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How to resolve the metabolic dark matter of microorganisms has long been a challenging problem in discovering active molecules. Diverse omics tools have been developed to guide the discovery and characterization of various microbial metabolites, which make it gradually possible to predict the overall metabolites for individual strains. The combinations of multi-omic analysis tools effectively compensates for the shortcomings of current studies that focus only on single omics or a broad class of metabolites. In this review, we systematically update, categorize and sort out different analysis tools for microbial metabolites prediction in the last five years to appeal for the multi-omic combination on the understanding of the metabolic nature of microbes. First, we provide the general survey on different updated prediction databases, webservers, or software that based on genomics, transcriptomics, proteomics, and metabolomics, respectively. Then, we discuss the essentiality on the integration of multi-omics data to predict metabolites of different microbial strains and communities, as well as stressing the combination of other techniques, such as systems biology methods and data-driven algorithms. Finally, we identify key challenges and trends in developing multi-omic analysis tools for more comprehensive prediction on diverse microbial metabolites that contribute to human health and disease treatment. [ABSTRACT FROM AUTHOR]

Motivation Metabolomics has developed rapidly in recent years, and metabolism-related databases are also gradually constructed. Nowadays, more and more studies are being carried out on diverse microbes, metabolites and diseases. However, the logics of various associations among microbes, metabolites and diseases are limited understanding in the biomedicine of gut microbial system. The collection and analysis of relevant microbial bioinformation play an important role in the revelation of microbe–metabolite–disease associations. Therefore, the dataset that integrates multiple relationships and the method based on complex heterogeneous graphs need to be developed. Results In this study, we integrated some databases and extracted a variety of associations data among microbes, metabolites and diseases. After obtaining the three interconnected bilateral association data (microbe–metabolite, metabolite–disease and disease–microbe), we considered building a heterogeneous graph to describe the association data. In our model, microbes were used as a bridge between diseases and metabolites. In order to fuse the information of disease–microbe–metabolite graph, we used the bipartite graph attention network on the disease–microbe and metabolite–microbe bipartite graph. The experimental results show that our model has good performance in the prediction of various disease–metabolite associations. Through the case study of type 2 diabetes mellitus, Parkinson's disease, inflammatory bowel disease and liver cirrhosis, it is noted that our proposed methodology are valuable for the mining of other associations and the prediction of biomarkers for different human diseases. Availability and implementation: https://github.com/Selenefreeze/DiMiMe.git [ABSTRACT FROM AUTHOR]

Objectives The present study aimed to determine the correlation between serum carcinoembryonic antigen (CEA) level and the severity of interstitial lung disease (ILD) in clinically amyopathic DM (CADM) patients. Methods We performed a retrospective study including 41 Chinese CADM patients without malignancy. Serum CEA levels, clinical and laboratory findings were collected. Association tests between CEA levels and disease activity parameters were performed. Results Among the 41 patients, 16 (39.0%) developed rapidly progressive (RP)-ILD; of them, 14 (87.5%) had elevated serum CEA levels. Multivariate logistic regression analysis indicated that an elevated serum CEA level was an independent risk factor for RP-ILD. The incidence of elevated CEA level was significantly higher in patients with RP-ILD than in those without RP-ILD (87.5 vs 16.0%, P  < 0.001). Furthermore, CEA levels were higher in patients with CADM with RP-ILD [26.87 (6.71) μg/l] than in those without RP-ILD [3.23 (0.64) μg/l] (P  < 0.001). CEA levels in CADM patients were associated with the ferritin, alanine aminotransferase, aspartate aminotransferase and lactate dehydrogenase levels, and CT scores of the lungs. Also, elevated CEA levels are related to the organizing pneumonia pattern and lower lung zone consolidation in high-resolution CT. Moreover, the cumulative survival rate was significantly lower (68.4 vs 31.6%, P  < 0.001) in the group with a CEA level >8.75 μg/l than that in the group with a CEA level <8.75 μg/l. Conclusions An elevated serum CEA level is common in patients with CADM, and a higher serum CEA level is a powerful indicator of RP-ILD and poor prognosis in those patients. [ABSTRACT FROM AUTHOR]

Quorum sensing interference (QSI), the disruption and manipulation of quorum sensing (QS) in the dynamic control of bacteria populations could be widely applied in synthetic biology to realize dynamic metabolic control and develop potential clinical therapies. Conventionally, limited QSI molecules (QSIMs) were developed based on molecular structures or for specific QS receptors, which are in short supply for various interferences and manipulations of QS systems. In this study, we developed QSIdb (http://qsidb.lbci.net/), a specialized repository of 633 reported QSIMs and 73 073 expanded QSIMs including both QS agonists and antagonists. We have collected all reported QSIMs in literatures focused on the modifications of N-acyl homoserine lactones, natural QSIMs and synthetic QS analogues. Moreover, we developed a pipeline with SMILES-based similarity assessment algorithms and docking-based validations to mine potential QSIMs from existing 138 805 608 compounds in the PubChem database. In addition, we proposed a new measure, pocketedit , for assessing the similarities of active protein pockets or QSIMs crosstalk, and obtained 273 possible potential broad-spectrum QSIMs. We provided user-friendly browsing and searching facilities for easy data retrieval and comparison. QSIdb could assist the scientific community in understanding QS-related therapeutics, manipulating QS-based genetic circuits in metabolic engineering, developing potential broad-spectrum QSIMs and expanding new ligands for other receptors. [ABSTRACT FROM AUTHOR]

Cell wall is closely related to bacterial robustness and adsorption capacity, playing crucial roles in nisin production in Lactococcus lactis. Peptidoglycan (PG), the essential component of cell wall, is usually modified with MurNAc O-acetylation and GlcNAc N-deacetylation, catalyzed by YvhB and XynD, respectively. In this study, increasing the two modifications in L. lactis F44 improved autolysis resistance by decreasing the susceptibility to PG hydrolases. Furthermore, both modifications were positively associated with overall cross-linkage, contributing to cell wall integrity. The robust cell wall rendered the yvhB/xynD-overexpression strains more acid resistant, leading to the increase of nisin production in fed-batch fermentations by 63.7 and 62.9%, respectively. Importantly, the structural alterations also reduced nisin adsorption capacity, resulting in reduction of nisin loss. More strikingly, the co-overexpression strain displayed the highest nisin production (76.3% higher than F44). Our work provides a novel approach for achieving nisin overproduction via extensive cell wall remodeling. [ABSTRACT FROM AUTHOR]

Farnesylation, which is catalyzed by farnesyltransferase, promotes membrane association of the modified protein and protein-protein interactions, and plays an important role in a number of physiological processes of pathogenic fungi, including stress response, environmental adaption and virulence. Lonafarnib is an orally bioavailable nonpeptide tricyclic farnesyltransferase inhibitor with excellent pharmacokinetic and safety profile. In the present study, we investigated the in vitro activities of lonafarnib alone or combined with azoles, including itraconazole, voriconazole, and posaconazole, against 22 strains of Aspergillus spp. and 18 strains of Exophiala dermatitidis via broth microdilution checkerboard technique. Lonafarnib alone was inactive against all isolates tested. However, synergistic effects between lonafarnib and itraconazole were observed in 86% Aspergillus strains and 94% E. dermatitidis strains. In addition, lonafarnib/posaconazole combination also exhibited synergism against 59% of Aspergillus strains and 100% E. dermatitidis strains. However, synergistic effects of lonafarnib/voriconazole were only observed in 32% Aspergillus strains and 28% E. dermatitidis strains. The effective working ranges of lonafarnib were 2--4 μg/ml and 1--4 μg/ml against Aspergillus isolates and E. dermatitidis isolates, respectively. No antagonism was observed in all combinations. This study demonstrated that lonafarnib could enhance the in vitro antifungal activity of itraconazole, posaconazole and voriconazole against Aspergillus spp. and E. dermatitidis, suggesting that azoles, especially itraconazole and posaconazole, combined with farnesyltransferase inhibitor might provide a potential strategy to the management of Aspergillus and Exophiala infections. However, further studies are warranted to elucidate the underlying mechanism and to investigate the potential of reliable and safe application in clinical practice. [ABSTRACT FROM AUTHOR]

NAD and NADP, a pivotal class of cofactors, which function as essential electron donors or acceptors in all biological organisms, drive considerable catabolic and anabolic reactions. Furthermore, they play critical roles in maintaining intracellular redox homeostasis. However, many metabolic engineering efforts in industrial microorganisms towards modification or introduction of metabolic pathways, especially those involving consumption, generation or transformation of NAD/NADP, often induce fluctuations in redox state, which dramatically impede cellular metabolism, resulting in decreased growth performance and biosynthetic capacity. Here, we comprehensively review the cofactor engineering strategies for solving the problematic redox imbalance in metabolism modification, as well as their features, suitabilities and recent applications. Some representative examples of in vitro biocatalysis are also described. In addition, we briefly discuss how tools and methods from the field of synthetic biology can be applied for cofactor engineering. Finally, future directions and challenges for development of cofactor redox engineering are presented. [ABSTRACT FROM AUTHOR]

The polyether ionophore antibiotic monensin is produced by Streptomyces cinnamonensis and is used as a coccidiostat for chickens and growth-promoting agent for cattle. Monensin biosynthetic gene cluster has been cloned and partially characterized. The GntR-family transcription factor DasR regulates antibiotic production and morphological development in Streptomyces coelicolor and Saccharopolyspora erythraea. In this study, we identified and characterized the two-level regulatory cascade of DasR to monensin production in S. cinnamonensis. Forward and reverse genetics by overexpression and antisense RNA silence of dasR revealed that DasR positively controls monensin production under nutrient-rich condition. Electrophoresis mobility shift assay (EMSA) showed that DasR protein specifically binds to the promoter regions of both pathway-specific regulatory gene monRII and biosynthetic genes monAIX, monE and monT. Semi-quantitative RT-PCR further confirmed that DasR upregulates the transcriptional levels of these genes during monensin fermentation. Subsequently, co-overexpressed dasR with pathway-specific regulatory genes monRI, monRII or monH greatly improved monensin production. [ABSTRACT FROM AUTHOR]

In this study, polyurethane foam (PUF) was chemically treated to immobilize Streptomyces thermotolerans 11432 for semi-continuous production of acetylisovaleryltylosin (AIV). Based on experimental results, positive cross-linked PUF (PCPUF) was selected as the most effective carrier according to immobilized cell mass. The effect of adsorption time on immobilized mass was investigated. AIV concentration (33.54 mg/l) in batch fermentations with immobilized cells was higher than with free cells (20.34 mg/l). In repeated batch fermentations with immobilized S. thermotolerans 11432 using PCPUF cubes, high AIV concentrations and conversion rates were attained, ranging from 25.56 to 34.37 mg/l and 79.93 to 86.31 %, respectively. Significantly, this method provides a feasible strategy for efficient AIV production and offers the potential for large-scale production. [ABSTRACT FROM AUTHOR]

Aspergillus fumigatus, an important human fungal pathogen, encounters high levels of reactive oxygen species following its ingestion by phagocytes. Reactive oxygen species are important mediators of the fungicidal activities of phagocytes. In yeasts, YAP1 encodes for transcriptional factors that contribute to their oxidative stress response and given the importance of the stress response, we hypothesized that the YAP1 homologue in A. fumigatus plays a similar role in this fungus. In this study, we found that Afyap1, the Yap1 homologue of A. fumigatus, confers protection against oxidative stress. Replacement of Afyap1 with the marker gene pyrG (ΔAfyap1) resulted in hypersensitivity of A. fumigatus to oxidants such as H2O2 and menadione. In contrast, an A. fumigatus strain harboring multiple-copy Afyap1 was resistant to these two oxidants as well as the oxidant diamide. However, ΔAfyap1 and strain harboring multiple-copy Afyap1 were comparable in their virulence to a wild-type A. fumigatus strain in a murine model of invasive pulmonary aspergillosis. Taken together, these results demonstrate that Afyap1 is involved in oxidative stress response but is not an essential virulence factor for A. fumigatus. [ABSTRACT FROM AUTHOR]

The cholesterol-lowering agents known as statins have in vitro activities against human pathogenic fungi, such as Candida species, Cryptococcus neoformans, and Zygomycetes. Synergy between statins and azoles against these fungi has also been reported. We evaluated the in vitro activities of two statins, lovastatin and simvastatin, alone and in combination with azoles and amphotericin B, against clinical isolates of Aspergillus spp. A disk diffusion assay showed that both statins were active against Aspergillus spp. The minimal inhibitory concentration (MIC) ranges for lovastatin and simvastatin against Aspergillus spp. were 16 to >256 µg/ml and 4 to >256 µg/ml, respectively. Although both statins were fungicidal for A. fumigatus, the MICs were vastly higher than clinically achievable concentrations. The results of a combined agar dilution-Epsilometer test as well as a disk diffusion assay showed that neither statin had any effect on the in vitro activities of itraconazole, voriconazole, or amphotericin B against Aspergillus spp. [ABSTRACT FROM AUTHOR]

Penicillium marneffei is an important thermal dimorphic fungus that is endemic to Southeast Asia and China and causes penicilliosis, an AIDS-defining disease. Dimorphic switching is considered an important growth characteristic associated with its pathogenicity. In recent years, the molecular mechanisms underlying both dimorphic switching and monomorphic growth have been studied. However, little is known about the physical and chemical factors that impact either dimorphic switching or monomorphic growth of this organism. Further, the natural history of the disease is unclear. Our experiments focus upon the effects of temperature, pH and salinity on both growth phases of P. marneffei. We compared 11 isolates of P. marneffei and found that all could grow at a wide temperature range (8.0-39.8°C), but growth was dramatically inhibited at 40°C. The morphological switch from hyphae to yeast growth was initiated at 32°C. However, the sensitivity to elevated temperatures during this transition varied among isolates. Both hyphae and yeast growth forms grew much better at acidic (pH 5, 6) and neutral pH than at alkaline conditions. While similar sensitivities were observed at high concentrations of NaCl and CaCl2, in general, yeast cells displayed a greater sensitivity to both compounds. Our data demonstrate that isolate differences occur in growth patterns. Importantly, the growth requirements defined in our study may shed light on the environmental conditions that favor its survival, a subject that is not completely resolved in the current literature. [ABSTRACT FROM AUTHOR]