholate were reduced. Conclusions: In rendering mice resistant to obesogenic diet-induced MASLD and obesity, cooked bean consumption sequesters bile acids, increasing their hepatic synthesis and enhancing their diversity through microbial metabolism. Bean-induced changes in bile acid metabolism have potential to improve dyslipidemia.

Impact of antimicrobial exposure at delivery and siblings on early Bifidobacterium succession and allergy development up to 24 months of age

BACKGROUND

Allergic diseases such as asthma, eczema, and food allergies are rising globally. The infant gut microbiota, particularly the dominance of Bifidobacterium, shapes immune development and allergy risk. In Japan-where Bifidobacterium prevalence is notably high-longitudinal investigations focusing on the pre-weaning period, when external influences are relatively limited, remain scarce. Therefore, based on consistent hypotheses and findings from previous studies, we investigated how two important early factors-antibiotic exposure at birth and the presence of older siblings-influence the gut environment in early infancy and subsequent allergy development.

RESULTS

In a prospective cohort of 121 Japanese infants, stool samples were collected at seven time points from birth through 24 months. We quantified the relative abundances of Bifidobacterium, Bacteroides, Clostridium, and Faecalibacterium and recorded allergic outcomes at 2 years. Both antimicrobial exposure at delivery and sibling presence significantly altered gut microbiota composition and overall diversity in early infancy. Although the full cohort showed no consistent diversity or Bifidobacterium differences by allergic status, in several subgroups where these two factors were excluded, infants who had an allergy by 24 months exhibited marked shifts in early gut microbiota community structure-particularly in beta diversity-and reduced Bifidobacterium occupancy during the pre-weaning period (1-6 months) versus non-allergic peers. Moreover, infants whose gut microbiota was initially affected by these factors showed a recovery in diversity after weaning, a rebound more pronounced in non-allergic individuals.

CONCLUSIONS

These findings indicate that both the initial community configuration and its capacity to rebound after perturbation are critical determinants of allergy risk. By focusing on dynamic changes through weaning and adjusting for decisive confounders, this study refines insight beyond prior cross-sectional work. Early interventions that preserve or restore microbial diversity and Bifidobacterium dominance may therefore offer a promising strategy to mitigate allergic disease development.

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

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

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

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

IMPORTANCE

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

Comprehensive quantitative evaluation and mechanism analysis of influencing factors on yield and quality of cultivated Gastrodia elata Blume

Gastrodia elata Blume (G. elata Bl.) is a dual-purpose herb for medicine and food. Wild resources are depleted, and there is a significant decrease in yield or quality when they are cultivated artificially. However, what factors led to the decline is still unclear. In this study, based on comprehensive data under multiple production regions, hierarchical partitioning and partial least squares path modeling were used for the first time to quantitatively evaluate the dominant influencing factors and mechanism for the yield and quality of cultivated G. elata Bl.. The results showed that all G. elata Bl. were categorized into two cultivated subspecies G. elata Bl. f. elata and G. elata Bl. f. glauca. The Proteobacteria was the most dominant phylum for bacteria with 33.59%, and Ascomycota for fungi with 46.33% based on the amplicon sequencing. Armillaria relative abundance, soil available potassium, and temperature seasonality were the key factors. Their independent effects were 74.14%, 24.78%, and 20.36% on yield, and 36.83%, 25.63%, and 21.30% on quality, respectively. Plant subspecies directly determined the yield and quality (P < 0.01). Soil physical properties affected chemical properties, which in turn affected biological properties and ultimately yields (P < 0.05). Meanwhile, soil physical properties affected quality by influencing soil chemical properties (P < 0.01). In conclusion, our study contributed novel insight to optimize cultivation strategies of G. elata Bl..

Investigating dose-dependent effects of chemical compounds targeting rumen fermentation pathways using an in-vitro rumen fermentation system

BACKGROUND

Ruminal fermentation leads to the formation of methane (CH4) as a byproduct, which is one of the major greenhouse gases. Despite extensive research efforts involving the use of various anti-methanogenic and hydrogen sink compounds, the current understanding of the dose-response effects of these compounds on the rumen microbiome and fermentation profile is limited. In this study, potential methanogenesis inhibitors or electron acceptors were evaluated for their effects on methane production, fermentation, and prokaryotic community composition. Dose-response effects of sodium 2-bromoethanesulfonate (BES: 0, 2.5, 5, 10 mmol/L), p-hydrocinnamic acid (HoC: 0, 5, 10 mmol/L), and sodium fumarate dibasic (DFS: 0, 5, 10, 20 mmol/L) on dry matter degradation, total gas production, methane concentration and yield, composition and yield of volatile fatty acids, and prokaryote composition were studied during 48 h rumen fermentations.

RESULTS

The BES decreased the yield (ml/ g DM) and concentration (%) of CH4, acetic, isobutyric, and total VFA (t-VFA) concentrations (mmol/g DM), and increased propionic and butyric acid concentrations (mmol/g DM) without affecting dry matter degradability (dDM) as the dose increased. The HoC decreased dDM, total gas production (TGP), CH4 yield (ml/ g DM) and increased tVFA concentration (mmol/g DM) as the dose increased. The increasing dose of DFS increased the pH, propionic acid and tVFA concentrations (mmol/g DM) and decreased the yield (ml/ g DM) and concentration (%) of CH4 without affecting dDM. Sodium 2-bromoethanesulfonate, HoC, and DFS doses did not significantly change the alpha-diversity and beta-diversity indices of the prokaryotic communities at the amplicon sequence variant level, although the relative abundances of specific phyla were affected by the treatments. The major bacterial phyla across all samples were Bacteroidetes, Proteobacteria, Firmicutes, Spirochaetota, Verrucomicrobiota, and Patescibacteria.

CONCLUSIONS

This study demonstrated that (i) all the evaluated compounds affected the targeted metabolic pathways without influencing the structure of the rumen microbial community, (ii) BES inhibited methanogenesis without affecting dry matter degradability, and (iii) HoC and DFS shifted hydrogen utilization towards acetate and propionate production. The recommended doses, to reduce methane during in-vitro rumen fermentation for BES, HoC, and DFS were determined to be 2.5 mmol/L, 5 mmol/L, and 10 mmol/L, respectively. Further research is suggested to understand the interactive effects of methane inhibition compounds, such as BES, in conjunction with H2 sink compounds such as HoC and DFS. However, caution is advised when using halogenated compounds like BES, as some methanogens have developed resistance and BES is not approved for use as a feed additive for live animals.

Sex-induced alterations in rumen microbial communities and metabolite profiles: implications for lamb body weight

BACKGROUND

Microbiota-metabolome interactions play a crucial role in host physiological regulation and metabolic homeostasis. The aim of this study was to investigate that sex induces alterations in rumen microbial community composition and metabolite profiles in lambs and the influence on body weight. This study aimed to demonstrate that sex- induced alterations in rumen microbial community and metabolite profiles and blood indices and their linkage to growth performance in lambs.

RESULTS

This study examined (growth indices, serum indices, rumen fermentation parameters, rumen fluid microbiota community and metabolome profiles) in 180 Hu lambs (90 males, and 90 females) with the same age and diet. At six months, male lambs showed significantly greater body weight, serum indices (glutamic pyruvic transaminase, glutamic oxalacetic transaminase, growth hormone, glucagon-like peptide 1, and ghrelin), and molar percentage of propionic acid, isobutyric acid, butyric acid, isovaleric acid and valeric acid compared to female. However, male had lower VFA molar concentrations (acetic acid, propionic acid, butyric acid, and TVFAs), acetic acid/propionic acid, and VFA molar percentage (acetic acid) than female. Significant sex-related differences were observed in rumen microbiota and metabolic enrichment between genders. Moreover, compared with the females lambs, the relative abundance of Succiniclasticum, uncultured_rumen_bacterium, NK4 A214_group, Veillonellaceae_UCG_001 and Butyrivibrio in the male lambs has been significantly increased, while the relative abundance of Prevotella has been significantly decreased (P < 0.05). Notably, there were significant rumen microbiota-metabolite interactions, especially Firmicutes and Bacteroidota as dominant phyla in the sheep rumen with significant differences in correlation with rumen metabolic modules. Additionally, there are pronounced correlations among the microbiota, particularly within the Firmicutes phylum. Furthermore, the up-regulated metabolites in the rumen fluid of male lambs were predominantly enriched in the amino acid metabolite pathway, and these metabolites exhibited a significant positive correlation with body weight. However, the metabolites that were up-regulated in ewe lambs were predominantly enriched in the lipid metabolic pathway, and these metabolites exhibited a significant negative correlation with body weight. Moreover, lamb rumen microbial markers (Lachnospiraceae_UCG_008, Saccharofermentans, unclassified_Clostridia, Christensenellaceae_R_7_group, Anaerovorax, Mogibacterium, and unclassified_Erysipelotrichaceae) and metabolic markers (C75, 4-Coumarate, Flibanserin,3-Amino-5-mercapto-1,2,4-triazole, 1,3-Propane sultone, Fingolimod phosphate ester, S-,) were significantly positively correlated with body weight, but lamb rumen microbial markers (Anaeroplasma, unclassified_Acholeplasmataceae, uncultured_rumen_bacterum_4c28 d_15) and metabolic markers (Mozenavir, Reduced riboflavin, PG(18:2(9Z,12Z)/0:0), Cowanin) were significantly negatively correlated body weight.

CONCLUSIONS

This study shows that sex-induced alterations in rumen microbial communities and metabolite profiles, adapting to the growth and development of lambs. The findings may help develop targeted strategies to optimize sheep rumen microbiota and improve productivity.

Exploring tarhana's prebiotic potential using different flours in an in vitro fermentation model

Tarhana, a traditional fermented food important to Turkish and Central Asian cuisines, is known for its unique composition of yoghurt, flour, vegetables, and herbs, and its potential health benefits through fermentation. The aim of this study was to evaluate tarhana's potential prebiotic and postbiotic properties using an in vitro colonic fermentation model. We explored how ingredient variations, particularly flour types and fermentation methods, influence gut microbial diversity and metabolite production. Tarhana was prepared using wheat, chickpea, einkorn, and purple potato flours, fermented with baker's yeast (Saccharomyces cerevisiae) or chickpea sourdough. Gut microbial composition and levels of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were analysed following in vitro colonic fermentation. Flour type and fermentation method significantly influenced gut microbial composition and metabolite production. Sourdough-fermented tarhana made with purple potato (q = 1.23 × 10-7), chickpea (q = 1.23 × 10-7), and einkorn (q = 2.51 × 10-7) flours reduced Veillonella levels compared to baker's yeast variants. Sourdough purple potato tarhana also decreased Escherichia-Shigella levels in faecal samples, which were higher in baker's yeast-fermented faecal samples (q = 0.003). SCFA levels, particularly acetate and propionate, were higher in chickpea and purple potato tarhana fermented faecal samples, with sourdough variants showing the strongest effects. Bifidobacterium abundance increased in einkorn sourdough tarhana, while chickpea flour tarhana slightly increased isobutyrate levels. This study demonstrates that specific flour types combined with sourdough fermentation enhance tarhana's functional properties by promoting beneficial microbial shifts and increasing SCFA production. These findings suggest tarhana's potential as a personalized functional food to support gut health, warranting further validation through clinical trials.

The forensic footprint: Elemental and microbial evidence in relocated remains

Here, we investigate the microbial and elemental signatures left behind at the sites of relocated remains, providing insights into postmortem processes that can assist forensic investigations of clandestine burials and relocated remains. We allowed two 90.7 kg (200lbs) clothed porcine models to decompose in open, varied environments in Arizona for a period of 25 days prior to the removal of the remains to secondary burial locations. After a period of 9 months, we collected soil samples from both the primary and secondary sites, as well as from control sites nearby. Our findings support the prevailing suggestion that microbial communities associated with decomposing remains exhibit distinct signatures, here dominated by Gammaproteobacteria and Clostridium, and demonstrate for the first time that these signatures remain detectable at a primary site for an extended period after a short decomposition period and relocation of remains to a secondary site. Additionally, elemental analyses identified significant differences in soil composition, particularly in macronutrients such as phosphorus and sulfur, between control and both primary and secondary deposition sites. These findings suggest that the traces left behind by decomposing remains can serve as forensic markers for an extended period after relocation. Our results highlight the potential of combining microbial and elemental analyses to enhance the understanding of decomposition and inform investigative strategies in forensic contexts. This research underscores the importance of microbial signatures in forensic science and calls for further exploration of their broader applicability in various burial environments.

A pilot study using eDNA collected from soil and active air samplers to detect terrestrial vertebrates in an open grassland habitat of central Queensland, Australia

OBJECTIVE

Small mammals such as the Julia Creek dunnart (Sminthopsis douglasi) may be difficult to detect using traditional trapping methods. Here, we conducted a pilot study to determine whether eDNA collected from soil and/or air could detect the presence of terrestrial vertebrates, including S. douglasi, in a semi-arid, open grassland environment.

RESULTS

Airborne eDNA analysis returned vertebrate DNA from five sample sites (n = 7), whereas soil eDNA analysis returned vertebrate DNA from a single site (n = 7). The Julia Creek dunnart was not detected in any of the experimental samples. However, several airborne eDNA samples did return strong matches to three terrestrial vertebrates, the long-haired rat (Rattus villosissimus), red kangaroo (Osphranter rufus) and brown quail (Synoicus ypsilophorus), all native species known to occur commonly in the study area. Overall, our preliminary findings suggest that the effectiveness of airborne and soil-derived eDNA in detecting terrestrial vertebrates was constrained by high human signal and low sampling intensity. For future studies, we recommend a number of field and lab-based refinements to increase the likelihood of detecting more taxa, particularly those that occur at low density.

CLINICAL TRIAL NUMBER

Not applicable.

Impact of fluoroquinolone and heavy metal pollution on antibiotic resistance maintenance in aquatic ecosystems

BACKGROUND

Freshwater pollution with compounds used during anthropogenic activities could be a major driver of antibiotic resistance emergence and dissemination in environmental settings. Fluoroquinolones and heavy metals are two widely used aquatic pollutants that show a high stability in the environment and have well-known effects on antibiotic resistance selection. However, the impact of these compounds on antibiotic resistance maintenance in aquatic ecosystems remains unknown. In this study, we used a microcosm approach to determine the persistence of two fluoroquinolones (ciprofloxacin, ofloxacin) and two heavy metals (copper and zinc) in the Rhône river over 27 days. In addition, we established links between antibiotic and metal pollution, alone and in combination, and the composition of freshwater bacterial communities, the selection of specific members and the selection and maintenance of antibiotic and metal resistance genes (ARGs and MRGs) using a metagenomics approach.

RESULTS

Whereas ofloxacin was detected at higher levels in freshwater after 27 days, copper had the strongest influence on bacterial communities and antibiotic and metal resistance gene selection. In addition, heavy metal exposure selected for some ARG-harboring bacteria that contained MRGs. Our research shows a heavy metal-driven transient co-selection for fluoroquinolone resistance in an aquatic ecosystem that could be largely explained by the short-term selection of Pseudomonas subpopulations harboring both fluoroquinolone efflux pumps and copper resistance genes.

CONCLUSION

This research highlights the complexity and compound-specificity of dose-response relationships in freshwater ecosystems and provides new insights into the medium-term community structure modifications induced by overall sub-inhibitory levels of antibiotic and heavy metal pollution that may lead to the selection and maintenance of antibiotic resistance in low-impacted ecosystems exposed to multiple pollutants.

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

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

Gut bacterial diversity in bovines infected with Mycobacterium tuberculosis var. bovis: insights on tuberculosis pathogenesis

Bovine tuberculosis susceptibility and pathogenesis are influenced by host immunity, which may be modulated by the host microbiota. While intestinal microbiota composition affects pulmonary diseases in humans, its role in bovine tuberculosis remains unclear. This study explores the intestinal microbiota of cattle and its association with tuberculosis to better understand disease pathophysiology. A case-control study was conducted using small intestine content samples from cattle with and without tuberculosis, slaughtered in Rio Grande do Sul, Brazil. DNA extraction, 16S rRNA (V4) sequencing, and bioinformatics analyses assessed alpha and beta diversity, taxa characterization, differential abundance, and metabolic pathways. No significant differences in alpha and beta diversities between the groups were detected. However, the Bacillota/Bacteroidota ratio suggested dysbiosis associated with bovine tuberculosis. Differential abundance analysis showed that microorganisms belonging to the Bacillota phylum, the Eubacterium cellulosolvens group, Colidextribacter and Coprococcus genera were enriched in healthy cattle. Conversely, animals with tuberculosis showed higher abundances of Verrucomicrobiota phylum, Sphingomonadaceae and Eubacteriaceae families, and Solobacterium and Clostridia-UCG-014 genera. Moreover, metabolic pathways related to carbohydrate degradation were enriched in healthy animals, and biosynthetic pathways related to disease were enriched in tuberculosis animals. This study highlights associations between intestinal microbiota and bovine tuberculosis, providing insights into disease mechanisms.

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

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

Effects of Grazing in a Low Deciduous Forest on Rumen Microbiota and Volatile Fatty Acid Production in Lambs

The aim of the present study was to evaluate the effect of grazing the low deciduous forest (LDF) vegetation on the diversity of the rumen microbiome in growing lambs and its relationship with volatile fatty acid (VFA) profiles. After a 35-day indoor acclimatization (stabilization period), the lambs were assigned to two groups: housed (CG, n = 4) and grazing (EG, n = 4). The grazing lambs had a 14-day habituation period in the LDF (4 h/day) and a further 30 grazing days when fodder intake was observed. Ruminal samples were collected at the end of the stabilization, on day 14 post-stabilization (14DPS), and on day 44 post-stabilization (44DPS). The ruminal butyrate concentration showed a progressive decrease of approximately 23% over the time (p = 0.0130). The qualitative composition (p = 0.001) and relative proportions of bacteria (p = 0.004) in EG-44DPS exhibited a greater diversity, with 107 total genera and 19 unique, significant abundances in 13 genera with a higher presence of Bacteroidales_RF16_group, Lachnospiraceae_ND3007_group, and WCHB1-41. Moreover, significant functional profiles are associated with key metabolic pathways in bacteria and are interconnected by the need to generate energy and biosynthetic precursors and to manage available nitrogen and carbon. Finally, eight bacterial genera were identified as biomarkers correlated with the increase in VFA in EG-44DPS.

Integrated faecal microbiota and blood metabolic changes following different dietary zinc oxide levels in weaned piglets

This study investigated faecal microbial composition and blood metabolome profile of piglets fed different levels of supplementary zinc oxide (ZnO) after weaning. A dose-response study was conducted with four experimental diets containing 153 (D153), 1022 (D1022), 1601 (D1601), and 2407 (D2407) ppm zinc (Zn) in the feed. At the end of the trial, blood and faeces samples were obtained for analyses. Multivariate analysis of the blood metabolomics dataset and Principal Coordinate Analysis (PCoA) of faecal microbiota data showed that pigs receiving D2407 had a different metabolic and microbial profile to the other groups, whereas no differences were observed in pigs fed with D153, D1022, and D1601. The highest dietary Zn inclusion was associated with significant increase in the abundance of Clostridium sensu stricto, Terrisporobacter, Dorea, and Prevotellaceae_NK3B31_group and a decrease in relative abundances of Methanobrevibacter, Treponema, Megasphaera, and UCG 002 genera. Pearson's correlation analysis showed positive correlations between the abundance of Christensenellaceae R7-group with amino acids metabolism and production of microbial metabolites. The results suggest that only 2407 ppm Zn altered gut microbiota and modulated blood metabolic profile, which may impact the health status of piglets through specific microbial metabolites.

Characteristic gene expression profile of intestinal mucosa early in life promotes bacterial colonization leading to healthy development of the intestinal environment

The gut microbiome early in life plays a crucial role in development of the host and affects health throughout life. The definition of a healthy microbiome early in life has not been established, and the underlying mechanism of how a young host selects appropriate microbes for colonization remains unclear. Understanding the mechanism may provide insights into novel preventive and therapeutic strategies by correcting dysbiosis early in life. We employed germ-free mice early in life (4 weeks of age) and later in life (10 weeks of age) for fecal microbiota transfer (FMT) from specific pathogen-free mice. We performed age-unmatched FMT between recipients early in life and donors early or later in life, in addition to common age-matched FMT. Age-matched FMT resulted in significantly different bacterial compositions between recipients early vs. later in life. When the gut microbiome from donors early or later in life was transferred to recipients early in life, bacterial compositions of recipients from donors later in life were similar to those of recipients from donors early in life. This finding suggests that the host early in life has mechanisms to select microbes appropriate for age from the exposed microbiome. We hypothesized that the age-specific intestinal environment promotes age-appropriate intestinal microbiome colonization and examined gene expression in the intestinal mucosa of germ-free mice. We observed that gene expression profiles were different between early vs. later in life. Correlation analysis demonstrated that genera Lachnospiraceae NK4A136 group and Roseburia were positively correlated to genes expressed predominantly early in life, but negatively with genes expressed predominantly later in life. We confirmed that the relative abundance of these genera was significantly higher in specific pathogen-free mice early in life compared with mice later in life. The characteristic gene expression of the intestinal mucosa early in life might play roles in selecting specific bacteria in the intestinal microbiome early in life.

Impact of Post-Harvest Apple Scab on Peel Microbiota, Fermentation Dynamics, and the Volatile/Non-Volatile Composition of Cider

Apple scab is a disease caused by Venturia inaequalis; it alters the vegetative cycle of apple trees and affects the fruits in orchards or during post-harvest storage. Utilizing rotten apples in cidermaking is a promising technique to mitigate crop losses; nonetheless, uncertainties persist regarding the beneficial effects of damaged fruits. This study involves a thorough chemical analysis of cider produced from both healthy and scab-infected fruits to identify compositional changes caused by microbial proliferation and to assess their impact on cider quality. Apples infected by post-harvest apple scab, as opposed to uninfected apples, were employed in cidermaking. The peel microbiota was described by plate count, and next-generation sequencing-based metabarcoding methods were used to describe the peel microbiota, while HPLC and GC MS-MS were used to characterize the cider compositions. Apples infected with post-harvest scab host a specific fungal consortium with higher biodiversity, as evidenced by the Shannon evenness index, especially in the fungi kingdom. The presence of apple scab slows fermentation by up to 23%, lowers ethanol accumulation by up to 0.4%, and affects certain cider constituents: sugars, alcohols, amino acids, fatty acids, and esters. The statistical treatment of data relative to the chemical profile (PLS and PCA on the 31 compounds with VIP > 1) distinguishes ciders made from altered or safe fruits. Scab-infected apples can be valorized in the agri-food industry; however, microbiota alterations must not be underestimated. It is necessary to implement adequate mitigation strategies.

AFB1 exacerbates testicular and intestinal inflammation by increasing stearoyl ethanolamide and homocysteine levels

In environmental toxicology, aflatoxin B1 (AFB1) is recognized for its detrimental effects on reproductive and intestinal health. This study elucidates how AFB1-induced elevations in stearoyl ethanolamide (SEA) and homocysteine (HCY) impact male fertility and intestinal function in mice. AFB1 was found to markedly reduce sperm concentration and exacerbate sperm damage in mice, primarily by increasing serum SEA and HCY levels. These metabolites compromise testicular structure and function, disrupt the blood-testicular barrier, and downregulate critical testicular proteins including DAZL, SYCP1, SYCP2, StAR, and CYP17A1. Transcriptomic analysis revealed that SEA and HCY broadly alter testicular gene expression, activate NOD-like receptor signaling pathways, induce testicular inflammation, and promote apoptosis. Additionally, SEA and HCY impair intestinal barrier function by reducing the expression of tight junction proteins ZO-1 and Occludin. Functional network analysis indicated that SEA and HCY regulate intestinal immune responses by promoting M1 macrophage polarization and the upregulation of pro-inflammatory cytokines, while simultaneously inhibiting anti-inflammatory factors. This study underscores the multifaceted adverse effects of SEA and HCY on male reproductive health and gut integrity, and highlights the need for further research into mechanisms and potential interventions to mitigate these harmful outcomes.

Microbial communities in the rhizosphere of tropical soils cultivated with maize as a function of nitrogen and phosphorus fertilizers

Phosphorus (P) has a strong affinity with soil colloids in humid tropical conditions, reducing its availability to plants. The use of alternative sources of P can provide nutrients to plants and reduce countries' dependence on imports of phosphate fertilizers. Some nitrogen (N) sources can acidify the soil and affect the efficiency of P fertilizers. In this study, evaluated the changes in the microbial community of the rhizosphere of maize (Zea mays) affected by N and P fertilizers in soils with contrasting textures. The N sources used were calcium nitrate (CN) and ammonium sulphate (AS), and the P sources: triple superphosphate (TSP), organomineral (OR) and struvite (ST), and two control treatments without the addition of N and P fertilizers, with (Control) and without plant (Control NP). The rhizosphere samples were subjected to genetic sequencing of the 16S rRNA region, and the structures, diversity, richness and differential abundance of the microbial communities were assessed. Distinct microbial compositions were identified between medium-textured (MT) and clayey (CT) soils, influenced by soil texture, organic matter and fertilizers. Nitrogen fertilizers had the greatest impact on the structure of microbial communities in MT soil. Differential abundance analysis revealed specific variations in microbial taxa in response to nutrient sources, with an impact on nutrient cycling and acquisition. The ST + CN treatment in MT soil was enriched with pollutant bioremediating genera such as Sphingbium, Flavitalea, Devosia and Rubellimicrobium. The study highlights the intricate interaction between soil type, fertilizer sources and microbial community dynamics, with an impact on overall productivity.

From mother to piglet: the lasting influence of the maternal microbiome

BACKGROUND

Given their crucial roles in agriculture and biomedical research, promoting pig health is essential. A balanced gut microbiota is vital for immune development, metabolism and pathogen resistance, and requires optimal initial colonization by beneficial bacteria. This becomes particularly evident during early life stages, like suckling and weaning, where disruptions can lead to long-term health issues. Understanding the factors influencing microbiome development during these phases is fundamental for enhancing pig health. On these basis, rectal swab samples from eighteen sow-piglet pairs were collected at multiple time points from 7 days after birth to 10 days post-weaning, and analyzed through 16S rRNA gene sequencing. This study aims to understand the maternal influence on piglet microbiota development during the suckling-weaning period, exploring microbial diversity, composition and additional influencing factors such as age, piglet and weaning.

RESULTS

α diversity significantly increased with piglet age (p < 0.001) and stabilized upon weaning, with maternal influence and differences between individual piglet affecting variability before weaning. Post-weaning α diversity was influenced by the pen environment (contributing to 14.5-16% of the variability between piglets) rather than age. Both the sow (~ 9.6%) and age of the piglets (20-30%) had a significant impact on the microbial β diversity over the entire timeframe. Moreover, at 10 days post-weaning a significant influence of the cage mates on piglets microbial β diversity was observed (~ 24.6%). Source-tracking analysis revealed a significant maternal contribution to piglet microbiome at 7 days (31.68%), which decreased over time but remained at 13.33% post-weaning. Piglet microbiome exhibited consistency across time, with 22.55-61.23% of bacteria retained from previous stages. Cage mates contributed 53.54% to the microbiome at 10 days post-weaning. Additionally, 68.32% of piglets microbiome at 7 days was derived from sources not included in the study, decreasing to 37.6% by 10 days post-weaning. ASV-level analysis showed that the majority of maternally transmitted ASVs pre-weaning persisted until the last time point, with both beneficial bacteria and pathobionts being transmitted.

CONCLUSIONS

This study highlights the significant influence of maternal microbiota on piglet gut microbiome development, affecting both diversity and composition. Beneficial bacteria are transmitted from mothers to offspring and persist through early developmental stages, thereby emphasizing the long-lasting impact of maternal microbiome and the importance of early microbial colonization for piglet health.

Investigating the Role of Gut Microbiota in the Pathogenesis and Progression of Rheumatoid Arthritis in a Collagen-Induced Arthritis Mouse Model

Rheumatoid arthritis (RA) is a chronic systemic autoimmune disorder whose precise etiology remains unclear, though growing evidence implicates gut microbiota in its pathogenesis. This study aimed to investigate the role of gut microbiota in the onset and progression of RA by employing fecal microbiota transplantation (FMT) in a collagen-induced arthritis (CIA) mouse model using DBA/1J and Aire-/- strains. Mice received FMT from healthy donors, treatment-naïve RA patients, or treated RA patients in relapse, followed by assessment of microbiota composition via 16S rRNA sequencing, arthritis severity scoring, histological evaluations, and systemic inflammatory markers. The findings revealed distinct microbiota clustering patterns post-FMT across experimental groups, highlighting strain-specific colonization effects. Notably, genera such as Bifidobacterium and Paraprevotella correlated positively with arthritis severity in DBA/1J mice, whereas Corynebacterium, Enterorhabdus, and Odoribacter exhibited negative correlations, suggesting potential protective roles. Despite these microbial differences, minor variations in arthritis scores, paw inflammation, or systemic inflammation were observed among FMT groups. This indicates that although gut microbiota alterations are associated with RA pathogenesis, further investigation with larger cohorts and comprehensive sequencing approaches is essential to elucidate the therapeutic potential of microbiome modulation in autoimmune diseases.

Characterization and potential causes of a whiting event in the Mar Menor coastal lagoon (Mediterranean, SE Spain)

The Mar Menor is a hypersaline coastal lagoon in the southeast of Spain, which has experienced several eutrophication episodes in recent years. In 2022, an area of milky white turbid water appeared covering about 10 % of its surface, and it has been there ever since. A comprehensive field research was set up to assess the origin of this possible whiting event, including identification of continental water inputs, satellite imagery and analyses of physico-chemical properties of the water column, sediment, and the planktonic and benthic communities. Our observations indicate that the water turned white due to precipitation of authigenic (formed where it is currently located) calcite as described in whiting events occurring in other marine areas. In addition to very high turbidity, the affected area showed increased nutrient and chlorophyll a concentrations compared to the rest of the lagoon. The altered conditions in this area also affected the planktonic communities and led to a complete disappearance of the previously abundant benthic vegetation (Caulerpa prolifera), thus influencing the biogeochemical cycles. Satellite images coupled with sediment core analysis suggest that this whiting event, which appears to have begun in 2022, is unprecedented in the Mar Menor. The enhanced alkalinity due to the semi-enclosed nature of the lagoon, along with the inflow of continental water may be producing favorable conditions for calcium carbonate supersaturation since rising groundwater levels in the adjacent aquifer seem to have intensified the groundwater discharge, which contains high concentrations of HCO3-. This rise is likely due to a long-term increase in recharge, induced by the expansion of irrigation practices, in combination with oscillations in rainfall cycles.

Optimization of genome editing by CRISPR ribonucleoprotein for high efficiency of germline transmission of Sox9 in zebrafish

Primordial germ cells (PGCs) are the first germline stem cells to emerge during early embryonic development and are essential for the propagation and survival of species. Genome editing creates mutagenesis possibilities in vivo, but the generation of precise mutations in PGCs is still challenging. Here, we report an optimized approach for highly efficient genome editing via introducing biallelic variations in early embryos in zebrafish. We adopted an extended, GC-rich, and chemically modified sgRNA along with microinjection of the CRISPR ribonucleoprotein (RNP) complex into the yolk sac at the 1-cell stage. We found that genome editing of Sox9a generated a high proportion of heterozygotes with edited alleles in the F1 generation, indicating biallelic editing. Deep sequencing and mapping the edited cells from early embryos to future tissues revealed that the edited founder has a dominantly edited allele, sox9a M1, accounting for over 99 % of alleles in the testis. Specifically, all offspring of the founder inherited the edited allele, suggesting nearly complete editing of the alleles in early germline cells. Overall, the optimization delineates biallelic editing of sox9a in early embryos and transmission of edited alleles to offspring, thus presenting a method to create a desired genetic mutation line of Sox9a avoiding lengthy traditional crossbreeding.

Microbial community enrichment and transition in landfill for the biotransformation of unpretreated low-density polyethylene (LDPE) under aerobic and anaerobic conditions

Low density polyethylene (LDPE), prevalent in single-use plastics, poses a significant environmental challenge due to its limited biodegradation. This study aims to enrich and characterize unpretreated LDPE degrading microorganisms from a nearly 50-year-old municipal landfill under aerobic and anaerobic conditions. Detailed analysis of the microbial communities through 16S rRNA gene based metataxonomy, whole genome metagenomics as well as thorough characterization of LDPE films exposed to the enriched microorganisms are done. Distinct shifts between plastisphere and bulk communities were observed. Shotgun metagenomics enabled reconstruction of thirty high-quality metagenome-assembled genomes (MAGs), revealing genes for plastic and hydrocarbon degradation, and biosurfactant production. Several plastic degradation-associated bacteria were identified, including Pseudomonas, Streptomyces, Burkholderia, Bacillus, Thermobifida, Saccharomonospora, Methylocaldum, Methylobacter, Ilumatobacter, Rubrivivax, and archaeal candidates like Methanosarcina and Nitrosarchaeum were observed. MAGs from Burkholderiales and Chlamydiales showed higher potential for LDPE degradation. Scanning electron microscopy showed biofilm formation on plastics, atomic force microscopy indicated surface topological changes, and Fourier transform infrared spectroscopy revealed increased carbonyl groups. Aerobic enrichments allowed up to 60% weight reduction of LDPE, with a degradation rate of 0.00766 mg/day and reaching half-life in nearly 90.49 days, confirming the biodegradation potential of the microbial community. From these observations, this study suggests two potential mechanisms of LDPE degradation under aerobic and anaerobic conditions by enriched communities. This study highlights role of landfill microbiomes in LDPE degradation, offering valuable insights into microbial succession of plastisphere and contributing to the development of effective plastic-degrading community. Future research could explore optimizing these for large-scale plastic waste management.

Exploiting taxonomic information from metagenomes to infer bacterial bioindicators and environmental quality at salmon aquaculture installations

Environmental DNA (eDNA) metabarcoding has emerged as a powerful method for assessing the environmental impacts of marine Atlantic salmon aquaculture by identifying bacterial bioindicators and inferring biotic indices. However, because this approach relies on the PCR amplification of 16S rRNA gene fragments, it may introduce errors that compromise bioindicator reliability. In contrast, metagenomic analysis which captures the complete set of genetic material directly extracted from environmental samples circumvents biases inherent to PCR amplification. We hypothesized that metagenomic data could offer superior assessments of benthic environmental impacts associated with salmon aquaculture compared to metabarcoding. To test this, we compared bacterial community structures derived from both metabarcoding and metagenomic analyses of 68 sediment samples obtained from aquaculture installation sites characterized by varying degrees of benthic impact as determined by macroinvertebrate inventories. Bacterial bioindicators were identified from each dataset, and Random Forest models were used to predict the degrees of benthic impacts. Metagenomics identified a greater number of bioindicators at both the family and individual sequence variant levels, resulting in higher predictive accuracy for impact assessments. Notably, only a few bioindicators were common to both methods, suggesting that methodological limitations and distorted abundance patterns in metabarcoding data may lead to spurious indicators. These findings highlight both the challenges and potential advantages of employing metagenomics for reliable environmental impact assessments.

Mycobiome of Pinus pinaster trees naturally infected by the pinewood nematode Bursaphelenchus xylophilus

Fungi are important biological elements in the Pine wilt disease (PWD) complex. In the late stages of the disease, the pinewood nematode (PWN) Bursaphelenchus xylophilus feeds on the fungal flora available in the pine tree for survival and multiplication. Previous studies have confirmed a close relation between the PWN and blue-stain fungi (Ophiostomatales), which are necrotrophic pathogens associated with bark beetles (Coleoptera: Scolytidae). The PWN is able to grow densely in the presence of these fungi, which results in a higher number of nematodes transferred to the insect-vector Monochamus spp. To understand the spatial diversity and structure of Pinus pinaster mycobiome, wood samples from PWN-infected and non-infected pine trees were collected in three locations of Continental mainland Portugal with different PWD records, during the maturation phase of the insect-vector M. galloprovincialis (winter 2019-spring 2020). The PWN-mycobiome from the PWN-infected P. pinaster was also characterized. A total of 27 samples of P. pinaster and 13 samples of PWN from PWN-infected trees were characterized using ITS2 amplicon sequencing. The diversity and structure of the fungal communities in P. pinaster varied with disease status suggesting that the PWN presence affects the endophytic fungal communities. For both P. pinaster and PWN fungal communities, differences were also associated with locations (recent PWD loci Seia, and long-term PWN locus Companhia das Lezírias and Tróia). Ophiostomatales were mainly detected in PWN-infected P. pinaster. This research contributes to increase the knowledge on the ecology of the fungal communities in PWD complex.

Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.)

Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.

Assessing the effects of urban effluent pollution on freshwater biodiversity and community networks using eDNA metabarcoding

Aquatic ecosystems provide essential services, yet they face increasing pressures from anthropogenic activities, including land-use change, eutrophication, browning, and contaminant pollution. While the ecological effects of these stressors are documented, the impacts of complex contaminant mixtures, particularly those from wastewater treatment plant (WWTP) effluents, remain poorly understood. Mixtures effects are typically assessed using traditional species-by-species toxicological approaches, which, though the gold standard, are time-intensive, require test animals, and have limited extrapolability. New Approach Methodologies (NAMs), such as environmental DNA (eDNA), offer a non-invasive alternative, enabling broader assessments of taxa responses across trophic levels. Here, we apply an eDNA approach to assess community-wide responses to effluent discharge in the St. Lawrence River, one of North America's most diverse freshwater ecosystems. We sampled water and aquatic communities along the effluent plume of the Montréal WWTP, analyzing taxa-specific responses across trophic levels using high-throughput sequencing. We evaluated the influence of water physico-chemistry and per- and polyfluoroalkyl substances (PFAS) on aquatic beta diversity and network structure. To validate our eDNA results, we compared fish-specific detections with traditional fishing surveys. Our findings highlight how wastewater-derived contaminants influence biodiversity patterns and species interactions, with taxonomic responses varying across trophic levels. Network analyses revealed shifts in ecological stability, with changes in species connectivity and modularity influenced by effluent exposure. This study demonstrates the value of eDNA for characterizing biodiversity responses to anthropogenic stressors and provides insights into the broader implications of point-source pollution for freshwater ecosystem resilience.

Context-dependent anaerobic oxidation of methane: Insight for methane emission mitigation

Anaerobic oxidation of methane (AOM) exhibits context-dependent metabolic versatility, governed by electron acceptor heterogeneity and anthropogenic perturbations. This study investigates the AOM potential by simulating three environments, high-dissolved organic carbon (DOC), high-nitrate with moderate sulfate, and sulfate-enhanced conditions, to investigate AOM potential under controlled perturbations. Substrate conversion dynamics were observed by monitoring the variation of methane, sulfate, nitrate, iron, etc., and microbial community shifts were analyzed by 16S rDNA high-throughput sequencing. In the high-carbon condition, characterized by high DOC (5.65-21.83 mmolC·L-1) but low nitrate and sulfate (both <1 mmol L-1) levels, methanogens such as Methanobacterium sp. IM1 and Thermoplasmata dominated the stage, overpowering anaerobic methanotrophic archaea (ANME), while no methane oxidation but obvious methane production occurred. Shifting to the scenario with high nitrate (3.51 mmolN·L-1) and moderate sulfate (1.36 mmolS·L-1), ammonium accumulation played the role of a spoiler. It weakened AOM process (Kmo = 0.58 d-1) and stirred up a competitive relationship between sulfur-driven ammonium-oxidizing archaea (e.g., Nitrososphaeraceae, Nitrosotaleaceae) and methanotrophs (e.g., Marine group II, Wosearchaeales, Roseiarcus). However, once nitrate was consumed to a low level, sulfate reduction relieved the ammonium pressure and re-activated iron, the suppression of AOM eased (Kmo = 1.44 d-1). Under the sulfate-enhanced circumstances, where the sulfate level increased to 1.47-2.55 mmolS·L-1, the AOM process accelerated (Kmo = 4.02 d-1) even under high-nitrate conditions (1.66 ± 0.12 mmolN·L-1). Methanotrophs and sulfur-metabolizing bacteria then co-thrived, showing a close display of cooperation. Our findings offer a pivotal framework to clarify AOM's contribution to natural methane emissions and give a new perspective for the development of methane mitigation technologies.

Anthelmintic resistance against benzimidazoles and macrocyclic lactones in strongyle populations on cattle farms in northern Germany

Anthelmintic resistance (AR) in cattle gastrointestinal nematodes (GIN) is an increasing global concern, with low to moderate levels recently documented in Central Europe. This study reports on resistance against both macrocyclic lactones (MLs) and benzimidazoles (BZs) in northern Germany, highlighting that AR is spreading. The fecal egg count reduction test (FECRT) remains the primary tool for AR assessment, yet differing methodologies and recent guideline updates complicate resistance interpretation across studies. Statistical methods, such as Bayesian approaches used by eggCounts and bayescount, yield varying confidence intervals, further influencing results. Notably, the nemabiome analysis identified Ostertagia ostertagi and Cooperia oncophora as predominant species in the region, though unexpected diversity among farms with additional GIN species occurring sometimes even at high frequency, suggests morphological analysis of coprocultures may underestimate species prevalence. Detecting AR against both drug classes on some farms underscores the urgency of implementing sustainable strategies, such as targeted selective treatment and combinations of anthelmintics with different mode of action, to prevent scenarios of multi-drug resistance observed elsewhere. Effective resistance management requires immediate discussions with veterinarians and stakeholders to steer toward informed, preventive measures in cattle farming.

Metabolic allocation strategies of Geobacter in electroactive biofilms to adapt to varying acetate supply concentrations

Geobacter species play a key role in acetate-fed electroactive biofilms (EABs), but their competitiveness varies with acetate supply concentration for unclear reasons. By continuously supplying different concentrations of acetate, we discovered an adaptive metabolic strategy of Geobacter biofilms, centered on regulating carbon allocation to protein synthesis, polysaccharide production, and the TCA cycle. Growth and reproduction were prioritized in response to acetate limitation under low supply concentrations, whereas catabolic efficiency was enhanced when acetate was sufficient. Excess acetate also induced the toxic effects of intracellular acetyl-CoA accumulation, triggering metabolic processes including stress responses, acetyl-CoA hydrolase synthesis, and carbon source storage. These metabolic adaptations ultimately determined the competitive niche of Geobacter in wastewater EABs, allowing for population dominance under acetate limitation and enhancing current production when acetate was abundant. Our findings give new insights into Geobacter's survival strategies in various environments with different acetate availability, and provide a theoretical basis for targeted regulation of the performance and stability of EABs to achieve environmental functions.

Root Exudates Mediate Bacillus velezensis FZB42's Colonization-Independent Biocontrol in Maize

Bacillus inoculants often show unstable performance due to poor colonization, making it crucial to explore colonization-independent biocontrol mechanisms. While rhizosphere microbial communities and root exudates influence plant disease resistance, it remains unclear if these changes depend on Bacillus colonization. This study analyzed the rhizosphere bacterial community and root exudates of maize in response to Bacillus velezensis FZB42 and the colonization-defective mutant FZB42ΔcheA. Both treatments significantly altered the root exudate composition. Notably, hydrocinnamic acid and tryptophol, which were upregulated more than 50-fold in both FZB42 and ΔcheA treatments, were confirmed to enhance maize resistance against Dickeya zeae. These compounds significantly reduced the pathogenicity of D. zeae with minimal effects on bacterial survival. Moreover, inoculation with FZB42 and the ΔcheA mutant reduced bacterial community diversity while increasing the abundance of beneficial bacteria, such as Cyanobacteria and Azospirillum, thereby indirectly enhancing maize resistance. This study offers a new understanding of the colonization-independent biocontrol mechanisms of Bacillus spp.

PCR bias in 16S rRNA genes caused by GC content leads to insufficient detection of some abundant species in amplicon sequencing analyses of thermophilic microbial communities

Amplicon sequencing is a widely used method for surveying biological diversity. However, the technique is disturbed by PCR bias leading to errors in community composition analyses. In this study, microbial community composition was evaluated in twenty-eight locations of hot spring water with temperatures between 87-48°C at Nakabusa Hot Springs, Japan, using amplicon sequencing analysis with the V4 region of the 16S rRNA gene. In discrepancy with the greenish color and the absorption spectra of the microbial samples, the relative abundance of amplicon sequence variants (ASVs) in the major photosynthetic organisms, Chloroflexus spp., were scarce in any sample when using the annealing temperature of 50°C in amplicon PCR. Changing the annealing temperature to 68ºC significantly improved the detection efficiency of Chloroflexus ASVs, and the obtained numbers were consistent with the presence of the photosynthetic pigments. The abundance of many other microbial ASVs was also dependent on the annealing temperature. The log ratio in the abundance of major ASVs between two annealing temperatures was correlated with the GC content of the 16S rRNA gene, suggesting that even some other major ASVs in the community are seriously affected by PCR bias due to the GC content. Combined usage of results from two different annealing temperatures, rather than a result using a single annealing temperature, seems to be a better way to obtain community structure information with less PCR bias in thermophilic organisms of high 16S rRNA GC content.

Light-Driven Changes in Macrophyte Tissue Quality Affect the Composition of Associated Microbial Communities

Microbial biofilms are important components in macrophyte decomposition, and their composition depends on the decomposition stage and host plant quality. Here, we investigated how macrophyte tissue quality (i.e., C:N:P stoichiometry and phenolic contents) influences epiphytic microbial biofilms during litter decomposition. Consecutive experiments were conducted to (1) modify the C:N:P stoichiometry and phenolic content of the freshwater macrophyte Elodea nuttallii by manipulating light and nutrient availability and (2) test how the modified tissue quality affected epiphytic microbial biofilm diversity and community composition before and during macrophyte decomposition. Our results showed that shading led to lower C:N ratios (28.6 to 12.6) and higher phenolic content (10.8 to 19.2 µg/mg dry weight). Simultaneously, shading affected the epiphytic bacterial and fungal community composition, and these shifts correlated with the macrophyte C:N ratio. While no effects of macrophyte tissue quality on decomposition rates were observed, the epiphytic bacterial community composition on the litter was significantly affected by light treatment, time, and their interaction. Bacterial community composition shifted from a high abundance of Comamonadaceae to a more diverse community over time. Overall bacterial diversity was lower on the litter grown in the shaded mesocosms. Fungal diversity and community composition during litter decomposition were not affected by litter quality. Overall, our results reveal a structuring role of macrophyte tissue quality on its associated microbial biofilm and uniquely show a continuation of light-driven changes in epiphytic bacterial community composition after exposure. We conclude that light-driven changes in C:N stoichiometry are a crucial factor in shaping epiphytic microbial communities during macrophyte decomposition.