Other affiliations: Renmin University of China
Bio: Libing Dong is an academic researcher from Chinese Academy of Sciences. The author has contributed to research in topics: Growing season & Animal science. The author has an hindex of 4, co-authored 6 publications receiving 172 citations. Previous affiliations of Libing Dong include Renmin University of China.
TL;DR: The microfluidic streak plate is described, a facile method for high-throughput microbial cell separation and cultivation in nanoliter sessile droplets that led to the discovery of several species with high degradation efficiency including four Mycobacterium isolates and a previously unknown fluoranthene-degrading Blastococcus species.
Abstract: This paper describes the microfluidic streak plate (MSP), a facile method for high-throughput microbial cell separation and cultivation in nanoliter sessile droplets. The MSP method builds upon the conventional streak plate technique by using microfluidic devices to generate nanoliter droplets that can be streaked manually or robotically onto petri dishes prefilled with carrier oil for cultivation of single cells. In addition, chemical gradients could be encoded in the droplet array for comprehensive dose-response analysis. The MSP method was validated by using single-cell isolation of Escherichia coli and antimicrobial susceptibility testing of Pseudomonas aeruginosa PAO1. The robustness of the MSP work flow was demonstrated by cultivating a soil community that degrades polycyclic aromatic hydrocarbons. Cultivation in droplets enabled detection of the richest species diversity with better coverage of rare species. Moreover, isolation and cultivation of bacterial strains by MSP led to the discovery of several species with high degradation efficiency, including four Mycobacterium isolates and a previously unknown fluoranthene-degrading Blastococcus species.
TL;DR: An ultra-high throughput screening pipeline for lipase-producing strains based on fluorescence-activated droplet sorting (FADS) using a compact optical system that could be easily set up in an alignment-free manner is developed.
Abstract: Lipases are ubiquitous enzymes of great physiological significance that have been used extensively in multiple industries. Environmental microorganisms are a major source for the discovery of novel lipases with high catalytic efficiency and selectivity. However, current plate-based screening of lipase-producing strains is time consuming, labour intensive and inefficient. In this study, we developed an ultra-high throughput screening pipeline for lipase-producing strains based on fluorescence-activated droplet sorting (FADS) using a compact optical system that could be easily set up in an alignment-free manner. The pipeline includes droplet generation, droplet incubation, picoinjection of the fluorescence probe, and sorting of droplets with a throughput of 2 × 106 drops per h. We applied the pipeline to screen samples collected from different locations, including sediments from a hot spring in Tibet, soils from the Zoige wetland, contaminated soils from an abandoned oilfield, and a Chinese Daqu starter. In total, we obtained 47 lipase-producing bacterial strains belonging to seven genera, including Staphylococcus, Bacillus, Enterobacter, Serratia, Prolinoborus, Acinetobacter, and Leclercia. We believe that this FADS-based pipeline could be extended to screen various enzymes from the environment, and may find wide applications in breeding of industrial microorganisms.
TL;DR: A microfluidic device for automated sorting and cultivation of chemotactic microbes from pure cultures or mixtures that can be widely used in chemotaxis studies without necessarily relying on fluorescent labelling, and isolation of functional microbial species from various environments.
Abstract: We report a microfluidic device for automated sorting and cultivation of chemotactic microbes from pure cultures or mixtures. The device consists of two parts: in the first part, a concentration gradient of the chemoeffector was built across the channel for inducing chemotaxis of motile cells; in the second part, chemotactic cells from the sample were separated, and mixed with culture media to form nanoliter droplets for encapsulation, cultivation, enumeration, and recovery of single cells. Chemotactic responses were assessed by imaging and statistical analysis of droplets based on Poisson distribution. An automated procedure was developed for rapid enumeration of droplets with cell growth, following with scale-up cultivation on agar plates. The performance of the device was evaluated by the chemotaxis assays of Escherichia coli (E. coli) RP437 and E. coli RP1616. Moreover, enrichment and isolation of non-labelled Comamonas testosteroni CNB-1 from its 1:10 mixture with E. coli RP437 was demonstrated. The enrichment factor reached 36.7 for CNB-1, based on its distinctive chemotaxis toward 4-hydroxybenzoic acid. We believe that this device can be widely used in chemotaxis studies without necessarily relying on fluorescent labelling, and isolation of functional microbial species from various environments.
TL;DR: In this paper, the effect of eCO2 on N2O emissions from maize field under the free-air CO2 enrichment (FACE) conditions in the warm temperate zone was investigated.
Abstract: The elevated atmospheric CO2 concentration (eCO2) is expected to increase the labile C input to the soil, which may stimulate microbial activity and soil N2O emissions derived from nitrification and denitrification. However, few studies studied the effect of eCO2 on N2O emissions from maize field under the free-air CO2 enrichment (FACE) conditions in the warm temperate zone. Here, we report a study conducted during the 12th summer maize season under long-term eCO2, aiming to investigate the effect of eCO2 on N2O emissions. Moreover, we tested zero and conventional N fertilization treatments, with maize being grown under either eCO2 or ambient CO2 (aCO2). We hypothesized that N2O emissions would be increased under eCO2 due to changes in soil labile C and mineral N derived from C-deposition, and that the increase would be larger when eCO2 was combined with conventional N fertilization. We also measured the activities of some soil extracellular enzymes, which could reflect soil C status. The results showed that, under eCO2, seasonal N2O and CO2 emissions increased by 12.4–15.6% (p < 0.1) and 13.8–18.5% (p < 0.05), respectively. N fertilization significantly increased the seasonal emissions of N2O and CO2 by 33.1–36.9% and 17.1–21.8%, respectively. Furthermore, the combination of eCO2 and N fertilization increased the intensity of soil N2O and CO2 emissions. The marginal significant increase in N2O emissions under eCO2 was mostly due to the lower soil water regime after fertilization in the study year. Dissolved organic C (DOC) and microbial biomass C (MBC) concentration showed a significant increase at most major stages, particularly at the tasseling stage during the summer maize growth period under eCO2. In contrast, soil mineral N showed a significant decrease under eCO2 particularly in the rhizospheric soils. The activities of C-related soil extracellular enzymes were significantly higher under eCO2, particularly at the tasseling stage, which coincided with concurrent increased DOC and MBC under eCO2. We conclude that eCO2 increases N2O emissions, and causes a higher increase when combined with N fertilization, but the increase extent of N2O emissions was influenced by environmental factors, especially by soil water, to a great extent. We highlighted the urgent need to monitor long-term N2O emissions and N2O production pathways in various hydrothermal regimes under eCO2.
TL;DR: The metabolic benefits of Parabacteroides distasonis (PD) on decreasing weight gain, hyperglycemia, and hepatic steatosis in ob/ob and high-fat diet (HFD)-fed mice is demonstrated and succinate and secondary bile acids produced by P. distasonis played key roles in the modulation of host metabolism.
Abstract: Summary We demonstrated the metabolic benefits of Parabacteroides distasonis (PD) on decreasing weight gain, hyperglycemia, and hepatic steatosis in ob/ob and high-fat diet (HFD)-fed mice. Treatment with live P. distasonis (LPD) dramatically altered the bile acid profile with elevated lithocholic acid (LCA) and ursodeoxycholic acid (UDCA) and increased the level of succinate in the gut. In vitro cultivation of PD demonstrated its capacity to transform bile acids and production of succinate. Succinate supplementation in the diet decreased hyperglycemia in ob/ob mice via the activation of intestinal gluconeogenesis (IGN). Gavage with a mixture of LCA and UDCA reduced hyperlipidemia by activating the FXR pathway and repairing gut barrier integrity. Co-treatment with succinate and LCA/UDCA mirrored the benefits of LPD. The binding target of succinate was identified as fructose-1,6-bisphosphatase, the rate-limiting enzyme in IGN. The succinate and secondary bile acids produced by P. distasonis played key roles in the modulation of host metabolism.
TL;DR: An overview of the recent literature referring to the usage of bacteria as biodegraders is provided, barriers regarding the implementation of this microbial technology are discussed, and suggestions for further developments are provided.
Abstract: With the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.
TL;DR: Applications of droplet microfluidics in various fields of microbiology are presented: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains.
Abstract: Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.
University of Wisconsin-Madison1, University of Minnesota2, Montana State University3, Purdue University4, University of Tennessee5, Oak Ridge National Laboratory6, Joint BioEnergy Institute7, University of California, Santa Barbara8, University of Michigan9, Delft University of Technology10, Great Lakes Bioenergy Research Center11
TL;DR: This Review presents key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function.
Abstract: Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.
19 Aug 2021
Saarland University1, University of Parma2, Technical University of Denmark3, University of Giessen4, Pasteur Institute5, University of Lorraine6, Max Planck Society7, Goethe University Frankfurt8, University of Lisbon9, National Museum of Natural History10, Wageningen University and Research Centre11, University of Paris12, John Innes Centre13, University of Manchester14, University of Perugia15, University of Tübingen16, University of Strasbourg17, Jacobs University Bremen18, University Hospital Bonn19, University of Bristol20, Uppsala University21, University of Ljubljana22, Drugs for Neglected Diseases Initiative23, University of Dundee24, Novartis25
TL;DR: In this paper, the authors present a strategic blueprint to substantially improve our ability to discover and develop new antibiotics, and propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding.
Abstract: An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.