Biosynthesis Of Vitamin Research Articles

The Di-Symbiotic Systems in the Aphids Sipha maydis and Periphyllus lyropictus Provide a Contrasting Picture of Recent Co-Obligate Nutritional Endosymbiosis in Aphids.

Dependence on multiple nutritional bacterial symbionts forming a metabolic unit has repeatedly evolved in many insect species that feed on nutritionally unbalanced diets such as plant sap. This is the case for aphids of the subfamilies Lachninae and Chaitophorinae, which have evolved di-symbiotic systems in which the ancient obligate nutritional symbiont Buchnera aphidicola is metabolically complemented by an additional nutritional symbiont acquired more recently. Deciphering how different symbionts integrate both metabolically and anatomically in such systems is crucial to understanding how complex nutritional symbiotic systems function and evolve. In this study, we sequenced and analyzed the genomes of the symbionts B. aphidicola and Serratia symbiotica associated with the Chaitophorinae aphids Sipha maydis and Periphyllus lyropictus. Our results show that, in these two species, B. aphidicola and S. symbiotica complement each other metabolically (and their hosts) for the biosynthesis of essential amino acids and vitamins, but with distinct metabolic reactions supported by each symbiont depending on the host species. Furthermore, the S. symbiotica symbiont associated with S. maydis appears to be strictly compartmentalized into the specialized host cells housing symbionts in aphids, the bacteriocytes, whereas the S. symbiotica symbiont associated with P. lyropictus exhibits a highly invasive phenotype, presumably because it is capable of expressing a larger set of virulence factors, including a complete flagellum for bacterial motility. Such contrasting levels of metabolic and anatomical integration for two S. symbiotica symbionts that were recently acquired as nutritional co-obligate partners reflect distinct coevolutionary processes specific to each association.

Proteomic profile of Candida albicans biofilm

Candida albicans biofilms are characterized by structural and cellular heterogeneity that confers antifungal resistance and immune evasion. Despite this, biofilm formation remains poorly understood. In this study, we used proteomic analysis to understand biofilm formation in C. albicans related to morphophysiological and architectural features. LC-MS/MS analysis revealed that 64 proteins were significantly modulated, of which 31 were upregulated and 33 were downregulated. The results indicate that metabolism (25 proteins), gene expression (13 proteins), stress response (7 proteins), and cell wall (5 proteins) composition are modulated. The rate of oxidative phosphorylation (OxPhos) and biosynthesis of UDP-N-acetylglucosamine, vitamin B6, and thiamine increased, while the rate of methionine biosynthesis decreased. There was a significant modification of the cell wall architecture due to higher levels of Sun41, Pir1 and Csh1 and increased glycosylation of proteins. It was observed that C. albicans induces hyphal growth by upregulating the expression of genes involved in cAMP-PKA and MAPK pathways. This study is significant in that it suggests an increase in OxPhos and alteration of cell wall architecture that could be contributing to the recalcitrance of C. albicans cells growing in biofilms. Nevertheless, a deeper investigation is needed to explore it further. SignificanceCandida sps is included in the list of pathogens with potential drug resistance threat due to the increased frequency especially colonization of medical devices, and tissues among the patients, in recent years. Significance of our study is that we are reporting traits like modulation in cell wall composition, amino acid and vitamin biosynthesis and importantly energy generation (OxPhos) etc. These traits could be conferring antifungal resistance, host immune evasion etc. and thus survival, in addition to facilitating biofilm formation. These findings are expected to prime the further studies on devising potent strategy against biofilm growth among the patients.

Advances and prospects in the biosynthesis of vitamin B6 and its bioengineering as a cofactor of other chemicals

AbstractVitamin B6 is an essential nutrient, which is widely used in food products, feed additives, pharmaceuticals, disease diagnosis, and other fields. Pyridoxal‐5′‐phosphate (PLP), the active form of vitamin B6, is an important coenzyme participating in a variety of enzyme reactions. At present, the oxazole method is mainly used for the production of vitamin B6, but toxic and corrosive intermediates produced in the synthesis process, which does not conform to the green manufacturing. Therefore, there is considerable interest in shifting from chemical processes to sustainable fermentation techniques and research on PLP metabolism of other valuable compounds. In this review, we will briefly describe the enzymes that PLP participated and focus on the advances in vitamin B6 biosynthesis and discuss its application to engineering bacteria that overproduce other commercially valuable substances including cadaverine, 3,4‐dihydroxyphenylacetate‐l‐alanine, γ‐aminobutyric acid, and l‐phosphinothricin. It will provide a reference for the biosynthesis of vitamin B6 or other valuable compounds in which PLP participates in the reaction, and we also look forward to the future development prospect of PLP.

Gut Microbial and Metabolic Signatures are Altered in Adolescents with Type 1 Diabetes

BackgroundEvidence suggests that the pathogenesis and development of Type 1 Diabetes (T1D) are driven by both genetic predisposition and immune dysfunction which may be influenced by gut microbiota. The present study aimed to investigate the composition and functional pathways of the gut microbiome in adolescents with T1D, determine the association between gut microbes and clinical and dietary factors in T1D, and identify features predictive of T1D.MethodsHealthy adolescents (n=35) and adolescents with T1D (n=30) were recruited and microbial profiling in participants’ stool samples was performed using deep shotgun metagenomic sequencing. The bioBakery3 pipeline (Kneaddata, Metaphlan3 and HUMAnN) was used to analyze the reads to assign taxonomy and functional annotations. The differences in taxonomic abundances were identified using Linear Discriminant Analysis (LDA) Effect Size (LEfSe) and ecological measures (diversity) were assessed using standard methods. The association between the abundance of specific bacterial species and the metadata (HbA1C, skin carotenoids, diet and physical activity) was assessed by performing Spearman’s correlation. Random forest modeling (using the MUVR package) was used to identify features predictive of T1D.ResultsAdolescents with T1D exhibited a significant increase in Simpson α‐diversity index as compared to healthy adolescents. β‐diversity was similar between the two groups. LEfSe indicated a significant difference in the microbial community at different taxonomic levels between the two groups. Seven taxa were enriched in adolescents with T1D at the species level that includes Alistipes Shahii, Asaccharobacter celatus, Blautia obeum, Coprococcus eutactus, Coprobacillus cateniformis, Clostridium symbiosum, and Eggerthella lenta. Three species Alistripes Putredins, Dialister invisus, and Eubacterium ventriosum were enriched in healthy adolescents. Further, 33 out of 400 microbial metabolic pathways were significantly different between the two groups. Importantly, biosynthesis of amino acids, vitamins, enzyme cofactors, and electron carrier were downregulated whereas fermentation pathways were upregulated in adolescents with T1D as compared to healthy adolescents. Association analysis indicated that specific bacterial species are correlated with HbA1C, skin carotenoids, dietary factors and physical activity. Most of the bacterial species associated with these measures were different between the two groups. MUVR identified bacterial taxa predictive of T1D status (0.82 sensitivity and 0.63 specificity). The top features in using genus level abundance included Coprococcus, Faecalibaterium and Streptococcus.ConclusionThe present study indicates an extensive alteration in the composition and functional capacity of gut microbiota in adolescents with T1D providing new insight into microbial and metabolic signatures in adolescents with T1D.

Compositional changes in human gut microbiota reveal a putative role of intestinal mycobiota in metabolic and biological decline during aging

BACKGROUND: Age-related alterations in the composition and function of gut microbiota may influence human health and disease mechanisms. However, connections between compositional changes in gut bacterial and fungal communities, and their role in the aging process, remain poorly understood. OBJECTIVE: Compare the gut microbiota and mycobiota composition in different age groups and evaluate the functionality. METHODS: In this study, we performed 16S rRNA and ITS2 gene-based microbial profiling analysis and shotgun metagenomics using the NextSeq platform. RESULTS: We observed a shift in compositional changes of human gut microbiota with age. Older individuals revealed a significantly different gut microbiota profile compared to younger individuals. For example, gut microbiota composition of the older individuals showed increase in genera Bacteroides, Blautia, Ruminococcaceae, and Escherichia coli. Additionally, older individuals had significant reduction in fungi belonging to saccharomyces cerevisiae and candida albicans in comparison to their younger counterparts. Moreover, metagenomics functional profiling analysis using shotgun metagenomics sequencing data showed substantial differences in the enrichment of 48 pathways between the young and older age groups. Metabolic pathways such as amino acid biosynthesis, carbohydrate metabolism, cell structure biosynthesis and vitamin biosynthesis were declined in the older age group, in comparison with the younger individuals. CONCLUSIONS: The identified differences provide a new insight to enrich our understanding of age-related changes in gut microbiota, their metabolic capabilities, and potential impact on health and disease conditions.

Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata).

BackgroundGut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level.MethodsGut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3–V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing.ResultsThe gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.

Mutants lacking global regulators, fis and arcA, in Escherichia coli enhanced growth fitness under acetate metabolism by pathway reprogramming.

Global regulatory transcription factors play a significant role in controlling microbial metabolism under genetic and environmental perturbations. A system-level effect of carbon sources such as acetate on microbial metabolism under disrupted global regulators has not been well established. Acetate is one of the major substrates available in various nutrient niches such as the mammalian gut and a keto diet. A substantial amount of acetate gets secreted in aerobic metabolism. Therefore, investigating the study on acetate metabolism is highly significant. It is known that the global regulatorsfisandarcAregulate acetate uptake genes inE. coliunder glucose conditions. This study deciphered the growth and flux distribution ofE. colitranscription regulatory knockouts Δfis,ΔarcAand double deletion mutant, ΔarcAΔfisunder acetate using 13C-metabolic flux analysis (MFA), which has not been investigated before. We observed that the mutants exhibited an expeditious growth rate (~ 1.2-1.6-fold) with a proportionate increase in acetate uptake rates compared to the wild type. 13C-MFA displayed the distinct metabolic reprogramming of intracellular fluxes via the TCA cycle, anaplerotic pathway and gluconeogenesis, which conferred an advantage of a faster growth rate with better carbon usage in all the mutants. This resulted in higher metabolic fluxes through the TCA cycle (~ 18-90%), lower gluconeogenesis (~ 15-35%) and higher CO2 and ATP production with the proportional increase in growth rate. The study reveals a novel insight by stating the sub-optimality of the wild-type strain grown under acetate substrate aerobically. These mutant strains efficiently oxidize acetate, thus acting as potential candidates for the biosynthesis of isoprenoids, biofuels, vitamins and various pharmaceutical products.Key Points• Mutants exhibited a better balance between energy and precursor synthesis than WT.• Leveraged in the unravelling of regulatory control under various nutrient shifts.• Metabolic readjustment resulted in optimal biomass requirement and faster growth.

Selective biosynthesis of retinol in S. cerevisiae

The vitamin A component retinol has become an increasingly sought-after cosmetic ingredient. In previous efforts for microbial biosynthesis of vitamin A, a mixture of retinoids was produced. In order to efficiently produce retinol at high purity, the precursor and NADPH supply was first enhanced to improve retinoids accumulation in the S. cerevisiae strain constructed from a β-carotene producer by introducing β-carotene 15,15ʹ-dioxygenase, following by screening of heterologous and endogenous oxidoreductases for retinal reduction. Env9 was found as an endogenous retinal reductase and its activity was verified in vitro. By co-expressing Env9 with the E. coli ybbO, as much as 443.43 mg/L of retinol was produced at 98.76% purity in bi-phasic shake-flask culture when the antioxidant butylated hydroxytoluene was added to prevent retinoids degradation. The retinol titer reached 2479.34 mg/L in fed-batch fermentation. The success in selective biosynthesis of retinol would lay a solid foundation for its biotechnological production.Graphical

Identification of QTLs and candidate genes for 100-seed weight trait using PyBSASeq algorithm in soybean

<p id="C3">The PyBSASeq algorithm, based on quantifying the enrichment of likely trait-associated SNPs in a chromosomal interval, was proved more suitable for genetic analysis of complex quantitative traits in bulked segregant analysis. In this study, to identify the loci and candidate genes of 100-seed weight (SW) in soybean using the PyBSASeq algorithm, 149 RILs derived from the hybrid of ‘Huapidou’ and ‘Qihuang 26’ were used as materials. As a result, 11 candidate regions closely associated with SW were identified by mining the 100-grain weight related loci of soybean, which were located on chromosomes 1, 2, 4, 7, 9, 14, and 16, respectively. Among these regions, <italic>qSW4-1</italic>, <italic>qSW9-1</italic>, <italic>qSW9-2</italic>, and <italic>qSW7-1</italic> were consistent with the QTLs for 100-seed weight reported previously, and a total of 218 coding genes were included in the candidate regions. Among these genes, <italic>Glyma.02G075000</italic> and <italic>Glyma.04G082500 </italic>were predicted to be candidate genes using gene expressional and haplotype analysis. Bioinformatics analysis showed that the candidate genes were mainly involved in sugar transport and biosynthesis of Vitamin E. The results will be helpful to elucidate the genetic mechanism of seed weight regulation in soybean and provide a reference for the study of quantitative trait based on BSA-Seq method.

Influence of Blanching on the Gene Expression Profile of Phenylpropanoid, Flavonoid and Vitamin Biosynthesis, and Their Accumulation in Oenanthe javanica.

Field blanching is a process used in agriculture to obtain sweet, delicious, and tender stems of water dropwort by obstructing sunlight. The nutritional and transcriptomic profiling of blanched water dropwort has been investigated in our previous studies. However, the effect of blanching on the production of secondary metabolites and different vitamins in water dropwort has not been investigated at the transcriptomic level. This study explored the transcriptomic variations in the phenylpropanoid biosynthesis, flavonoid biosynthesis, and different vitamin biosynthesis pathways under different blanching periods in the water dropwort stems (pre-blanching, mid-blanching, post-blanching, and control). The results show that polyphenol and flavonoid contents decreased; however, the contents of vitamins (A, B1, B2, and C) and antioxidant activity increased significantly after blanching. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of blanched water dropwort showed the downregulation of many important genes involved in phenylpropanoid and flavonoid biosynthesis pathways, and the downregulation of these genes might be the reason for the reduction in polyphenol and flavonoid contents. We also examined and highlighted the genes involved in the higher vitamin content, antioxidant activity, pale color, tenderness, and sweetness of the blanched stem of water dropwort. In conclusion, the present study explored the role of phenylpropanoid and vitamin biosynthesis, and it will provide a basis for future investigation and application in the blanch cultivation of water dropwort.

Anti-obesity effects of Chenpi: an artificial gastrointestinal system study.

SummaryThe gut microbiota plays a significant role in human health; however, the complex relationship between gut microbial communities and host health is still to be thoroughly studied and understood. Microbes in the distal gut contribute to host health through the biosynthesis of vitamins and essential amino acids and the generation of important metabolic by‐products from dietary components that are left undigested by the small intestine. Aged citrus peel (Chenpi) is used in traditional Chinese medicine to lower cholesterol, promote weight loss and treat various gastrointestinal symptoms. This study investigated how the microbial community changes during treatment with Chenpi using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME). Two preparations of Chenpi extract were tested: Chenpi suspended in oil only and Chenpi in a viscoelastic emulsion. Short‐chain fatty acids (SCFAs) were measured during treatment to monitor changes in the microbial community of the colon presenting a decrease in production for acetic, propionic and butyric acid (ANOVA (P < 0.001) during the 15 days of treatment. 16S rRNA sequencing of microbial samples showed a clear difference between the two treatments at the different sampling times (ANOSIM P < 0.003; ADOSIM P < 0.002 [R 2 = 69%]). Beta diversity analysis by PcoA showed differences between the two Chenpi formulations for treatment day 6. These differences were no longer detectable as soon as the Chenpi treatment was stopped, showing a reversible effect of Chenpi on the human microbiome. 16S rRNA sequencing of microbial samples from the descending colon showed an increase in Firmicutes for the treatment with the viscoelastic emulsion. At the genus level, Roseburia, Blautia, Subdoligranulum and Eubacterium increased in numbers during the viscoelastic emulsion treatment. This study sheds light on the anti‐obesity effect of a polymethoxyflavone (PMFs)‐enriched Chenpi extract and creates a foundation for the identification of ‘obesity‐prevention’ biomarkers in the gut microbiota.

Improved Enzymatic Assay and Inhibition Analysis of Redox Membranotropic Enzymes, AtGALDH and TcGAL, Using a Reversed Micellar System

Reversed micelles are helpful to solubilize otherwise insoluble membranotropic or membrane-bound enzymes in their functional form, thus enabling activity assay and inhibition analysis. However, in the case of redox enzymes, this task is further complicated by the necessity to select an appropriate electron-acceptor (EA) which, ideally, should be compatible with spectrophotometric measurements in reversed micelles. Here, we have identified such an EA and successfully used it in a reversed micellar environment to assay the activity of two homologous enzymes from mitochondria: l-galactone-1,4-lactone dehydrogenase (EC 1.3.2.3) from Arabidopsis thaliana (AtGALDH) and galactonolactone oxidase (EC 1.3.3.12) from Trypanosoma cruzi (TcGAL), differing in their membranotropic properties, with TcGAL being almost insoluble in water and particularly difficult to assay. Furthermore, we have demonstrated the possibility to use this assay for inhibition analysis, with an elucidation of the mechanism and inhibition parameters, which otherwise could not be possible. In order to perform inhibition analysis, we improved the approach for the determination of activity of such membrane enzymes based on a reversed micellar system as membrane matrix, necessary for the functioning of membrane enzymes. A number of electron acceptors (EA) were tested for AtGALDH and optimal conditions of activity determination for AtGALDH were found. The suggested method was successfully applied to the study of the inhibition of AtGALDH by lycorine, and the mixed competitive mechanism of inhibition of AtGALDH by lycorine was determined. The developed approach to inhibitor analysis was applied for TcGAL, insoluble in water membrane, and the method provides new opportunities for searching effective inhibitors that may be potential drugs. Indeed, galactonolactone oxidase from Trypanosoma cruzi (TcGAL) and AtGALDH are homologues, and the inhibition of TcGAL stops the vital biosynthesis of vitamin C in parasite Trypanosoma cruzi from causing Chagas disease. The approach proposed can be applied for the screening of inhibitors of AtGALDH and TcGAL, as well as to study properties of other membrane enzymes including determination of the mechanisms of inhibition, structure and catalytic properties, the impact of membrane components (for example lipids), and so on.

The Role of Cytochrome P450 Enzymes in COVID-19 Pathogenesis and Therapy.

Coronavirus disease 2019 (COVID-19) has become a new public health crisis threatening the world. Dysregulated immune responses are the most striking pathophysiological features of patients with severe COVID-19, which can result in multiple-organ failure and death. The cytochrome P450 (CYP) system is the most important drug metabolizing enzyme family, which plays a significant role in the metabolism of endogenous or exogenous substances. Endogenous CYPs participate in the biosynthesis or catabolism of endogenous substances, including steroids, vitamins, eicosanoids, and fatty acids, whilst xenobiotic CYPs are associated with the metabolism of environmental toxins, drugs, and carcinogens. CYP expression and activity are greatly affected by immune response. However, changes in CYP expression and/or function in COVID-19 and their impact on COVID-19 pathophysiology and the metabolism of therapeutic agents in COVID-19, remain unclear. In this analysis, we review current evidence predominantly in the following areas: firstly, the possible changes in CYP expression and/or function in COVID-19; secondly, the effects of CYPs on the metabolism of arachidonic acid, vitamins, and steroid hormones in COVID-19; and thirdly, the effects of CYPs on the metabolism of therapeutic COVID-19 drugs.

GDP-Mannose 3,5-Epimerase: A View on Structure, Mechanism, and Industrial Potential.

GDP-mannose 3,5-epimerase (GM35E, GME) belongs to the short-chain dehydrogenase/reductase (SDR) protein superfamily and catalyses the conversion of GDP-d-mannose towards GDP-l-galactose. Although the overall reaction seems relatively simple (a double epimerization), the enzyme needs to orchestrate a complex set of chemical reactions, with no less than 6 catalysis steps (oxidation, 2x deprotonation, 2x protonation and reduction), to perform the double epimerization of GDP-mannose to GDP-l-galactose. The enzyme is involved in the biosynthesis of vitamin C in plants and lipopolysaccharide synthesis in bacteria. In this review, we provide a clear overview of these interesting epimerases, including the latest findings such as the recently characterized bacterial and thermostable GM35E representative and its mechanism revision but also focus on their industrial potential in rare sugar synthesis and glycorandomization.

Unraveling of Chlorella-associated bacterial load, diversity, and their imputed functions at high- and low-yield conditions through metagenome sequencing.

Chlorella-associated bacteria can have a significant influence on facilitating higher Chlorella biomass yield due to their symbiotic relationship. In this study, non-axenic Chlorella was cultivated in an airlift photobioreactor at high and low-yield conditions. The associated bacterial diversity was analyzed using 16S rRNA metagenome sequencing. At high-yield conditions, the bacterial load was observed in the range of 108 -1010 CFU · mL-1 , whereas at low-yield conditions, bacteria were more dominant and observed in the range of 1014 -1015 CFU · mL-1 . The majority of the bacterial species associated with Chlorella at high-yield conditions belongs to Proteobacteria and Bacteroidetes. Further, Bacteroidetes levels were decreased at low-yield conditions and were highly diversified with Planctomycetes, Firmicutes, and 18 others. Predicted functional genes indicated that Chlorella-associated bacteria have the enzymes involved in the metabolism and biosynthesis of B-complex vitamins (i.e., vitamin B12 , thiamin, biotin, pyridoxine, and riboflavin). A critical evaluation revealed that vitamin biosynthesis genes were more abundant at low-yield conditions; however, vitamin B12 transport genes (B12 transport ATP-binding protein, B12 substrate-binding transportation, and B12 permease protein) were less abundant, indicating even though vitamins production occurs, but their availability to Chlorella was limited due to the lack of vitamin transport genes. Further, at high yield, Chlorella-associated bacteria enabled higher growth by supplementing the vitamins. In contrast, at low-yield condition-an increased bacterial load, diversity, and limited vitamin transport functional genes affected the Chlorella yield. It can be inferred that Chlorella yield was significantly affected by three factors: associated bacterial load, diversity, and transport functional genes of vitamins.

Faecal microbiome and metabolic signatures in rectal neuroendocrine tumors.

Background: The prevalence of rectal neuroendocrine tumors (RNET) has increased substantially over the past decades. Little is known on mechanistic alteration in the pathogenesis of such disease. We postulate that perturbations of human gut microbiome-metabolome interface influentially affect the development of RNET. The study aims to characterize the composition and function of faecal microbiome and metabolites in RNET individuals.Methods: We performed deep shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling of faecal samples from the discovery cohort (18 RNET patients, 40 controls), and validated the microbiome and metabolite-based classifiers in an independent cohort (15 RNET participants, 19 controls).Results: We uncovered a dysbiotic gut ecological microenvironment in RNET patients, characterized by aberrant depletion and attenuated connection of microbial species, and abnormally aggregated lipids and lipid-like molecules. Functional characterization based on our in-house and Human Project Unified Metabolic Analysis Network 2 (HUMAnN2) pipelines further indicated a nutrient deficient gut microenvironment in RNET individuals, evidenced by diminished activities such as energy metabolism, vitamin biosynthesis and transportation. By integrating these data, we revealed 291 robust associations between representative differentially abundant taxonomic species and metabolites, indicating a tight interaction of gut microbiome with metabolites in RNET pathogenesis. Finally, we identified a cluster of gut microbiome and metabolite-based signatures, and replicated them in an independent cohort, showing accurate prediction of such neoplasm from healthy people.Conclusions: Our current study is the first to comprehensively characterize the perturbed interface of gut microbiome and metabolites in RNET patients, which may provide promising targets for microbiome-based diagnostics and therapies for this disorder.

Gut microbial ecology of Xenopus tadpoles across life stages

Background: The microorganism world living in amphibians is still largely under-represented and under-studied in the literature. Among anuran amphibians, African clawed frogs of the Xenopus genus stand as well-characterized models with an in-depth knowledge of their developmental biological processes including their metamorphosis. In this study, we analyzed the succession of microbial communities and their activities across diverse body habitats of Xenopus tropicalis using different approaches including flow cytometry and 16s rDNA gene metabarcoding. We also evaluated the metabolic capacity of the premetamorphic tadpoles gut microbiome using metagenomic and metatranscriptomic sequencing. Results: We analyzed the bacterial components of the Xenopus gut microbiota, the adult gut biogeography, the succession of communities during ontogeny, the impact of the alimentation in shaping the tadpoles gut bacterial communities and the transmission of skin and fecal bacteria to the eggs. We also identified the most active gut bacteria and their metabolic contribution to tadpole physiology including carbohydrate breakdown, nitrogen recycling, essential amino-acids and vitamin biosynthesis. Conclusions: We present a comprehensive new microbiome dataset of a laboratory amphibian model. Our data provide evidences that studies on the Xenopus tadpole model can shed light on the interactions between a vertebrate host and its microbiome. We interpret our findings in light of bile acids being key molecular components regulating the gut microbiome composition during amphibian development and metamorphosis. Further studies into the metabolic interactions between amphibian tadpoles and their microbiota during early development and metamorphosis should provide useful information on the evolution of host-microbiota interactions in vertebrates.

Shedding light on the bacterial resistance to toxic UV filters: a comparative genomic study.

UV filters are toxic to marine bacteria that dominate the marine biomass. Ecotoxicology often studies the organism response but rarely integrates the toxicity mechanisms at the molecular level. In this study, in silico comparative genomics between UV filters sensitive and resistant bacteria were conducted in order to unravel the genes responsible for a resistance phenotype. The genomes of two environmentally relevant Bacteroidetes and three Firmicutes species were compared through pairwise comparison. Larger genomes were carried by bacteria exhibiting a resistant phenotype, favoring their ability to adapt to environmental stresses. While the antitoxin and CRISPR systems were the only distinctive features in resistant Bacteroidetes, Firmicutes displayed multiple unique genes that could support the difference between sensitive and resistant phenotypes. Several genes involved in ROS response, vitamin biosynthesis, xenobiotic degradation, multidrug resistance, and lipophilic compound permeability were shown to be exclusive to resistant species. Our investigation contributes to a better understanding of UV filters resistance phenotypes, by identifying pivotal genes involved in key pathways.

Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods.

Metabolic cross-feeding frequently underlies mutualistic relationships in natural microbial communities and is often exploited to assemble synthetic microbial consortia. We systematically identified all single-gene knockouts suitable for imposing cross-feeding in Escherichia coli and used this information to assemble syntrophic communities. Most strains benefiting from shared goods were dysfunctional in biosynthesis of amino acids, nucleotides, and vitamins or mutants in central carbon metabolism. We tested cross-feeding potency in 1,444 strain pairs and mapped the interaction network between all functional groups of mutants. This network revealed that auxotrophs for vitamins are optimal cooperators. Lastly, we monitored how assemblies composed of dozens of auxotrophs change over time and observed that they rapidly and repeatedly coalesced to seven strain consortia composed primarily from vitamin auxotrophs. The composition of emerging consortia suggests that they were stabilized by multiple cross-feeding interactions. We conclude that vitamins are ideal shared goods since they optimize consortium growth while still imposing member co-dependence.

The role of the gut microbiota in the dietary niche expansion of fishing bats

BackgroundDue to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet.ResultsWe first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish.ConclusionsOur results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory.