The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities ...influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.
Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable ...physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.
We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster.
The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.
Nonribosomal peptide synthetases (NRPSs) are a class of cytosolic enzymes that synthesize a range of bio-active secondary metabolites including antibiotics and siderophores. They are widespread among ...both prokaryotes and eukaryotes but are considered rare among animals. Recently, several novel NRPS genes have been described in nematodes, schistosomes, and arthropods, which led us to investigate how prevalent NRPS genes are in the animal kingdom. We screened 1059 sequenced animal genomes and showed that NRPSs were present in 7 out of the 19 phyla analyzed. A phylogenetic analysis showed that the identified NRPSs form clades distinct from other adenylate-forming enzymes that contain similar domains such as fatty acid synthases. NRPSs show a remarkably scattered distribution over the animal kingdom. They are especially abundant in rotifers and nematodes. In rotifers, we found a large variety of domain architectures and predicted substrates. In the nematode Plectus sambesii, we identified the beta-lactam biosynthesis genes L-δ-(α-aminoadipoyl)-L-cysteinyl-D-valine synthetase, isopenicillin N synthase, and deacetoxycephalosporin C synthase that catalyze the formation of beta-lactam antibiotics in fungi and bacteria. These genes are also present in several species of Collembola, but not in other hexapods analyzed so far. In conclusion, our survey showed that NRPS genes are more abundant and widespread in animals than previously known.
Fluoroquinolone (FQ) is a potent antibiotic class. However, resistance to this class emerges quickly which hinders its application. In this study, mechanisms leading to the emergence of ...multidrug-resistant (MDR) Staphylococcus aureus (S. aureus) strains under FQ exposure were investigated.
S. aureus ATCC 29213 was serially exposed to ciprofloxacin (CIP), ofloxacin (OFL), or levofloxacin (LEV) at sub-minimum inhibitory concentrations (sub-MICs) for 12 days to obtain S. aureus -1 strains and antibiotic-free cultured for another 10 days to obtain S. aureus-2 strains. The whole genome (WGS) and target sequencing were applied to analyze genomic alterations; and RT-qPCR was used to access the expressions of efflux-related genes, alternative sigma factors, and genes involved in FQ resistance.
A strong and irreversible increase of MICs was observed in all applied FQs (32 to 128 times) in all S. aureus-1 and remained 16 to 32 times in all S. aureus-2. WGS indicated 10 noticeable mutations occurring in all FQ-exposed S. aureus including 2 insdel mutations in SACOL0573 and rimI; a synonymous mutation in hslO; and 7 missense mutations located in an untranslated region. GrlA, was found mutated (R570H) in all S. aureus-1 and -2. Genes encoding for efflux pumps and their regulator (norA, norB, norC, and mgrA); alternative sigma factors (sigB and sigS); acetyltransferase (rimI); methicillin resistance (fmtB); and hypothetical protein BJI72_0645 were overexpressed in FQ-exposed strains.
The emergence of MDR S. aureus was associated with the mutations in the FQ-target sequences and the overexpression of efflux pump systems and their regulators.
Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen ...generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. Prevotella was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to Prevotella. Besides, Prevotella possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in E. coli. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5–6.5, temperature 40–50 °C, and was capable to be used in practices. Based on these findings, we confirm that Prevotella plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.
A bibliometric analysis of 309 publications related to Education 4.0 published in both Scopus and Web of Science (WoS) databases has been conducted to analyze the development of this research field ...since the first articles published in 2017. Although being an emerging field, the number of publications increased quickly. Scholars from developing countries (i.e., Malaysia, Indonesia, Mexico, Brazil, and Philippines) are among the most productive authors, but internal and cross-country collaborations between them are very limited. Quality of the publication collection is not high as within the top ten most popular journals, five journals are not qualified to the Scopus database since 2020, and only three journals belong to the WoS core collections. Research topics related to Education 4.0 can be classified into five main clusters, including application of modern technologies on Education 4.0, effects of Industry 4.0 on teaching and learning activities, Education 4.0 in engineering education, education innovations in Education 4.0, and empirical research and quantitative analyses using questionnaires on different aspects of Education 4.0.
As a successful solution applied to electrical discharge machining (EDM), powder-mixed electrical discharge machining (PMEDM) has been proposed as an upgrade of the EDM process. The optimization of ...the process parameters of PMEDM is essential and pressing. In this study, Taguchi methods and analysis of variance (ANOVA) were used to find the main parameters affecting surface roughness in the EDM process with SiC powder-mixed-dielectric of hardened 90CrSi steel. The PMEDM parameters selected were the powder concentration, the pulse-on-time, the pulse-off-time, the pulse current, and the server voltage. It was found that SiC powder exhibits positive effects on reducing surface roughness. The roughness obtained with the optimum powder concentration of 4 g/L was reduced by 30.02% compared to that when processed by conventional EDM. Furthermore, the pulse-off-time was found to be the most influential factor that gave an important effect on surface roughness followed by the powder concentration. The EDM condition including a powder concentration of 4 g/L, a pulse-on-time of 6 µs, a pulse-off-time of 21 µs, a pulse current of 8 A, and a server voltage of 4 V resulted in the best surface roughness.
The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel ...lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats’ rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes’ modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.
The blasting technique has been broadly utilized to prepare new surfaces for painting, engraving, etc., in industry. In fact, the minimization of the cleaning cost system is essential. However, the ...knowledge of this technique in terms of optimization has been poor so far. The aim of this study is to find the optimum replaced boron carbide nozzle diameter for the abrasive blasting system. The basis of the study is to find the replaced nozzle diameter to minimize the cost of the blasting system. Seven main parameters are adopted for examining their influences on the response and the optimum replaced nozzle diameter. The design of experiment (DOE) technique is utilized by using Minitab@19. The results reveal that the initial nozzle diameter has the strongest impact on the optimum replaced nozzle diameter. Furthermore, the proposed regression model has been found to be entirely insistent to the experiments. The utilization of this model can provide an effective way to simplify the calculation of the optimum initial nozzle diameter for boron carbide.
We aimed to investigate the microbial diversity, mine lignocellulose-degrading enzymes/proteins, and analyze the domain structures of the mined enzymes/proteins in humus samples collected from the ...Cuc Phuong National Park, Vietnam. Using a high-throughput Illumina sequencer, 52 Gbs of microbial DNA were assembled in 2,611,883 contigs, from which 4,104,872 open reading frames (ORFs) were identified. Among the total microbiome analyzed, bacteria occupied 99.69%; the five ubiquitous bacterial phyla included Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Acidobacteria, which accounted for 92.59%. Proteobacteria (75.68%), the most dominant, was 5.77 folds higher than the second abundant phylum Bacteroidetes (13.11%). Considering the enzymes/proteins involved in lignocellulose degradation, 22,226 ORFs were obtained from the annotation analysis using a KEGG database. The estimated ratio of Proteobacteria/Bacteroidetes was approximately 1:1 for pretreatment and hemicellulases groups and 2.4:1 for cellulases. Furthermore, analysis of domain structures revealed their diversity in lignocellulose-degrading enzymes. CE and PL were two main families in pretreatment; GH1 and GH3-FN3 were the highest domains in the cellulase group, whereas GH2 and GH43 represented the hemicellulase group. These results validate that natural tropical forest soil could be considered as an important source to explore bacteria and novel enzymes/proteins for the degradation of lignocellulose.
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