Carbohydrate Metabolic Pathways Research Articles

Impacts of Aspergillus oryzae 3.042 on the flavor formation pathway in Cantonese soy sauce koji

To investigate the mechanism of flavor formation during the traditional preparation Cantonese soy sauce koji (TP), the changes of microorganisms, physicochemical properties, and flavor compounds in TP were comprehensively and dynamically monitored by absolute quantitative methods. Results demonstrated that inoculating Aspergillus oryzae 3.042 in TP was crucial role in enhancing enzyme activity properties. Absolute quantification of flavor combined with multivariate statistical analysis yielded 5 organic acids, 15 amino acids, and 2 volatiles as significantly different flavors of TP. Amplicon sequencing and RT-qPCR revealed that the dominant genera were Staphylococcus, Weissella, Enterobacter, Lactic streptococci, Lactobacillus, and Aspergillus, which exhibited a increasing trend in TP. Correlation analysis exhibited that Staphylococcus and Aspergillus were the pivotal genera contributing to the enzyme activities and flavor of TP. The flavor formation network involved lipid and protein degradation, carbohydrate metabolism and other pathways. Simultaneously, TP can appropriately increase the fermentation time to improve product quality.

Staphylococcus inoculation enhances the sensorial attributes of Chinese bacon by coordinating the composition of flavor compounds through amino acid metabolism

In this study, we aimed to uncover the potential underlying mechanisms of the flavor modulation of Chinese bacon by Staphylococcus. To that end, taste-enhancing S. cohnii WX-M8 and S. saprophyticus MY-A10 screened from Chinese bacon were used to investigate the effects of their individual and mixed fermentations and their synergistic fermentation with Lactobacillus plantarum BL-1 on the sensorial attributes, physicochemical properties, microbial diversity, and volatile compounds (VOCs) of Chinese bacon. Our results revealed that S. cohnii WX-M8 and S. saprophyticus MY-A10 significantly increased a* (redness) and Aw and reduced thiobarbituric acid reactive substances (TBARS) when fermented in a mixture. Moreover, they promoted the formation of esters, aldehydes (especially straight-chain aldehydes), and phenolic compounds through pathways related to amino acid metabolism, enhancing sensorial attributes. While synergistic fermentation with L. plantarum BL-1 resulted in an improved a* (redness) of Chinese bacon, and the increased microbial metabolism of the carbohydrate and lipid metabolic pathways, the increase in TBARS and the higher content of acidic volatiles, led to a change in the composition of the flavor substances. The advantage of co-fermentation of Staphylococci in sensory attributes can be attributed to their capability to metabolize amino acids and associates. These findings provide insights into the role of Staphylococcus as a starter in regulating bacon flavor.

Spatially resolved multi-omics unravels region-specific responses, microenvironment remodeling and metabolic reprogramming in aristolochic acid nephropathy

<p>Aristolochic acid nephropathy (AAN), primarily caused by overexposure to aristolochic acid I (AAI), is characterized by acute renal injury, interstitial nephritis, and metabolic dysfunction. Previous studies have revealed the cell-specific responses to AAI and its role in inducing metabolic dysfunction. However, the lack of structural information in these datasets hinders our full understanding of the spatially specific pathological mechanisms of AAN. To address this limitation, we propose an integration of spatial transcriptomics with spatial metabolomics methods to establish a spatial multi-omics analysis, which allows for deciphering region-specific responses, microenvironmental remodeling, and metabolic reprogramming <i>in situ</i> in AAN. The pathological differences between renal regions indicate that AAI-induced renal injury exhibits spatial heterogeneity. With prolonged AAI treatment, we observed an increased proportion and co-localization of the injured proximal tubule (PT-inj) and immune cells in the cortex region, accompanied by intercellular crosstalk involving the MHC-I and CCL pathways. In addition, we identified a divergent cellular response along nephron segments, with up-regulation of multiple renal stress markers and pathways after AAI treatment. Regional heterogeneity of metabolic activities was also observed, with PT-inj cells exhibiting dysregulation of carbohydrate, lipid, and amino acid metabolic pathways, as well as increased purine and pyrimidine metabolism after AAI treatment. These findings provide a more comprehensive understanding of the cellular and molecular mechanisms of AAN in a spatial context, and suggest potential intervention pathways to alleviate the global burden of AAN.</p>

Transcriptional Analysis of Antrodin C Synthesis in Taiwanofungus camphoratus (Syn. Antrodia camphorate, Antrodia cinnamomea) to Understand Its Biosynthetic Mechanism

Antrodin C, a bioactive component of Taiwanofungus camphoratus, exhibits good immunophysiological and antitumour activities, including a broad spectrum of anticancer effects. Exogenous additives can bind to metabolites during the submerged culture of T. camphoratus and affect secondary metabolite yields. However, the lack of molecular genetic studies on T. camphoratus has hindered the study of the antrodin C biosynthetic pathway. In this study, we conducted a ribonucleic acid-sequencing-based transcriptional analysis to identify the differentially expressed genes involved in the synthesis of antrodin C by T. camphoratus, using inositol and maleic acid (MAC) as exogenous additives. The addition of inositol significantly upregulated carbohydrate and sugar metabolism pathway genes (E3.2.1.14, UGDH, and IVD). When MAC was used, amino and nucleotide sugar metabolism and starch and sucrose metabolism pathways were significantly inhibited, and the associated genes (E3.2.1.14 and E3.2.1.58) were also significantly downregulated. The biosynthesis pathway genes for ubiquinone and other terpene quinones (COQ2, ARO8, and wrbA), which may play an important role in antrodin C synthesis, were significantly downregulated. This study advances our understanding of how the additives inositol and MAC affect metabolite biosynthesis in T. camphorates. This could be beneficial in proposing potential strategies for improving antrodin C production using a genetic approach.

Metagenomic shotgun sequencing reveals the enrichment of Salmonella and Mycobacterium in larynx due to prolonged ethanol exposure

The exposure of ethanol increases the risk of head and neck inflammation and tumor progression. However, limited studies have investigated the composition and functionality of laryngeal microbiota under ethanol exposure. We established an ethanol-exposed mouse model to investigate the changes in composition and function of laryngeal microbiota using Metagenomic shotgun sequencing. In the middle and late stages of the experiment, the laryngeal microbiota of mice exposed to ethanol exhibited obvious distinguished from that of the control group on principal-coordinate analysis (PCoA) plots. Among the highly abundant species, Salmonella enterica and Mycobacterium marinum were likely to be most impacted. Our findings indicated that the exposure to ethanol significantly increased their abundance in larynxes in mice of the same age, which has been confirmed through FISH experiments. Among the species-related functions and genes, metabolism is most severely affected by ethanol. The difference was most obvious in the second month of the experiment, which may be alleviated later because the animal established tolerance. Notable enrichments concerning energy, amino acid, and carbohydrate metabolic pathways occurred during the second month under ethanol exposure. Finally, based on the correlation between species and functional variations, a network was established to investigate relationships among microbiota, functional pathways, and related genes affected by ethanol. Our data first demonstrated the continuous changes of abundance, function and their interrelationship of laryngeal microbiota under ethanol exposure by Metagenomic shotgun sequencing. ImportanceEthanol may participate in the inflammation and tumor progression by affecting the composition of the laryngeal microbiota. Here, we applied the metagenomic shotgun sequencing instead of 16 S rRNA sequencing method to identify the laryngeal microbiota under ethanol exposure. Salmonella enterica and Mycobacterium marinum are two dominant species that may play a role in the reconstruction of the laryngeal microenvironment, as their local abundance increases following exposure to ethanol. The metabolic function is most evidently impacted, and several potential metabolic pathways could be associated with alterations in microbiota composition. These findings could help us better understand the impact of prolonged ethanol exposure on the microbial composition and functionality in the larynx.

Phosphorus-induced improvement of photosynthate synthesis and transport in the leaf subtending to cotton boll provided sufficient sucrose for fiber thickening during the crucial period and improved fiber bundle strength

ContextCotton fiber is an important natural textile raw material, and its quality directly affects spinning performance. Phosphorus (P) deficiency reduces fiber quality, particularly fiber strength. Fiber strength formation relies on sucrose supplied by the leaf subtending to cotton boll (LSCB), and low P may affect it by regulating sucrose supply and utilization in LSCB and fiber. ObjectiveOur study aimed to investigate how P regulates the formation of fiber bundle strength through essential carbohydrate metabolic pathways. MethodsA three-year experiment on Lu 54 (low-P sensitive) and Yuzaomian 9110 (low-P tolerant) was carried out to study the influence of P on sucrose synthesis and export in LSCB, sucrose absorption and utilization in fiber under 0 (Deficient P), 100 (Critical P), and 200 (Excessive P) kg P2O5 ha−1 in soil with 16.9 mg kg−1 available P. ResultsP application significantly increased fiber bundle strength (8.9 %−14.6 %), primarily attributed to the enhanced sucrose supply and utilization in LSCB and fiber during the crucial period for fiber bundle strength formation (17–24 days post anthesis). During this period, P application promoted the sucrose synthesis in LSCB by improving the net photosynthetic rate (9.0 %−16.8 %), and sucrose phosphate synthase (6.3 %−12.4 %) and sucrose synthase (10.0 %−17.4 %) activities. Concomitantly, P application up-regulated the expressions of sucrose transporter genes in LSCB and fiber, promoting sucrose transport and increasing the sucrose content (28.1 %−54.0 %) in fiber. Furthermore, P application markedly enhanced the sucrose utilization in fiber by increasing sucrose synthase (9.7 %−19.2 %) and invertase (14.0 %−35.7 %) activities, improving cellulose content (6.7 %−11.5 %) and fiber bundle strength. Lu 54 exhibited a greater sensitivity to P in the carbohydrate metabolism of LSCB and fiber than Yuzaomian 9110, making its cellulose content and fiber bundle strength increase more. Incremental effects of unit P on the above measurements attenuated markedly with P rates. The critical P content in LSCB (LPC) required for effective fiber bundle strength formation was 0.40 % for Lu 54 versus 0.36 % for Yuzaomain 9110, on the basis of the content of sucrose (the key substrate) in LSCB and fiber. ConclusionP application increased cotton fiber bundle strength mainly by enhancing sucrose synthesis in LSCB, sucrose transport between LSCB and fiber, and sucrose utilization in fiber during the crucial period. ImplicationThis report revealed the crucial carbohydrate metabolic path by which P regulated the fiber bundle strength formation and quantified its LPC demand during the crucial period, providing theoretical support for P diagnosis and regulation in cotton cultivation.

Genomic basis of metabolome-mediated cultivar-specific flavor formation in juice sacs of the pomelo (Citrus grandis (L.) Osbeck) cultivars Shatian and Guanxi honey

Shatian pomelo (Citrus grandis (L.) Osbeck cv. Shatian) (ST) is one of the main cultivars of pomelo, and its flavor, aroma and mastication traits exhibit marked specificity compared to those of another major pomelo cultivar, Guanxi honey pomelo (Citrus grandis (L.) Osbeck cv. Guanxi honey) (BR). As parents, both cultivars generated many offspring cultivars with excellent quality. However, the limited study of pomelo flavor-specific metabolites and their metabolic pathways has hindered the understanding of pomelo flavor diversity. In this work, genome resequencing and metabolome analyses were performed to reveal the differences in cultivar-specific flavor metabolic pathways and cultivar-specificity formation molecular bases in taste flavor, aroma and mastication. A total of 397,056 and 427,885 SNP-InDels were found, with 53.67% and 54.76% of the SNP-InDels located in the gene intervals in ST and BR, respectively. 148 candidate genes distributed in carbohydrate, amino acid, flavonoid, lipid, terpene and lignin metabolism pathways were screened to uncover the molecular basis of flavor, aroma and mastication trait formation biological processes. Overall, revealing the origin of the cultivar-specific flavor of ST and BR may provide novel insight into the pomelo flavor formation mechanism and genetic resources for pomelo genetic breeding.

Using low-protein diet in egg production for win-win of productivity and environmental benefits should be prudent: Evidence from pilot test

A shortage of feed protein resources restricts poultry productivity. Key strategies to alleviate this problem include improvements to the structure of the gut microbiota by the appropriate intake of high-quality protein, improvements to the comprehensive protein utilization rate, and reducing the consumption of protein raw materials. In addition, damage to the environment caused by nitrogen emissions needs to be reduced. The aim of the study was to evaluate the effects of dietary protein levels on laying performance, host metabolism, ovarian health, nitrogen emissions, and the gut microbial structure and function of laying hens. In total, 360 hens at the age of 38 weeks were randomly allotted four treatments. Each of the groups consisted of nine replicates, with 10 birds per replicate, used for 12 weeks of study. Dietary protein levels of the four groups were 13.85 %, 14.41 %, 15.63 %, and 16.30 %. Results revealed that, compared with the 13.85 % crude protein (CP) group, the 15.63 % CP group experienced significantly enhanced final body weight, average daily gain, egg production, and egg mass. Compared with the 16.30 % CP group, the other groups' serum concentrations of immunoglobulin G (IgG) and immunoglobulin M (IgM) were significantly reduced. Compared with the 16.30 % CP group, the 13.85 % and 15.63 % groups had increased CP utilization rates but reduced nitrogen emission rate, and daily per egg and per kilogram egg nitrogen emissions rose with increased dietary protein levels. Compared to the 13.85 % and 14.41 % CP groups, the 16.30 % CP group exhibited a significant increase in the expression of genes related to amino acids and carbohydrate metabolic pathways. According to the linear discriminant analysis effect size diagram, the predominant bacteria in the 15.63 % CP group (e.g., Subdoligranulum, and Ruminococcaceae_UCG-013) were significantly related to CP utilization. The results of this study emphasize that production performance is significantly reduced when protein levels are too low, whereas too high protein levels lead to gut microbiota imbalance and a reduction in the utilization efficiency of nutrients. Therefore, on the premise of ensuring the health of hens, the structure of the gut microbiota can be improved by appropriately reducing protein levels, which helps to balance the relationships among host health, productivity, resources, and the environment.

Polysaccharide degradation in Cellvibrionaceae: Genomic insights of the novel chitin-degrading marine bacterium, strain KSP-S5-2, and its chitinolytic activity

In this study, we present the genome characterization of a novel chitin-degrading strain, KSP-S5-2, and comparative genomics of 33 strains of Cellvibrionaceae. Strain KSP-S5-2 was isolated from mangrove sediment collected in Balik Pulau, Penang, Malaysia, and its 16S rRNA gene sequence showed the highest similarity (95.09%) to Teredinibacter franksiae. Genome-wide analyses including 16S rRNA gene sequence similarity, average nucleotide identity, digital DNA-DNA hybridization, and phylogenomics, suggested that KSP-S5-2 represents a novel species in the family Cellvibrionaceae. The Cellvibrionaceae pan-genome exhibited high genomic variability, with only 1.7% representing the core genome, while the flexible genome showed a notable enrichment of genes related to carbohydrate metabolism and transport pathway. This observation sheds light on the genetic plasticity of the Cellvibrionaceae family and the gene pools that form the basis for the evolution of polysaccharide-degrading capabilities. Comparative analysis of the carbohydrate-active enzymes across Cellvibrionaceae strains revealed that the chitinolytic system is not universally present within the family, as only 18 of the 33 genomes encoded chitinases. Strain KSP-S5-2 displayed an expanded repertoire of chitinolytic enzymes (25 GH18, two GH19 chitinases, and five GH20 β-N-acetylhexosaminidases) but lacked genes for agar, xylan, and pectin degradation, indicating specialized enzymatic machinery focused primarily on chitin degradation. Further, the strain degraded 90% of chitin after 10 days of incubation. In summary, our findings provided insights into strain KSP-S5-2's genomic potential, the genetics of its chitinolytic system, genomic diversity within the Cellvibrionaceae family in terms of polysaccharide degradation, and its application for chitin degradation.

Effects of Dietary β-Glucan Feeding Strategy on the Growth, Physiological Response, and Gut Microbiota of Pacific White Shrimp, Litopenaeus vannamei, under Low Salinity.

An eight-week feeding trial was conducted to investigate the effects of a dietary β-glucan application strategy on the growth performance, physiological response, and gut microbiota of Pacific white shrimp (Litopenaeus vannamei) (0.49 ± 0.17 g) under low salinity. Six feeding strategies were established, including a continuous β-glucan-free diet group (control), a continuously fed group with a 0.1% β-glucan diet (T1), and groups with the following intermittent feeding patterns: 1 day of β-glucan diet and 6 days of β-glucan-free diet (T2), 2 days of β-glucan diet and 5 days of β-glucan-free diet (T3), 3 days of β-glucan diet and 4 days of β-glucan-free diet (T4), and 4 days of β-glucan diet and 3 days of β-glucan-free diet (T5) each week. No significant differences in growth performance among all the groups were found, although the condition factor was significantly higher in the T3 group than in the T1 and T5 groups (p < 0.05). The T-AOC and GPX activities were significantly lower in the T3 group than in the control group (p < 0.05). The MDA content was also significantly lower in the T2 group than in the T3 and T4 groups (p < 0.05). Additionally, the mRNA expression of the Pen3a gene was significantly upregulated in the hepatopancreas of the T4 group compared to the control and T5 groups (p < 0.05), and the Toll gene was also significantly upregulated in the T3 group compared to the T1 and T2 groups (p < 0.05). Dietary β-glucan induced changes in the alpha diversity and composition of the gut microbiota in different feeding strategies. The beta diversity of the gut microbiota in the T2 group was significantly different from that in the control group. The results of a KEGG analysis showed that gut function in the carbohydrate metabolism, immune system, and environmental adaptation pathways was significantly enhanced in the T3 group. These findings provide evidence that the intermittent feeding strategy of β-glucan could alleviate immune fatigue, impact antioxidant ability, and change gut microbiota composition of L. vannamei under low salinity.

Oxidative stress is the active pathway in canola seed aging, the role of oxidative stress in the development of seedlings grown from aged canola seed

The widespread use of canola in the food sector has led to accelerated product growth, making it the second largest crop in the world. The analysis showed an increase in the content of proline (13.6%), H2O2 (12.7%), the levels of lipid peroxidation (30.7%), and antioxidant capacity (25.7%) in aged canola seed. The activity of CAT, SOD, and GPX enzymes increased by 1.40, 2.51, and 5.93 times respectively, while GR activity decreased by 8.8% in aged canola seed as compared to the control. An increase in GSSG content to 2.57 times and a decrease in GSH content of 0.76 times were observed in aged canola seeds. The increase in oxidative stress indices and the activity of antioxidant enzymes in canola seeds under accelerated aging indicate the role of free radicals in aging. Amylase enzyme activity increased 2.57 times in aged canola seed. Oxidative stress causes changes in the biological structures of seeds including cell membranes, lipids, pfroteins, and even in different tissue layers of seeds, which form different dimensions of the aging process. The analysis of canola seeds under accelerated aging showed that although aging reduced seed germination by 70%, the seedlings obtained from the seeds with the ability to germinate showed changes in the metabolic pathways of carbohydrates (0.26 times reduction) and proteins (1.36 times increase) of the seedlings. The phenolic compounds, flavonoid, and flavonol content of seedlings from aged seeds increased by 12.7%, 12.4%, and 12.1%, respectively. These seedlings showed significant changes in oxidative stress indexes compared to the control seedling.

Integrative Analysis of Metabolome and Transcriptome Provides Insights into the Mechanism of Flower Induction in Pineapple (Ananas comosus (L.) Merr.) by Ethephon.

Exogenous ethylene is commonly utilized to initiate flower induction in pineapple (Ananas comosus (L.) Merr.). However, the molecular mechanisms and metabolic changes involved are not well understood. In this study, we explored the genetic network and metabolic shifts in the 'Comte de Paris' pineapple variety during ethylene-induced flowering. This was achieved through an integrative analysis of metabolome and transcriptome profiles at vegetative shoot apexes (0 d after ethephon treatment named BL_0d), the stage of bract primordia (8 d after ethephon treatment named BL_8d), stage of flower primordia (18 d after ethephon treatment named BL_18d), and the stage of stopped floret differentiation (34 d after ethephon treatment named BL_34d). We isolated and identified 804 metabolites in the pineapple shoot apex and inflorescence, categorized into 24 classes. Notably, 29, 31, and 46 metabolites showed significant changes from BL_0d to BL_8d, BL_8d to BL_18d, and BL_18d to BL_34d, respectively. A marked decrease in indole was observed, suggesting its role as a characteristic metabolite during flower induction. Transcriptomic analysis revealed 956, 1768, and 4483 differentially expressed genes (DEGs) for BL_0d vs. BL_8d, BL_8d vs. BL_18d, and BL_18d vs. BL_34d, respectively. These DEGs were significantly enriched in carbohydrate metabolism and hormone signaling pathways, indicating their potential involvement in flower induction. Integrating metabolomic and transcriptomic data, we identified several candidate genes, such as Agamous-Like9 (AGL9), Ethylene Insensitive 3-like (ETIL3), Apetala2 (AP2), AP2-like ethylene-responsive transcription factor ANT (ANT), and Sucrose synthase 2 (SS2), that play potentially crucial roles in ethylene-induced flower induction in pineapple. We also established a regulatory network for pineapple flower induction, correlating metabolites and DEGs, based on the Arabidopsis thaliana pathway as a reference. Overall, our findings offer a deeper understanding of the metabolomic and molecular mechanisms driving pineapple flowering.

Compositional and functional alteration of gut microbiota profiles in response to anti-TNF-α therapy in inflammatory bowel disease: A Pilot study

Background and aimInflammatory bowel disease (IBD) is a chronic and relapsing disorder that is strongly linked to intestinal microbiota alteration (dysbiosis). Anti-tumor necrosis factor-alpha (anti-TNF-α) therapies have revolutionized IBD treatment over the last two decades. Clinical response to anti-TNF-α treatment generally involves alteration of the gut microbiota composition, although change in the microbiome following therapy has generated some contradictory theories. We examine the composition and function of the intestinal microbiota following treatment with TNF-α inhibitors and examine this relationship in the context of clinical and endoscopic response in a cohort of IBD patients in Saudi Arabia. MethodAn analysis of fecal-derived microbiota in 20 human samples was performed using 16S rRNA gene-based microbiota profiling and next generation sequencing, utilizing Illumina MiSeq. Ten samples were collected at baseline prior to treatment with TNF-α antagonists and ten samples were collected following treatment. Inter- and intra-species variation was tested using ɑ-diversity and β-diversity metrics along with appropriate statistical analysis. An examination of functional metagenomic profile variation was performed following biologics exposure. ResultsA total of 5 087 721 clean-paired sequence reads were generated across subjects before and after biologics treatment and assigned to 401 different operational taxonomic units (OTUs). The two taxonomic microbial groups (before and after treatment) demonstrated no clear separation. Anti-TNF-α treatments induced more specific variation, rather than involving a global impact on the gastrointestinal (GI) microbiota profiles, with a statistically significant increase in the Firmicutes (P = 0.01) and a statistically significant decrease in Proteobacteria (P = 0.04). This was accompanied by a remarkable increase in protective taxa, responsible for short-chain fatty acids production, such as the Lachnospiraceae family, which belongs to the Clostridiales order (P = 0.005). A notable increase in F. prausnitzii and a decrease in the relative abundance of E. coli were observed. At the functional level, an up-regulation in the carbohydrate metabolism pathway was shown in addition to a down-regulation in cellular process and signaling pathways (P = 0.04, P = 0.006, respectively). ConclusionTNF-α antagonists reduced GI microbiota with pro-inflammatory capacity enabling protective bacteria to thrive. The biologics caused specific compositional and functional variation rather than a global alteration of the gut microbiota profile in biologic-responsive IBD patients, leading to an improvement in treatment efficacy.

Integration of Metabolomes and Transcriptomes Provides Insights into Morphogenesis and Maturation in Morchella sextelata.

True morels (Morchella, Pezizales) are a popular edible and medicinal fungus with great nutritional and economic value. The dynamics and regulatory mechanisms during the morphogenesis and maturation of morels are poorly understood. In this study, the metabolomes and transcriptomes of the mycelium (MY), primordium differentiation (PR), young fruiting body (YFB), and mature fruiting body (MFB) were comprehensively analyzed to reveal the mechanism of the morphogenesis and maturation of Morchella sextelata. A total of 748 differentially expressed metabolites (DEMs) and 5342 differentially expressed genes (DEGs) were detected, mainly enriched in the carbohydrate, amino acid, and lipid metabolism pathways, with the transition from the mycelium to the primordium being the most drastic stage at both the metabolic and transcriptional levels. The integrated metabolomics and transcriptomics highlighted significant correlations between the DEMs and DEGs, and specific amino acid and nucleotide metabolic pathways were significantly co-enriched, which may play key roles in morphological development and ascocarp maturation. A conceptual model of transcriptional and metabolic regulation was proposed during morphogenesis and maturation in M. sextelata for the first time, in which environmental factors activate the regulation of transcription factors, which then promote metabolic and transcriptional regulation from vegetative to reproductive growth. These results provide insights into the metabolic dynamics and transcriptional regulation during the morphogenesis and maturation of morels and valuable resources for future breeding enhancement and sustainable artificial cultivation.

Comparative profiling of gut microbiota and metabolome in diet-induced obese and insulin-resistant C57BL/6J mice

Diet-based models are commonly used to investigate obesity and related disorders. We conducted a comparative profiling of three obesogenic diets HFD, high fat diet; HFHF, high fat high fructose diet; and HFCD, high fat choline deficient diet to assess their impact on the gut microbiome and metabolome. After 20 weeks, we analyzed the gut microbiota and metabolomes of liver, plasma, cecal, and fecal samples. Fecal and plasma bile acids (BAs) and fecal short-chain fatty acids (SCFAs) were also examined. Significant changes were observed in fecal and cecal metabolites, with increased Firmicutes and decreased Bacteroidetes in the HFD, HFHF, and HFCD-fed mice compared to chow and LFD (low fat diet)-fed mice. Most BAs were reduced in plasma and fecal samples of obese groups, except taurocholic acid, which increased in HFCD mice's plasma. SCFAs like acetate and butyrate significantly decreased in obesogenic diet groups, while propionic acid specifically decreased in the HFCD group. Pathway analysis revealed significant alterations in amino acid, carbohydrate metabolism, and nucleic acid biosynthesis pathways in obese mice. Surprisingly, even LFD-fed mice showed distinct changes in microbiome and metabolite profiles compared to the chow group. This study provides insights into gut microbiome dysbiosis and metabolite alterations induced by obesogenic and LFD diets in various tissues. These findings aid in selecting suitable diet models to study the role of the gut microbiome and metabolites in obesity and associated disorders, with potential implications for understanding similar pathologies in humans.

Allelic variations of WAK106-E2Fa-DPb1-UGT74E2 module regulate fibre properties in Populus tomentosa.

Wood formation, intricately linked to the carbohydrate metabolism pathway, underpins the capacity of trees to produce renewable resources and offer vital ecosystem services. Despite their importance, the genetic regulatory mechanisms governing wood fibre properties in woody plants remain enigmatic. In this study, we identified a pivotal module comprising 158 high-priority core genes implicated in wood formation, drawing upon tissue-specific gene expression profiles from 22 Populus samples. Initially, we conducted a module-based association study in a natural population of 435 Populus tomentosa, pinpointing PtoDPb1 as the key gene contributing to wood formation through the carbohydrate metabolic pathway. Overexpressing PtoDPb1 led to a 52.91% surge in cellulose content, a reduction of 14.34% in fibre length, and an increment of 38.21% in fibre width in transgenic poplar. Moreover, by integrating co-expression patterns, RNA-sequencing analysis, and expression quantitative trait nucleotide (eQTN) mapping, we identified a PtoDPb1-mediated genetic module of PtoWAK106-PtoDPb1-PtoE2Fa-PtoUGT74E2 responsible for fibre properties in Populus. Additionally, we discovered the two PtoDPb1 haplotypes that influenced protein interaction efficiency between PtoE2Fa-PtoDPb1 and PtoDPb1-PtoWAK106, respectively. The transcriptional activation activity of the PtoE2Fa-PtoDPb1 haplotype-1 complex on the promoter of PtoUGT74E2 surpassed that of the PtoE2Fa-PtoDPb1 haplotype-2 complex. Taken together, our findings provide novel insights into the regulatory mechanisms of fibre properties in Populus, orchestrated by PtoDPb1, and offer a practical module for expediting genetic breeding in woody plants via molecular design.

The composition and function of the gut microbiota of Francois' langurs (Trachypithecus francoisi) depend on the environment and diet.

The microbiota is essential for the extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. In this study, metagenomic sequencing technology was used to analyze the compositional structure and functional differences of the gut microbial community of Francois' langurs (Trachypithecus francoisi) under different environmental and dietary conditions. The results showed that in terms of the composition of the gut microbial community, there were significant differences among the gut microbiota of Francois' langurs (anthropogenic disturbed populations, wild populations, and captive populations) under different environmental and dietary conditions. The microbial communities with the highest abundance in Francois' langurs were Firmicutes and Bacteroidetes. Firmicutes was the most abundant phylum in anthropogenic disturbed Francois' langurs and the least abundant in captive Francois' langurs. The abundance of Bacteroidetes was highest in captive Francois' langurs. In the analysis and comparison of alpha diversity, the diversity of the gut microbiota of Francois' langurs affected by anthropogenic disturbance was the highest. The significant differences in gut microbiota between Francois' langurs in different environments and different diets were further supported by principal coordinate analysis (PCoA), with the disturbance group having a gut microbiota more similar to the wild group. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis indicated a high abundance of functional genes involved in carbohydrate metabolism, amino acid metabolism, replication and repair, cofactor and vitamin metabolism, and other amino acid metabolism pathways. Additionally, the functional genes involved in carbohydrate metabolism pathways were significantly enriched in the gut microbial community of Francois' langurs that were anthropogenic disturbed and captive. The gut microbiota of the Francois' langurs exhibited potential plasticity for dietary flexibility, and long-term food availability in captive populations leads to changes in gut microbiota composition and function. This study explored the composition and function of the gut microbiota of Francois' langurs and provided a scientific basis for understanding the physiological and health status of Francois' langurs, effectively protecting the population of wild Francois' langurs and reintroducing captive Francois' langurs into the wild.

Spontaneous nonsense mutation in the tuftelin 1 gene is associated with abnormal hair appearance and amelioration of glucose and lipid metabolism in the rat.

Recently, we have identified a recessive mutation, an abnormal coat appearance in the BXH6 strain, a member of the HXB/BXH set of recombinant inbred (RI) strains. The RI strains were derived from the spontaneously hypertensive rat (SHR) and Brown Norway rat (BN-Lx) progenitors. Whole genome sequencing of the mutant rats identified the 195875980 G/A mutation in the tuftelin 1 (Tuft1) gene on chromosome 2, which resulted in a premature stop codon. Compared with wild-type BXH6 rats, BXH6-Tuft1 mutant rats exhibited lower body weight due to reduced visceral fat and ectopic fat accumulation in the liver and heart. Reduced adiposity was associated with decreased serum glucose and insulin and increased insulin-stimulated glycogenesis in skeletal muscle. In addition, mutant rats had lower serum monocyte chemoattractant protein-1 and leptin levels, indicative of reduced inflammation. Analysis of the liver proteome identified differentially expressed proteins from fatty acid metabolism and β-oxidation, peroxisomes, carbohydrate metabolism, inflammation, and proteasome pathways. These results provide evidence for the important role of the Tuft1 gene in the regulation of lipid and glucose metabolism and suggest underlying molecular mechanisms.NEW & NOTEWORTHY A new spontaneous mutation, abnormal hair appearance in the rat, has been identified as a nonfunctional tuftelin 1 (Tuft1) gene. The pleiotropic effects of this mutation regulate glucose and lipid metabolism. Analysis of the liver proteome revealed possible molecular mechanisms for the metabolic effects of the Tuft1 gene.

Transcriptome Analysis Reveals the Stress Tolerance Mechanisms of Cadmium in Zoysia japonica.

Cadmium (Cd) is a severe heavy metal pollutant globally. Zoysia japonica is an important perennial warm-season turf grass that potentially plays a role in phytoremediation in Cd-polluted soil areas; however, the molecular mechanisms underlying its Cd stress response are unknown. To further investigate the early gene response pattern in Z. japonica under Cd stress, plant leaves were harvested 0, 6, 12, and 24 h after Cd stress (400 μM CdCl2) treatment and used for a time-course RNA-sequencing analysis. Twelve cDNA libraries were constructed and sequenced, and high-quality data were obtained, whose mapped rates were all higher than 94%, and more than 601 million bp of sequence were generated. A total of 5321, 6526, and 4016 differentially expressed genes were identified 6, 12, and 24 h after Cd stress treatment, respectively. A total of 1660 genes were differentially expressed at the three time points, and their gene expression profiles over time were elucidated. Based on the analysis of these genes, the important mechanisms for the Cd stress response in Z. japonica were identified. Specific genes participating in glutathione metabolism, plant hormone signal and transduction, members of protein processing in the endoplasmic reticulum, transporter proteins, transcription factors, and carbohydrate metabolism pathways were further analyzed in detail. These genes may contribute to the improvement of Cd tolerance in Z. japonica. In addition, some candidate genes were highlighted for future studies on Cd stress resistance in Z. japonica and other plants. Our results illustrate the early gene expression response of Z. japonica leaves to Cd and provide some new understanding of the molecular mechanisms of Cd stress in Zosia and Gramineae species.

Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.).

The nutritional value of soybean [Glycine max (L.) Merr.] for animals is influenced by soluble carbohydrates, such as sucrose and stachyose. Although sucrose is nutritionally desirable, stachyose is an antinutrient causing diarrhea and flatulence in non-ruminant animals. We conducted a genome-wide association study of 220 soybean accessions using 21,317 single nucleotide polymorphisms (SNPs) from the SoySNP50K iSelect Beadchip data to identify significant SNPs associated with sucrose and stachyose content. Seven significant SNPs were identified for sucrose content across chromosomes (Chrs.) 2, 8, 12, 17, and 20, while thirteen significant SNPs were identified for stachyose content across Chrs. 2, 5, 8, 9, 10, 13, 14, and 15. Among those significant SNPs, three sucrose-related SNPs on Chrs. 8 and 17 were novel, while twelve stachyose-related SNPs on Chrs. 2, 5, 8, 9, 10, 13, 14, and 15 were novel. Based on Phytozome, STRING, and GO annotation, 17 and 24 candidate genes for sucrose and stachyose content, respectively, were highly associated with the carbohydrate metabolic pathway. Among these, the publicly available RNA-seq Atlas database highlighted four candidate genes associated with sucrose (Glyma.08g361200 and Glyma.17g258100) and stachyose (Glyma.05g025300 and Glyma.13g077900) content, which had higher gene expression levels in developing seed and multiple parts of the soybean plant. The results of this study will extend knowledge of the molecular mechanism and genetic basis underlying sucrose and stachyose content in soybean seed. Furthermore, the novel candidate genes and SNPs can be valuable genetic resources that soybean breeders may utilize to modify carbohydrate profiles for animal and human usage.