Second generation biofuel production has been appeared as a sustainable and alternative energy option. The ultimate aim is the development of an industrially feasible and economic conversion process ...of lignocellulosic biomass into biofuel molecules. Since, cellulose is the most abundant biopolymer and also represented as the photosynthetically fixed form of carbon, the efficient hydrolysis of cellulose is the most important step towards the development of a sustainable biofuel production process. The enzymatic hydrolysis of cellulose by suites of hydrolytic enzymes underlines the importance of cellulase enzyme system in whole hydrolysis process. However, the selection of the suitable cellulolytic enzymes with enhanced activities remains a challenge for the biorefinery industry to obtain efficient enzymatic hydrolysis of biomass. The present review focuses on deciphering the novel and effective cellulases from different environmental niches by unculturable metagenomic approaches. Furthermore, a comprehensive functional aspect of cellulases is also presented and evaluated by assessing the structural and catalytic properties as well as sequence identities and expression patterns. This review summarizes the recent development in metagenomics based approaches for identifying and exploring novel cellulases which open new avenues for their successful application in biorefineries.
Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform ...standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association, network analysis to identify polymicrobial clusters, and functional profiling. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature; and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.
•Fe(III)-minerals promoted granule formation in the anammox system.•Ferrihydrite enhanced nitrogen removal (>4%) in the absence of Fe(II).•Ferrihydrite promoted the retention of phylum planctomycetes ...in the reactor.•Ferrihydrite facilitated the community resistance to environmental stress.•Fe(III)-mineral had a limited effect on anammox metabolism under Fe(II) sufficiency.
Iron is a recognized physiological requirement for microorganisms but, for anaerobic ammonium oxidation (anammox) bacteria, its role extends well beyond that of a nutritional necessity. In this study, the function of two typical Fe(III)-minerals (ferrihydrite and magnetite) in anammox processes was evaluated in the absence/presence of Fe(II) by integrated network and metagenomics analyses. Results showed that Fe-(III) minerals addition increased the activity of cellular processes and pathways associated with granule formation, enabling the peak values of particle size to increase by 144% and 115%, respectively. Notably, ferrihydrite (5 mM) enhanced nitrogen removal by 4.8% and 4.1%, respectively, in the short-term and long-term absence of Fe(II). Ferrihydrite also promoted the retention of anammox bacteria affiliated with phylum Planctomycetes in the reactor, contributing to an 11% higher abundance with ferrihydrite amendment when compared with the control (without iron additions) in the short-term absence of Fe(II). Network-based analyses revealed that ferrihydrite facilitated the microbial community to form densely clustered and complex topologies to improve resistance to environmental disturbance (i.e., Fe(II) deficiency), and effectively increased the underlying cooperation and facilitation in the community. Metagenomic analysis revealed that there was limited promotion of anammox central metabolism by the extra addition of Fe(III)-minerals in the presence of Fe(II), highlighting the poor utilization of Fe(III)-minerals by anammox bacteria under Fe(II) sufficiency. This study deepens our understanding of the function of Fe(III)-minerals in anammox systems at the community and functional level, and provides a fundamental basis for developing Fe-based anammox enhancement technologies.
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•The whole fermentation of Suanyu was divided into 3 stages using OPLS-DA model.•The aroma markers of different fermentation stage were confirmed.•The characteristic flavor metabolic ...network of Suanyu was constructed.•The different metabolic roles of key microbes in flavor formation were elucidated.
Microbial metabolism is crucial for the flavor development of traditional Suanyu. A total of 21 characteristic volatile compounds of Suanyu were identified according to GC-MS combined with GC-O analysis. HCA results indicated that the whole fermentation process could be divided into three stages: raw material (fresh), initial fermentation (0–2 week) and the late fermentation (2–4 week). Moreover, nine flavor markers in different fermentation stages were revealed using the OPLS-DA model and VIP values. Furthermore, metagenomic sequencing was used to analyze the possible formation pathways of the characteristic flavor compounds and identify the key microorganisms related to flavor formation at the gene level. The top 10 bacterial genera associated with flavor formation were Staphylococcus, Enterococcus, Vibrio, Kocuria, Lactobacillus, Macrococcus, Streptococcus, Enterobacter, Lactococcus and Pediococcus, accounting for large parts of flavor formation of fermented Suanyu. This study is helpful to elucidate the different metabolic roles of microorganisms in flavor formation during fermentation.
The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not truly present in the sample. Contaminants ...come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam ( https://github.com/benjjneb/decontam ), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls.
Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants.
Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.
Domestic wastewater is a significant reservoir of antibiotic resistance genes, which pose environmental and public health risks. We aimed to define an antibiotic resistome signature, represented by ...core genes, i.e., shared by ≥ 90% of the metagenomes of each of three conceptual environmental compartments – wastewater (influent, sludge, effluent), freshwater, and agricultural soil. The definition of resistome signatures would support the proposal of a framework for monitoring treatment efficacy and assessing the impact of treated wastewater discharge into the environment, such as freshwater and agricultural soil.
Metagenomic data from 163 samples originating from wastewater (n = 81), freshwater (n = 58), and agricultural soils (n = 24) across different regions (29 countries, 5 continents), were analysed regarding antibiotic resistance diversity, based on annotation against a database that merged CARD and ResFinder databases. The relative abundance of the total antibiotic resistance genes (corresponding to the ratio between the antibiotic resistance genes and total reads number) was not statistically different between raw and treated wastewater, being significantly higher than in freshwater or agricultural soils. The latter had the significantly lowest relative abundance of antibiotic resistance genes. Genes conferring resistance to aminoglycosides, beta-lactams, and tetracyclines were among the most abundant in wastewater environments, while multidrug resistance was equally distributed across all environments. The wastewater resistome signature included 27 antibiotic resistance genes that were detected in at least 90% of the wastewater resistomes, and that were not frequent in freshwater or agricultural soil resistomes. Among these were genes responsible for resistance to tetracyclines (n = 8), macrolide-lincosamide-streptogramin B (n = 7), aminoglycosides (n = 4), beta-lactams (n = 3), multidrug (n = 2), sulphonamides (n = 2), and polypeptides (n = 1). This comprehensive assessment provides valuable insights into the dynamics of antibiotic resistance in urban wastewater systems and their potential ecological implications in diverse environmental settings. Furthermore, provides guidance for the implementation of One Health monitoring approaches.
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•Wastewater, freshwater, and agricultural soil resistomes were screened for shared genes.•Wastewater (influent, sludge, effluent) resistome signature comprised >50 genes.•For freshwater it was not possible to define a signature resistome.•In agricultural soil the resistome signature contained 12 genes.•27 wastewater resistome signature genes are proposed to chase wastewater impacts.
Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine ...virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus-host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.
Sketching methods offer computational biologists scalable techniques to analyze data sets that continue to grow in size. MinHash is one such technique to estimate set similarity that has enjoyed ...recent broad application. However, traditional MinHash has previously been shown to perform poorly when applied to sets of very dissimilar sizes. FracMinHash was recently introduced as a modification of MinHash to compensate for this lack of performance when set sizes differ. This approach has been successfully applied to metagenomic taxonomic profiling in the widely used tool sourmash gather. Although experimental evidence has been encouraging, FracMinHash has not yet been analyzed from a theoretical perspective. In this paper, we perform such an analysis to derive various statistics of FracMinHash, and prove that although FracMinHash is not unbiased (in the sense that its expected value is not equal to the quantity it attempts to estimate), this bias is easily corrected for both the containment and Jaccard index versions. Next, we show how FracMinHash can be used to compute point estimates as well as confidence intervals for evolutionary mutation distance between a pair of sequences by assuming a simple mutation model. We also investigate edge cases in which these analyses may fail to effectively warn the users of FracMinHash indicating the likelihood of such cases. Our analyses show that FracMinHash estimates the containment of a genome in a large metagenome more accurately and more precisely compared with traditional MinHash, and the point estimates and confidence intervals perform significantly better in estimating mutation distances.
Aims
Metagenomic next‐generation sequencing (mNGS) has been utilized for diagnosing infectious diseases. It is a culture‐free and hypothesis‐free nucleic acid test for diagnosing all pathogens with ...known genomic sequences, including bacteria, fungi, viruses and parasites. While this technique greatly expands the clinical capacity of pathogen detection, it is a second‐line choice due to lengthy procedures and microbial contaminations introduced from wet‐lab processes. As a result, we aimed to reduce the hands‐on time and exogenous contaminations in mNGS.
Methods and Results
We developed a device (NGSmaster) that automates the wet‐lab workflow, including nucleic acid extraction, PCR‐free library preparation and purification. It shortens the sample‐to‐results time to 16 and 18·5 h for DNA and RNA sequencing respectively. We used it to test cultured bacteria for validation of the workflow and bioinformatic pipeline. We also compared PCR‐free with PCR‐based library prep and discovered no differences in microbial reads. Moreover we analysed results by automation and manual testing and found that automation can significantly reduce microbial contaminations. Finally, we tested artificial and clinical samples and showed mNGS results were concordant with traditional culture.
Conclusion
NGSmaster can fulfil the microbiological diagnostic needs in a variety of sample types.
Significance and Impact of the Study
This study opens up an opportunity of performing in‐house mNGS to reduce turnaround time and workload, instead of transferring potentially contagious specimen to a third‐party laboratory.
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