Microbial Pathways Research Articles

Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.

Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.

Engineering a Silk Protein-Mediated Customizable Compartment for Modular Metabolic Synthesis.

Microbial cell factories provide a nontoxic, economical way for the synthesis of various chemicals and drugs, garnering significant attention from researchers. However, excessive dispersion of enzymes and accumulation of intermediate metabolites in the production process will weaken the reaction efficiency of the pathway enzyme. In this study, a cellular compartment was constructed to isolate the enzyme reaction space and optimize the modular metabolic synthesis. First, a special spider silk protein was designed and constructed to form protein condensates in microbial cells, and its synthetic microcompartment effects were investigated. Second, the interaction of short peptide pairs or direct fusion based on the silk protein was used to recruit a variety of enzymes to improve the efficiency of enzyme catalysis. Third, the 2'-fucosyllactose (2'-FL) de novo synthesis pathway and its modular optimization were carried out to verify the mode. Finally, a synthetic compartment was introduced into the pathway to directly aggregate the 2'-FL synthesis pathway, thus obtaining synthetic-compartment-mediated multienzyme aggregates. The experimental results showed that the titer of 2'-FL was significantly improved compared with those of wild-type and modular-optimized free enzymes. The utilization of this cell microcompartment offers a novel avenue for the aggregation of diverse enzymes, thereby offering an innovative approach for enhancing the efficiency of the microbial modular metabolic pathway.

Pollution Status, Ecological Effects, and Bioremediation Strategies of Phthalic Acid Esters in Agricultural Ecosystems: A Review.

Phthalic acid esters (PAEs) are common organic contaminants in farmland soil throughout agricultural systems, posing significant threats to human health and thus closely associated with food safety concerns. Here, we consolidate the latest findings regarding the distribution, ecological effects, bioremediation methods, and microbial degradation pathways of PAEs in agricultural ecosystems. Generally, di(2-ethylhexyl) phthalate (DEHP), di-n-butyl phthalate (DnBP), and di-isobutyl phthalate (DiBP) exhibit the highest detection frequencies and concentrations in soil, air and agricultural products. The presence of these PAEs in agricultural ecosystems can significantly affect soil and plant-associated microbial communities, leading to decreased yield and quality of agricultural products. Bioremediation techniques, such as microbial degradation and phytoremediation, are frequently explored to address these issues. Overall, this review provides a comprehensive overview of current research on PAEs in China's agricultural systems and offers insights into potential problems and future research directions.

Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.

Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have an close interrelationship with intestinal microbiota. Recently, we utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenomics sequencing. We found that the gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (p < 0.001). No differences in microbial composition were observed between midgut NET patients with and without CS (p < 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsielle, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristic curve (AUROC) 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). This study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.

Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries

Despite extensive research on the gut microbiome of healthy individuals from a single country, there are still a limited number of population-level comparative studies. Moreover, the sequencing approach used in most related studies involves 16S ribosomal RNA (rRNA) sequencing with a limited resolution, which cannot provide detailed functional profiles. In the present study, we applied a combined analysis approach to analyze whole metagenomic shotgun sequencing data from 2035 healthy adult samples from six countries across four continents. Analysis of core species revealed that 13 species were present in more than 90% of all investigated individuals, the majority of which produced short-chain fatty acids (SCFA)-producing bacteria. Our analysis revealed consistently significant differences in gut microbial species and pathways between Western and non-Western countries, such as Escherichia coli and the relation of MetaCyc pathways to the TCA cycle. Specific changes in microbial species and pathways are potentially related to lifestyle and diet. Furthermore, we identified several noteworthy microbial species and pathways that exhibit distinct characteristics specific to China. Interestingly, we observed that China (CHN) was more similar to the United States (USA) and United Kingdom (GBR) in terms of the taxonomic and functional composition of the gut microbiome than India (IND) and Madagascar (MDG), which were more similar to the China (CHN) diet. The current study identified consistent microbial features associated with population and geography, which will inspire further clinical translations that consider paying attention to differences in microbiota backgrounds and confounding factors.

TssL2 of T6SS2 is required for mobility, biofilm formation, wrinkly phenotype formation, and virulence of Vibrio parahaemolyticus SH112

Type VI secretion system 2 (T6SS2) of Vibrio parahaemolyticus is required for cell adhesion and autophagy in macrophages; however, other phenotypes conferred by this T6SS have not been thoroughly investigated. We deleted TssL2, a key component of T6SS2 assembly, to explore the role of the T6SS2 in environmental adaptation and virulence. TssL2 deletion reduced Hcp2 secretion, suggesting that TssL2 played an important role in activity of functional T6SS2. We found that TssL2 was necessary for cell aggregation, wrinkly phenotype formation, and participates in motility and biofilm formation by regulating related genes, suggesting that TssL2 was essential for V. parahaemolyticus to adapt changing environments. In addition, this study demonstrated TssL2 significantly affected adhesion, cytotoxicity, bacterial colonization ability, and mortality in mice, even the levels of the proinflammatory cytokines IL-6 and IL-8, suggesting that TssL2 was involved in bacterial virulence and immunity. Proteome analysis revealed that TssL2 significantly affected the expression of 163 proteins related to ABC transporter systems, flagellar assembly, biofilm formation, and multiple microbial metabolism pathways, some of which supported the effect of TssL2 on the different phenotypes of V. parahaemolyticus. Among them, the decreased expression of the T3SS1 and T2SS proteins was confirmed by the results of gene transcription, which may be the main reason for the decrease in cytotoxicity. Altogether, these findings further our understanding of T6SS2 components on environmental adaption and virulence during bacterial infection.Key points• The role of T6SS2 in V. parahaemolyticus was far from clear.• TssL2 participates in cell aggregation, wrinkly phenotype formation, motility, and biofilm formation.• TssL2 is essential for cell bacterial colonization, cytotoxicity, virulence, and proinflammatory cytokine production.

Highway to health: Microbial pathways of soil organic carbon accrual in conservation farming systems

Increasing pressure on arable land related to climate change mitigation and adaptation within recent policy frameworks has generated widespread interest in the effect of sustainable agricultural management practices on soil organic carbon (SOC) storage. Current frameworks point to soil microorganisms and their functioning as the key drivers of SOC accrual. This study provides a comprehensive on-farm assessment of changes in SOC formation pathways (physico-chemical and microbial) and the underlying drivers comparing three soil use systems: conservation and conventional farming systems as well as permanently vegetated adjacent reference soils (i.e., field margins) without agricultural land-use.Overall, our results indicated substantial increases in extractable organic carbon (+22 %), microbial biomass carbon (+29 %) and necromass carbon stocks (+11 %) in soils of conservation farming systems as compared to conventional farming systems. Differences between all three soil use systems were strongly pronounced in the surface soil (0–5 cm) and declined in deeper soil layers. Structural equation modelling revealed a varying influence of SOC storage pathways among soil use systems, with microbial-mediated (‘in-vivo’) turnover and direct sorption being the most dominant pathways. Moreover, diversity of crop rotation and tillage intensity were identified as the most important factors influencing extractable organic carbon and carbon-liberating enzyme activity within conservation farming management. Our on-farm approach demonstrates that enhanced bioavailable carbon inputs and reduced soil disturbance are the key drivers for microbially-controlled SOC accrual in arable soils and that conservation farming systems with extended plant coverage and increased crop diversity can substantially advance the restoration of soil health.

Inorganic and organic additives differently regulate compost microbiomes in response to heavy metals immobilization

Various composting additives, both organic and inorganic, have been used to effectively reduce the bioavailability of heavy metals (HMs) in compost. However, a comprehensive assessment of their comparative contributions and the mechanisms involved is still lacking. In this study, we selected shell powder and biochar as representative amendments to assess their efficacy in immobilizing various HMs. Our results demonstrated that the addition of shell powder and biochar markedly enhanced the synthesis of humic acids (HA), reduced the bioavailability of HMs, and indirectly enhanced microbial carbon metabolism and growth pathways. This enhancement subsequently enriched the abundance of key HA synthesis contributors, including Enterobacter, Thermobispora, Pseudomonas, and Sphingobacterium, creating a positive feedback loop. Additionally, adding biochar altered the abundance of Pseudomonas, Chelatococcus, and Pseudoxanthomonas during the mesophilic phase, thereby reducing the expression of HMs resistance genes (HMRGs). In contrast, shell powder supplementation modulated the response to HMRGs reduction by regulating the abundance of Sphingobacterium, Pseudomonas, and Thermobispora during the thermophilic phase. Ultimately, regional cultivation trials confirmed the potential of these innovative organic fertilizers to significantly reduce the spread of HMs to plants. Collectively, these findings highlighted the similarities and differences between organic and inorganic additives to modulate microbial community responses during HMs immobilization, providing a theoretical framework for diminishing the risks associated with HMs dissemination and improving the quality of organic fertilizers.

SERS-AI Based Detection and Bioanalysis of Malodorous Components in Kitchen Waste.

The prevention and control of odor gas generated from kitchen waste are significant missions in research on environmental pollution. Because of the high complexity and variability of kitchen waste, the development of a suitable technique with high sensitivity for the accurate detection of odor gas is an urgent and core task in this frontier field. Here, a technique combining surface-enhanced Raman spectroscopy (SERS) and artificial intelligence (AI) is explored for detecting malodorous components in the leachate of kitchen waste. Initially, 1706 SERS spectra were collected from synthetic kitchen waste under various fermentation parameters. Several AI algorithms were used to classify three levels of odor intensity based on SERS spectra, among which the Random Forest Classifier algorithm model showed a high prediction accuracy of 86.5%. Then, by integrating Raman data, the AI algorithm model identified hydrogen sulfide (H2S) and ammonia (NH3) as the dominant malodorous components in the odor gas. Finally, the structural characteristics of the microbial communities are investigated. With the help of Raman's intensities of malodorous components, many more insights into microorganisms in the fermentation process are revealed, which has important research value in the prevention and controlling of odor gas generated from kitchen waste. Furthermore, the microbial metabolic pathways of sulfur and nitrogen are discussed here. This SERS-AI-based novel technique not only has a broad potential for odor pollution but also could be applied to another complicated biochemical system with functional bacteria.

Tryptophan Metabolism-Regulating Probiotics Alleviate Hyperuricemia by Protecting the Gut Barrier Integrity and Enhancing Colonic Uric Acid Excretion.

The balance of gut microbiota affects uric acid synthesis and excretion, influencing the development of hyperuricemia. This study aimed to investigate the effects and mechanisms of probiotics on hyperuricemia and adenine- and potassium oxonate-induced colonic damage. After two months of gavage at 109 CFU/day, the probiotic strains Lactobacillus rhamnosus UA260 and Lactobacillus plantarum YU28, identified through in vitro screening, significantly reduced serum uric acid levels in hyperuricemia mice from 109.71 ± 56.33 to 38.76 ± 15.06 and 33.22 ± 6.91 μmol/L, respectively. These strains attenuated inflammatory, repaired gut barrier damage, and enhanced colonic uric acid transporter function, thereby promoting uric acid excretion. Furthermore, the probiotics significantly reshaped gut microbiota by increasing the abundance of beneficial bacteria, including Lactobacillus and Coprococcus, while modulating tryptophan, purine, and riboflavin metabolism. Changes in tryptophan metabolites, specifically indole-3-propionic acid and indole-3-acetic acid, were correlated with xanthine oxidase activity, colonic injury, and the expression of the uric acid transporter protein ABCG2 during treatment. Probiotics intervention activated aryl hydrocarbon receptor pathways. These findings suggest that probiotics alleviate hyperuricemia and colonic inflammatory by regulating gut microbiota composition and tryptophan microbial metabolite pathways. Probiotics that modulate tryptophan microbial metabolism may provide a potential strategy for treating or preventing hyperuricemia.

Metagenomic Analysis Identifies Sex-Related Gut Microbial Functions and Bacterial Taxa Associated With Skeletal Muscle Mass.

This study aimed to explore the association between gut microbiota functional profiles and skeletal muscle mass, focusing on sex-specific differences in a population under 65 years of age. Stool samples from participants were analysed using metagenomic shotgun sequencing. Skeletal muscle mass and skeletal muscle mass index (SMI) were quantified (SMI [%] = total appendage muscle mass [kg]/body weight [kg] × 100) using bioelectrical impedance analysis. Participants were categorized into SMI quartiles, and associations between gut microbiota, functional profiling and SMI were assessed by sex, adjusting for age, BMI and physical activity. The cohort included 1027 participants (651 men, 376 women). In men, Escherichia coli (log2 fold change 3.08, q = 0.001), Ruminococcus_B gnavus (log2 fold change 2.89, q = 0.014) and Enterocloster sp001517625 (log2 fold change 2.47, q = 0.026) were more abundant in the lowest SMI compared to the highest SMI group. In contrast, Bifidobacterium bifidum (log2 fold change 3.13, q = 0.025) showed higher levels in the second lowest SMI group in women. Microbial pathways associated with amino acid synthesis (MET-SAM-PWY: log2 fold change 0.42; METSYN-PWY: log2 fold change 0.44; SER-GLYSYN-PWY: log2 fold change 0.20; PWY-5347: log2 fold change 0.41; P4-PWY: log2 fold change 0.53), N-acetylneuraminate degradation (log2 fold change 0.43), isoprene biosynthesis (log2 fold change 0.20) and purine nucleotide degradation and salvage (PWY-6353: log2 fold change 0.42; PWY-6608: log2 fold change 0.38; PWY66-409: log2 fold change 0.52; SALVADEHYPOX-PWY: log2 fold change 0.43) were enriched in the lowest SMI in men (q < 0.10). In women, the second lowest SMI group showed enrichment in energy-related pathways, including lactic acid fermentation (ANAEROFRUCAT-PWY: log2 fold change 0.19), pentose phosphate pathway (PENTOSE-P-PWY: log2 fold change 0.30) and carbohydrate degradation (PWY-5484: log2 fold change 0.31; GLYCOLYSIS: log2 fold change 0.29; PWY-6901: log2 fold change 0.27) (q < 0.05). This study highlights sex-specific differences in gut microbiota and functional pathways associated with SMI. These findings suggest that gut microbiota may play a role in muscle health and point toward microbiota-targeted strategies for maintaining muscle mass.

Multi-stage anoxic/oxic sequencing batch reactor realizes shortcut nitrogen removal for anaerobically co-digested liquor of municipal sludge and urban organic wastes

ABSTRACT Nitrogen removal from the combined anaerobic digestion dehydration liquor (CADDL) of municipal sludge and urban organic wastes is challenging due to high ammonium concentrations, low C/N ratio, and poor biodegradability. This study proposes a multi-stage anoxic/oxic (A/O) sequencing batch reactor with step feeding to realize partial nitrification and denitrification for shortcut nitrogen removal from the CADDL. We investigated the effects of external carbon source (acetate), dissolved oxygen (DO), A/O duration ratio, and A/O stage number on biological nitrogen removal. Moreover, we assessed the microbial community structure and nitrogen removal pathway. The results showed that the C/N consumption ratio for nitrite reduction to dinitrogen was 3.0 mg COD/mg N, and denitrifying bacteria yielded about 0.43. The optimal dosage of acetate was 2.2 mg COD/mg N. High DO concentration (1.5∼3.0 mg/L) in the aerobic stage improved the ammonia-oxidizing bacteria activity and nitrogen removal rather than worsening the nitritation. A high A/O duration ratio (50 min/60 min) was conducive to complete denitrification of nitrite. The three-stage A/O had an excellent nitrogen removal performance. Under optimal conditions, the nitrite accumulation ratio of nitritation and the total inorganic nitrogen removal reached 100% and 90.1%, respectively. The dominant ammonia-oxidizing bacteria was the genus Nitrosomonas (0.76% abundance), and the dominant denitrifying bacteria was Thauera (0.24% abundance). The nitrite-oxidizing bacteria were not detected, confirming that the biological nitrogen removal pathway was partial nitrification and denitrification. These findings provide a feasible option for the low-carbon nitrogen removal treatment for the CADDL of municipal sludge and urban organic wastes.

Gut microbes of a high-value marine fish, Snubnose Pompano (Trachinotus blochii) are resilient to therapeutic dosing of oxytetracycline

Trachinotus blochii is a high-value tropical mariculture species. The present study evaluated the gut microbial impact of therapeutic exposure (80 mg/day/kg biomass for 10 days) to oxytetracycline, the most common aquaculture antibiotic in T. blochii. The cultivable counts, α-diversity measures of taxonomic and functional metagenomics, microbial dysbiosis (MD) index, and microbial taxon abundances showed the resilience of gut microbiota at 16–26 days of treatment. A significant reduction in bacterial abundance, diversity measures, Firmicutes and Actinobacteria and an increase in γ-Proteobacteria was recorded on the 6th and 11th day of treatment. The increased metagenomic stress signatures, decreased beneficial bacterial abundances, decreased abundance of microbial pathways on energy metabolism, and MD index indicated short-term transient stress during the initial days of therapeutic withdrawal, warranting health management measures. Therapeutic exposure reduced the abundance of fish pathogens, including Vibrio spp., kanamycin and ampicillin-resistant bacteria. Strikingly, oxytetracycline treatment did not increase tetracycline-resistant bacterial counts and the predicted abundance of tetracycline resistance encoding genes in the gut, illustrating that therapeutic application would not pose a risk in the context of antimicrobial resistance in short term. Altogether, the present study provides a foundation for oxytetracycline treatment to develop suitable risk minimization tactics in sustainable aquaculture.

Biotransformation of Tetrabromobisphenol A and Its Analogs by Selected Gut Bacteria Strains: Implications for Human Health.

Knowledge of the biotransformation of tetrabromobisphenol A (TBBPA) and its related contaminants by human gut microbiota (GM) remains unexplored. Here, TBBPA and its four analogs were incubated with mixed GM strains, and nine rhamnosylated or debrominated transformation products (TPs) were discovered. Remarkably, rhamnosylation was identified as a common and unique microbial transformation pathway for these contaminants, and six of the seven rhamnosylated TPs were reported for the first time. Additionally, a kinetic transformation study also showed a rapid and strong bioaccumulation of TBBPA and TPs by Clostridium manihotivorum. Genomic analysis and phylogenetic studies identified C1.1_02053 as the gene encoding the C. manihotivorum working rhamnosyltransferase (CmRT), showing elevated gene expression with higher TBBPA exposure. Molecular docking identified five critical amino acid residues in CmRT that catalyze TBBPA rhamnosylation, and molecular dynamics simulations further confirmed the stability of the CmRT-TBBPA complex. Dynamic metabolomics analysis showed microbial growth-dependent disturbing effects in C. manihotivorum upon TBBPA exposure, and key metabolic pathways related to rhamnosyltransferase showed changes closely related to the transformation process. These findings provide insights into the unique transformation of environmental contaminants by the GM and highlight the disturbing effects of exogenous chemicals on the GM, as well as the potential impacts on overall human health.

Gut Microbial Metabolites and Future Risk of Parkinson's Disease: A Metabolome-Wide Association Study.

Alterations in gut microbiota are observed in Parkinson's disease (PD). Previous studies on microbiota-derived metabolites in PD were small-scale and post-diagnosis, raising concerns about reverse causality. Our goal was to prospectively investigate the association between plasma microbial metabolites and PD risk within a metabolomics framework. A nested case-control study within the prospective EPIC4PD cohort, measured pre-diagnostic plasma microbial metabolites using untargeted metabolomics. Thirteen microbial metabolites were identified nominally associated with PD risk (P-value < 0.05), including amino acids, bile acid, indoles, and hydroxy acid, although none remained significant after multiple testing correction. Three pathways were implicated in PD risk: valine, leucine, and isoleucine degradation, butanoate metabolism, and propanoate metabolism. PD-associated microbial pathways were more pronounced in men, smokers, and overweight/obese individuals. Changes in microbial metabolites may represent a pre-diagnostic feature of PD. We observed biologically plausible associations between microbial pathways and PD, potentially influenced by individual characteristics. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Novel Photoelectron-Assisted Microbial Reduction of Arsenate Driven by Photosensitive Dissolved Organic Matter in Mine Stream Sediments.

The microbial reduction of arsenate (As(V)) significantly contributes to arsenic migration in mine stream sediment, primarily driven by heterotrophic microorganisms using dissolved organic matter (DOM) as a carbon source. This study reveals a novel reduction pathway in sediments that photosensitive DOM generates photoelectrons to stimulate diverse nonphototrophic microorganisms to reduce As(V). This microbial photoelectrophic As(V) reduction (PEAsR) was investigated using microcosm incubation, which showed the transfer of photoelectrons from DOM to indigenous sediment microorganisms, thereby leading to a 50% higher microbial reduction rate of As(V). The abundance of two marker genes for As(V) reduction, arrA and arsC, increased substantially, confirming the microbial nature of PEAsR rather than a photoelectrochemical process. Photoelectron ion is unlikely to stimulate photolithoautotrophic growth. Instead, diverse nonphototrophic genera, e.g., Cupriavidus, Sphingopyxis, Mycobacterium, and Bradyrhizobium, spanning 13 orders became enriched by 10-50 folds. Metagenomic binning revealed their genetic potential to mediate the photoelectron-assisted reduction of As(V). These microorganisms contain essential genes involved in respiratory As(V) reduction, detoxification As(V) reduction, dimethyl sulfoxide reductase family, c-type cytochromes, and multiple heavy-metal resistance but lack a complete photosynthesis system. The novel microbial PEAsR pathway offers new insights into the interaction between photoelectron utilization and nonphototrophic As(V)-reducing microorganisms, which may have profound implications for arsenic pollution transportation in mine stream sediment.

Alterations in maternal–fetal gut and amniotic fluid microbiota associated with fetal growth restriction

BackgroundFetal growth restriction (FGR) is typically characterised as the fetus’ inability to reach its inherent growth potential. A growing body of evidence points to the important role of the maternal gut microbiota in FGR development. However, comprehensive research on changes in maternal–fetal gut and intrauterine microbiota related to FGR is lacking.MethodsIn this case–control study, we sequenced bacterial 16S rRNA from 35 maternal faecal, 35 meconium, and 31 amniotic fluid samples collected from 19 pregnant women diagnosed with FGR and 16 healthy controls. We identified putative bacterial taxonomic and functional characteristics associated with FGR by comparing these to control samples.ResultsWe identified 34 differential operational taxonomic units (OTUs) in amniotic fluid, seven differential OTUs in maternal faecal matter, and two differential OTUs in meconium. Compared to controls, FGR subjects exhibited enriched bacterial OTUs of the genus Bacteroides in the maternal gut. They also had depleted OTUs of the order Enterobacterales and genus Pseudomonas in the amniotic fluid and genus Stenotrophomonas in the fetal gut. These altered bacterial OTUs showed a significant correlation with neonatal weight and fetal ultrasonographic indexes. Additionally, we identified differential microbial functional pathways related to glycan and lipid metabolism in the maternal gut. We developed diagnostic biomarkers for FGR based on the maternal–fetal gut and amniotic fluid microbiota.ConclusionsThis study offers a comprehensive overview of the shifts in microbial composition and functional pathways in the maternal–fetal gut and amniotic fluid microbiota related to FGR, and present novel insights into the development and screening of FGR. However, the assessment of contamination’s impact on meconium and amniotic fluid remains inconclusive, necessitating further rigorous experimentation to address this scientific inquiry in future studies.

Short-term organic fertilizer substitution increases sorghum yield by improving soil physicochemical characteristics and regulating microbial community structure.

Chemical fertilizer reduction combined with organic fertilizer (organic fertilizer substitution) has a positive impact on crop productivity and sustainable development. However, the effects of short-term organic fertilizer substitution on microbial community structure and functions of sorghum rhizosphere soil and on sorghum yield remain unclear. Herein, this study investigated the short-term effects of organic fertilizer substitution on sorghum soil physicochemical properties, microbial community structure and enzyme activities using Metagenomic sequencing technology. The fertilization treatment included no fertilization (CK), pure chemical fertilizer N (CF), substitution of 25% chemical fertilizer N with organic N (NF25), substitution of 50% chemical fertilizer N with organic N (NF50), substitution of 75% chemical fertilizer N with organic N (NF75), and pure organic fertilizer N (NF100); soil samples were collected and analyzed in the flowering period of sorghum. The results showed that the suitable organic fertilizer substitution rate of sorghum field was 50%, and its yield was the highest among all treatments (9789.9 kg/hm2). Compared with the CF treatment, a medium ratio (50%) of organic fertilizer substitution significantly reduced soil alkalization (by 3.05%), improved soil nutrients, enhanced soil enzyme activities, and increased sorghum yield (P < 0.05). After organic fertilizer substitution treatment, higher protein, fat, and total starch levels accumulated in sorghum grains, and the tannin content of grains decreased. The effect of organic fertilizer substitution on bacterial diversity was greater than that on fungal diversity. Among the dominant bacterial phyla, the medium ratio of organic substitution treatment significantly increased the relative abundances of Proteobacteria (by 3.57%) and Actinomycetes (by 14.94%), and decreased the relative abundances of Acidobacteria (by 5.18%) and Planctomycetes (by 7.76%) compared with no fertilization, while the dominant fungal phyla did not respond significantly to the addition of organic fertilizer. Organic fertilizer substitution also improved soil microbial metabolic pathways, biosynthesis of secondary metabolites, and carbon metabolism. The biomarkers enriched in inorganic fertilizer treatment and organic fertilizer substitution treatments had similar relevant environmental elements but reversed correlation trends. Moreover, soil Alkali-hydrolyzable nitrogen and L-leucine aminopeptidase were important environmental factors influencing the structure of bacterial and fungal communities in sorghum soils, respectively. Soil nutrient levels and microbial communities together explained the variation in annual sorghum yield. The results of this study provide evidence that short-term organic fertilizer substitution increases sorghum yield by improving soil properties and regulating microbial community structure.

Screening and Functional Prediction of Rumen Microbiota Associated with Methane Emissions in Dairy Cows.

Agricultural activities are a significant contributor to global greenhouse gas emissions, accounting for 14.5% of total anthropogenic emissions. Specifically, greenhouse gas emissions from beef cattle and dairy cattle constitute 35% and 30% of total global livestock emissions, respectively. This study focuses on dairy cattle, exploring the complex relationships between rumen microbiota and methane emission. The methane emissions of 968 lactating Holstein cows were measured using a laser methane detector (LMD, Shanghai Hesai Technology Co., Ltd., Shanghai, China). Among the measured cows, 107 individuals were further selected into high (HME) and low methane-emitting (LME) groups, including 50 cows in the HME group and 57 in the LME group. This study analyzed differences in rumen microbiota and microbial functions between cows with varying levels of methane emissions. The results showed significant differences in the Simpson and Pielou indices of rumen bacterial communities between the HME and LME groups. Beta diversity analysis revealed significant differences in microbial community structure between the two groups. It was found that the abundance of Bacteroidales and Prevotellaceae in the rumen of cows in the HME group cows was significantly higher than that of cows in the LME group (LDA > 3, p < 0.05). Additionally, bacterial functions related to biosynthesis and carbohydrate metabolism were more active in the HME group. This study revealed distinct differences in the rumen bacterial communities between HME and LME cow in Chinese Holstein cattle, and identified specific bacteria and their functional differences in the HME group. The microbial characteristics and metabolic pathways provide new insights for developing strategies to reduce methane emissions, supporting the sustainable development of the dairy industry.

Microbial degradation mechanisms of the neonicotinoids acetamiprid and flonicamid and the associated toxicity assessments.

Extensive use of the neonicotinoid insecticides acetamiprid (ACE) and flonicamid (FLO) in agriculture poses severe environmental and ecological risks. Microbial remediation is considered a feasible approach to address these issues. Many ACE-and FLO-degrading microorganisms have been isolated and characterized, but few reviews have concentrated on the underlying degradation mechanisms. In this review, we describe the microbial degradation pathways of ACE and FLO and assess the toxicity of ACE, FLO and their metabolites. Especially, we focus on the enzymes involved in degradation of ACE and FLO, including cytochrome P450s, nitrile hydratases, amidases, and nitrilases. Those studies reviewed here further our understanding of the enzymatic mechanisms of microbial degradation of ACE and FLO, and aid in the application of microbes to remediate environmental ACE and FLO contamination.