DNA Separation Research Articles

Parallelized continuous flow dielectrophoretic separation ofDNA.

Numerous microfluidic separation applications have been shown in the past years providing a fast analysis of biological samples like DNA or proteins. Microfluidic separation based on dielectrophoresis (DEP), that is the migration of a polarizable object in an inhomogeneous electric field, provides numerous advantages. However, the main drawback of DEP separation devices is that they are not sufficient for large-scale sample purification due to the lack of high sample throughput. In this work, we present for the first time a microfluidic device with two parallelized dielectrophoretic separations of (biological) samples smaller than 1µm. The separation is carried out by means of insulator-based DEP, that is an insulating ridge reduced the flow through height and thus created a nanoslit at which the selective DEP forces occur. The device consists of a cross injector, two parallel operation regions and separate harvesting reservoirs where the samples are collected. Each DEP operation region contains an insulating ridge. We successfully demonstrate the separation of 100 and 40nm beads and 10 and 5kbp DNA with a separation purity of more than 80%. This states the proof-of-concept for up-scaling of dielectrophoretic separation by parallelization. As the present technique is virtually label-free, it offers a fast purification, for example in the production of gene vaccines.

Mechanistic Insights into the Phase Separation Behavior and Pathway-Directed Information Exchange in all-DNA Droplets.

Liquid-liquid phase separation provides a versatile approach to fabricating cell-mimicking coacervates. Recently, it was discovered that phase separation of single-stranded DNA (ssDNA) allows for forming protocells and microgels in multicomponent systems. However, the mechanism of the ssDNA phase separation is not comprehensively understood. Here, we present mechanistic insights into the metal-dependent phase separation of ssDNA and leverage this understanding for a straightforward formation of all-DNA droplets. Two phase separation temperatures are found that correspond to the formation of primary nuclei and a growth process. Ca2+ allows for irreversible, whereas Mg2+ leads to reversible phase separation. Capitalizing on these differences makes it possible to control the information transfer of one-component DNA droplets and two-component core-shell protocells. This study introduces new kinetic traps of phase separating ssDNA that lead to new phenomena in cell-mimicking systems.

Endogenous Stimuli-Responsive Autonomous Separation of Dual-Targeting DNA Guided Missile from Nanospacecraft for Intelligent Targeted Cancer Therapy.

Most conventional chemotherapeutics indiscriminately kill both cancerous and healthy cells and cause toxic side effects, limiting the maximum tolerated dose and thereby compromising therapeutic efficacy. To address this challenge, here dual-targeting intelligent DNA guided missile (GM)-integrated nanospacecraft (NSC) (abbreviated as GM-NSC) is demonstrated for staged chemotherapeutic drug delivery exclusively into cancer cells and then mitochondria (not into healthy cells). GM-NSC is essentially a core/shell nanocomposite composed of gold nanoparticles (AuNPs) surrounded by a high-density multilayer DNA crown that is self-assembled from DNA tetrahedral units (DNA Tetra) in a highly ordered manner. Each tetrahedral structural unit is equipped with three functional components: a cancer cell-targeting aptamer pointing toward the outside environment, a hidden mitochondria-targeting triphenylphosphonium (TPP), and an explosive bolt (E-bolt). GM-NSC can remain intact in fetal bovine serum solution over 12 h and has 53-fold improved systemic stability. Each GM-NSC accommodates 1250 anticancer doxorubicin (Dox), achieving a 48-63-fold improved drug payload capacity. When systemically administrated into a tumor-bearing xenograft murine model, Dox-loaded GM-NSC enters into tumor sites with 18-fold improved specificity followed by autonomous separation of GMs from the NSC core and specific mitochondrial accumulation due to the explosion of E-bolt upon stimuli of endogenous miRNAs. About 80% of Dox uptaken is transferred into mitochondria and induces mitochondria-mediated apoptosis. As a result, the growth of malignant tumor is almost 100% inhibited without detectable toxicity to healthy tissues. Due to the desirable systemic stability, good biocompatibility, high cargo loading capability, satisfactory in vivo biodistribution, and therapeutic efficacy without adverse effects, intelligible GM-NSC is expected to become an alternative drug delivery system for precision cancer therapy.

Cancer Classification Based on the Features of Itemset Sequence Pattern of TP53 Protein Code Using Deep Miden - KNN

Cancer is a disease that is still difficult to identify up to today. One of the causes of cancer is genetic modification that because of mutations in p53 gene. Healthy cells have a p53 wild type protein (normal) that is able to manage DNA separation. If DNA mutates, it will be difficult to detect cancer because the composition of the protein has changed. Bioinformatics is a combination of biology and information engineering (TI) that is utilized to manage data. One of the applications of data mining in bioinformatics is the development of pharmaceutical and medical industries. Data mining classification can use variety of methods including K-Nearest Neighbor (KNN), C45, ID3, and several other methods. One of the most reliable data classification methods is KNN. In this study, the development used two algorithms. The first was with the modification of the k-fold method, which divided two data into training data and test data, in which test-1 data and test-2 data were made into slices. The second was by a method for selecting an itemset sequence pattern that had the largest Gain Information, either 2 itemsets, 3 itemsets, and so on (Deep Miden). The best accuracy result of 96.00% was obtained through the process of computation testing in the server based on variations in terms of the number of patterns of Deep Miden itemset sequences and several k values on KNN classification method.

Designed assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade

AbstractIn this paper, we introduce a novel encapsulation system for DNA oligonucleotides. Supramolecular assembly of melamine cyanurate encapsulates DNA at pH 7 and start to release it at pH less than 6.5. We study the assembly and disassembly in time in specially designed reaction‐diffusion system. Magnesium ions allow spatial separation of DNA with the highest DNA concentration in the core of melamine cyanurate capsule. Molecular dynamics (MD) simulation shows that DNA acts as a nucleation centre for melamine cyanurate. Dataset of fluorescent images analysed by machine learning algorithms indicates correlation between structure of melamine cyanurate capsules for DNA trapping and concentration of magnesium ions. The concentration of magnesium ions can be recognized with 96% accuracy proving that all environmental conditions are extremely important during the self‐assembly and should be considered for laboratory and industrial applications of the suggested approach. Moreover, the encapsulated DNA can undergo a cascade reaction consisting of hybridization with complementary strand and its cleavage at a designated site. This reactivity opens a fresh avenue for various applications in biosensing, diagnostics, DNA compartmentalization, and even gives new hints for the origin‐of‐life questions.

Evaluation of Cassava (Manihot esculenta) and Sweet Potato (Ipomea batatas) Starch from South East Nigeria in the Separation of Deoxyribonucleic Acids as Alternative to Agarose Gel

Gel electrophoresis technique is an indispensable tool in biotechnology and among other related fields for separation of nucleic acids and proteins. This study determined the potential of selected cassava and sweet potato starch in the separation of DNA as alternative to agarose gel. The sample pH, gelling temperature and time were determined by Light transmittance method proposed by Craig et al. [1] Standard electrophoresis procedure was used for the starch gel electrophoresis. The result showed that composite starch gelled within 18-21 minutes while agarose and agar-agar gelled after 12 minutes. Cassava starch blended with agar-agar gelled at a temperature of 58oC while sweet potato starch blended with agar-agar gelled between 35oC - 47oC. Agarose and agar-agar maintained 54oC and 53oC respectively. There was no significant difference (P > 0.05) in pH value of the composite starch when compared to 1% agarose gel. Unblended starch samples did not form solid gel except when blended with some amount of agar-agar or agarose powder. Cassava and sweet potato composite starch formed good gel strength at 3% (2.2 g of starch and 0.8 g of agar-agar) but solid gel at 4% (3.6 g of starch and 0.8 g of agar-agar). This study demonstrated the possibilities for agarose cost reduction by 60% when cassava starch (3.6 g) was blended with 0.4 g of agarose. The cassava composite starch (4%) separated DNA molecules comparably to that of 1% agarose. Therefore, the use of these cheaper, accessible and readily available blended starch sources is highly recommended for separation of biomolecules such as DNA.

Recovery of integrated and surface trace DNA from illicit drug tablets

In many parts of the world, tablets are a commonly encountered form of illicit drug preparation. Whilst previous research has investigated the feasibility of detecting trace DNA on illicit drug capsules, this has not been performed for tablets. Tablets have a unique substrate surface and therefore the amount of DNA transferring to them and persisting on them may be different to capsules; there may also be differences in the collection efficiency and the outcome of downstream DNA processing and analysis steps. The ability to profile the DNA from individuals who handled tablets during their preparation and distribution would add another level of discrimination between various drug seizures or corroborate chemical profiling outcomes which may link various seizures to a common origin. DNA from two different individuals (male and female) was added to the tablets in two stages. Firstly, tablet powder was spiked with DNA from one individual to mimic the situation where DNA traces are incorporated during the drug synthesis or final drying stages. The powder was then pressed into tablets in a clean environment without intentional addition of DNA. Subsequently, a second individual counted out the tablets into bags of ten to mimic the preparation for distribution at a user level. The exterior of the tablet was swabbed and then the entire tablet and the swab were put through separate DNA extractions, yielding two DNA extracts for each tablet. Swabs of the exterior tablet surface yielded single source DNA profiles that identified the tablet handler in 100 % of samples. The tablet extract yielded the donor of the DNA intentionally added within the drug powder in 80% of samples with varying levels of support, however contributions of the exterior handler were detected in 60 % of samples. The identification of individuals potentially involved in the synthesis of the drugs compared to the distribution of the tablets will provide invaluable strategic intelligence related to illicit drug investigations and to law enforcement agencies.

Comparison of swab types & elution buffers for collection and analysis of intact cells to aid in deconvolution of complex DNA mixtures

Heightened sensitivity of forensic DNA techniques has led to an increased variety of samples tested, often yielding complex DNA mixtures, in turn making the interpretation of profiling results more complicated. Currently, there is no prescribed upstream laboratory method to separate complex DNA mixtures by their contributors; therefore, a method is needed that could reduce mixtures into their component parts. Various cell sorting applications have the potential to be this method, if intact cells can be reliably obtained from forensic samples. Here, the effects of elution buffer and swab substrate on the recovery of intact, human, white blood cells from dried blood samples were evaluated. Approximately 328,000 cells per swab were deposited onto cotton, flocked, and dissolvable swabs. The whole-cell elution of the dried samples was evaluated with water, phosphate buffered saline, and AutoMACS® elution buffers. We demonstrate that AutoMACS® buffer is superior for the elution of intact cells, compared to phosphate buffered saline and water. When swab type was considered, the highest yield of intact cells resulted from flocked swabs, as opposed to cotton or dissolvable swabs.

Topology and kinetics of R-loop formation

R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. They can be formed upon “invasion” of an RNA strand into a DNA duplex, during which the RNA displaces the homologous DNA strand and binds the complementary strand. R-loops have many significant beneficial or deleterious biological effects, so it is important to understand the mechanisms for their generation and processing. We propose a model for co-transcriptional R-loop formation, in which their generation requires passage of the nascent RNA “tail” through the gap between the separated DNA strands. This passage becomes increasingly difficult with lengthening of the RNA tail. The length of the tail increases upon increasing distance between the transcription start site and the site of R-loop initiation. This causes reduced yields of R-loops with greater distance from the transcription start site. However, alternative pathways for R-loop formation are possible, involving either transient disruption of the transcription complex or the hypothetical formation of a triple-stranded structure, as a “collapsed R-loop.” These alternative pathways could account for the fact that in many systems R-loops are observed very far from the transcription start site. Our model is consistent with experimental data and makes general predictions about the kinetics of R-loop formation.

Mechanisms of phase-separation-mediated cGAS activation revealed by dcFCCS.

Cyclic GMP-AMP synthase (cGAS), as a DNA sensor, plays an important role in cGAS-STING pathway, which further induces expression of type I interferon as the innate immune response. Previous studies reported that liquid-liquid phase separation (LLPS) driven by cGAS and long DNA is essential to promote catalytic activity of cGAS to produce a second messenger, cyclic GMP-AMP (cGAMP). However, the molecular mechanism of LLPS promoting cGAS activity is still unclear. Here, we applied dual-color fluorescence cross-correlation spectroscopy (dcFCCS), a highly sensitive and quantitative method, to characterize phase separation driven by cGAS and DNA from miscible individual molecule to micronscale. Thus, we captured nanoscale condensates formed by cGAS at close-to-physiological concentration and quantified their sizes, molecular compositions and binding affinities within condensates. Our results pinpointed that interactions between DNA and cGAS at DNA binding sites A, B, and C and the dimerization of cGAS are the fundamental molecular basis to fully activate cGAS in vitro. Due to weak binding constants of these sites, endogenous cGAS cannot form stable interactions at these sites, leading to no activity in the absence of LLPS. Phase separation of cGAS and DNA enriches cGAS and DNA by 2 to 3 orders of magnitude to facilitate these interactions among cGAS and DNA and to promote cGAS activity as an on/off switch. Our discoveries not only shed lights on the molecular mechanisms of phase-separation-mediated cGAS activation, but also guided us to engineer a cGAS fusion, which can be activated by 15bp short DNA without LLPS.

Synthesis of magnetic Fe3O4@Al3+ particles and its application in DNA extraction

The rapid nucleic acid extraction is essential, particularly the communicable diseases pandemic. In this work, aluminum modified Fe3O4 (Fe3O4@Al3+) particles were successfully synthesized by solvthermal method, epoxidation, covalent binding of iminodiacetic acid and Al3+ ions coordination for DNA extraction. Fe3O4@Al3+ particles could greatly improve the efficiency of DNA extraction and the extraction could be totally completed within 15 minutes at the optimum condition. The simple and rapid method is mainly based on the Fe3O4@Al3+ particles, which have large specific surface area, superparamagnetism, and Al3+ ions affinity to DNA. Additionally, several characterizations were carried out to further investigate the features of Fe3O4@Al3+ particles. According to SEM image, the average dimension of monodispersed Fe3O4@Al3+ spheres was around 200 nm. XPS results showed the existence of Al3+ on the surface of Fe3O4 particles, which further demonstrated the success of metal chelation in this material synthesis. The XRD patterns indicated that the Fe3O4@Al3+ particles were the inverse spinel structure as the bare Fe3O4 particles. Good magnetism of Fe3O4@Al3+ particles determined by VSM indicated that this material could be easily separated from the reaction system. To summarize, Fe3O4@Al3+ particles is expected to play an important role in future DNA extraction due to remarkable performance. Highlights The DNA separation media Fe3O4@Al3+ particles were successfully synthesized. DNA adsorption was effectively achieved by Fe3O4@Al3+ particles based on metal chelation. DNA extraction was significantly boosted by Fe3O4@Al3+ particles.

A Turn Off Fluorescence Probe Based on Carbon Dots for Highly Sensitive Detection of BRCA1 Gene in Real Samples and Cellular Imaging.

In this research, DNA-modified carbon dots (CDs) were exploited to construct a fluorescence assay for breast cancer genes (BRCA1, a potential marker for cancer diagnosis) detection. For this purpose, water-soluble synthesized CDs were functionalized with 19 mer-modified oligonucleotides (capture probe). By adding the DNA target, the specific binding between the DNA probe and DNA target causes fluorescence quenching. The assay displayed a fine capability of sensing the BRCA1 gene with a linear range (R2 = 0.9918) of 36 attomolar (aM) to 532 femtomolar (fM) and a detection limit of 2 attomolar. This homogeneous process does not need additional separation and washing steps of un-hybridized DNA. To assess the selectivity, the prepared biosensor responses were evaluated in solutions containing single-base mismatched DNA sequences, three-base mismatched DNA sequences, or non-complementary DNA sequences, separately. To demonstrate the practical application of the designed biosensor, the extracted DNA from blood samples of breast cancer patients was utilized as real samples. When the CDs-DNA bioassay was exploited in the imaging of MCF-7 cancer cells, strong fluorescence emission was observed. After incubation times, both the cells' size and shape remained unchanged. The results validated that the CDs are an extremely great bioimaging candidate in disease diagnosis, biomedicine investigation, and managing cancer diseases.

Periodontal disease progression and gene polymorphisms: results after 3 years of active periodontal treatment.

Although non-surgical periodontal treatment is considered the gold standard, a subgroup of patients displays recurrence/progression of periodontitis after treatment. The aim of the present prospective study was to assess the effect of IL-6 -572 G/C and IL-10 -592 C/A gene polymorphisms on the risk of disease recurrence/progression at 3 years following non-surgical periodontal treatment. Thirty-seven patients diagnosed with chronic periodontitis received oral hygiene instructions and non-surgical periodontal treatment and were monitored for 3 years. All individuals were clinically evaluated for PPD, CAL and BOP at baseline and 3 years. Based on the clinical findings at 3 years, all subjects were considered either "at risk" or "not at risk" of periodontal disease progression based on specific criteria. Blood samples were collected at baseline and genotyping of the polymorphisms in IL-6 (rs1800796) and IL-10 (rs1800872) genes were performed by PCR. Following DNA separation and genotyping, 70.3% of the patients were homozygous carriers of the IL-6 -572G and 45.9% were carriers of the IL-10 -592A allele. Individuals at risk of disease progression ranged from 16.2% to 56.8% based on the criteria used. IL-6 -572 G/C and IL-10 -592 C/A polymorphisms were not associated with an increased risk of further disease progression (P>0.05) when the three criteria were examined. All examined periodontal clinical measures were significantly improved (P<0.05) after treatment. Males showed a significantly higher risk of disease progression than females when full-mouth BOP ≥30% was considered (P=0.008). Within the limitations of this 3-year prospective study, individuals susceptible to periodontal disease as determined by the presence of the IL-6 -572GG genotype or the IL-10 -592A allele were not associated with an increased risk of further disease progression and the potential need for further treatment following non-surgical periodontal treatment. Males were more prone to be at risk of disease progression than females.

Vacuolar fragmentation promotes fluxes of microautophagy and micronucleophagy but not of macroautophagy

Vacuoles and lysosomes are organelles involved in the degradation of cytoplasmic proteins and organelles. Vacuolar morphology is dynamically regulated by fission and fusion in budding yeast. Vacuolar fusion is elicited in nutrient-depleted conditions and mediated by inactivation of target of rapamycin complex 1 (TORC1) protein kinase. However, it is unknown whether and how vacuolar morphology affects macroautophagy and microautophagy, which are induced by nutrient starvation and TORC1 inactivation. Here, we developed a system to control vacuolar fission in budding yeast. Vacuolar fragmentation promoted microautophagy but not macroautophagy. Vacuolar fragmentation caused multiple nucleus–vacuole junctions. Multiple vacuoles caused by vacuolar fragmentation also improved micronucleophagy (microautophagic degradation of a portion of the nucleus). However, vacuolar morphology did not impact nucleolar remodeling, condensation of the rDNA (rRNA gene) region, or separation of ribosomal DNA from nucleolar proteins, which is evoked by TORC1 inactivation. Thus, this study provides insights into the impacts of vacuolar/lysosomal morphology on macroautophagy and microautophagy.

Nonlinear electrophoretic velocity of DNA in slitlike confinement.

We have applied zero-time-averaged alternating electric fields to DNA molecules in a cross-shaped nanofluidic slit. We observed a net drift of DNA molecules, the magnitude of which depends on the square of the electric field amplitude. From the rate of accumulation of DNA at the center of the device, we derive an estimate for the second-order electrophoretic mobility, μ_{2}. We observe that focusing is absent at a dipole rotation frequency >20 Hz, which suggests that μ_{2} depends on the frequency of the alternating fields. The observation of a nonzero μ_{2} raises the possibility of frequency-dependent electrophoretic DNA separation by length achievable in the absence of a sieving matrix.

Sequence to size-based separation using microfluidic electrophoresis for targeted cell-free DNA analysis

The aim of this research is to present a new method to identify and separate target DNA of the same size, in base pairs (bp), into different sizes based on the targeted sequences. This sequence-specific analysis can then be used to evaluate the presence of multiple targeted analytes in a sample without the need for fluorescence detection. This work displays the feasibility of this method using multiple different 150 bp target sequences separated via microfluidic electrophoresis into 230 bp to 330 bp peaks. Using a combination of denaturation, hybridization, ligation, purification, and universal amplification, this represents a simple, robust method for targeted analysis of short DNA sequences. This work shows a limit of detection of 3 pg (∼1.825 x 107 copies) of input DNA using 20 PCR cycles and the ability for the method to be used for short DNA sequences extracted from a plasma sample, most importantly cell-free DNA. Overall, this method has the potential to be used for mutation detection and multiplexed analysis without the need for multiple fluorophores or significant optimization due to varying melting temperatures between PCR primers and can qualitatively evaluate the presence of specific target sequences in a variety of molecular diagnostic applications.

Ultrasensitive immuno-PCR for detecting aflatoxin B1 based on magnetic separation and barcode DNA

It was desired to develop the ultrasensitive and efficient strategy for detecting ultratrace aflatoxin B1 (AFB1) and protecting consumers' health. In this study, a magnetic immuno-PCR method (MIPCR) based on the barcode DNA was described and evaluated for detecting AFB1 in agricultural by-product samples. Under the optimal MIPCR, the limit of detection (LOD) was 0.01 pg mL−1, the half inhibitive concentration (IC50) was 1.72 pg mL−1, and the detection range was between 0.01 and 100 pg mL−1. The LOD and IC50 showed 480-fold and 21-fold lower than that of ELISA, respectively. The sensitivity of MIPCR had reached an ultratrace level and considerably improved. The reasonable specificity, precision and accuracy had been demonstrated. Furthermore, the high reliability and applicability of the MIPCR had been further confirmed by the good correlation of LC-MS/MS for the authentic samples. The proposed MIPCR had significantly shortened the analytical procedure, testing time and workload through the powerful probes and magnetic separation, which indicated the high-efficiency performance. This study could provide an alternative approach to detect the AFB1 contamination, and a critical reference for the ultrasensitive and efficient detection of other hazardous chemicals.

Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate.

DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.

Article Review: Staphylococcus Aurous Virulence Factors and it´s Resistance to Antibiotics

Staphylococcus aureus is naturally colonizing the skin and the naris of healthy people and Staphylococcus aureus exhibits different surface factors of the cell, which play a role in their virulence. This study explained the increasing β-lactamase secrtion by Methicillin Resistant. S. aureus primarily decreases the antibiotic affect, and Methicillin Resistant. S. aureus (MRSA) has increasingly become the most prevalent resistance pathogens in the world. This study stated that Quinolones function antibacterial by inhibiting bacterial topoisomerases, important in the removal of DNA super-coiling and separation of concatenated DNA-strands.

Ileal Microbiota Alters the Immunity Statues to Affect Body Weight in Muscovy Ducks.

The ileum is mainly responsible for food absorption and nutrients transportation. The microbes in its intestinal lumen play an essential role in the growth and health of the host. However, it is still unknown how the ileal microbes affect the body weight of the host. In this study, we used Muscovy ducks as an animal model to investigate the relationship between the ileal microbes and body weight and further explore the potential mechanism. The ileum tissue and ileal contents of 200 Muscovy ducks were collected for mRNA extraction and real-time quantitative PCR, as well as DNA separation and 16S rRNA gene sequencing. With body weight being ranked, the bottom 20% (n = 40) and top 20% (n = 40) were set as the low and high groups, respectively. Our results showed that in the ileum of Muscovy ducks, the Bacteroides, Firmicutes, and Proteobacteria were the predominant phyla with the 10 most abundant genera, namely Candidatus Arthromitus, Bacteroides, Streptococcus, Vibrio, Romboutsia, Cetobacterium, Clostridium sensu stricto 1, Terrisporobacter, Escherichia-Shigella, and Lactobacillus. We identified Streptococcus, Escherichia-Shigella, Candidatus Arthromitus, Bacteroides, Faecalibacterium, and Oscillospira were closely correlated to the growth of Muscovy ducks. Streptococcus and Escherichia-Shigella were negatively related to body weight (BW), while Candidatus Arthromitus, Bacteroides, Faecalibacterium, and Oscillospira were positively associated with BW. In addition, we found that the relative expression levels of tight junction proteins (Claudin 1, Claudin 2, ZO-1 and ZO-2) in the high group showed an upward trend, although this trend was not significant (P > 0.05). The expression of pro-inflammatory factors (IL-1β, IL-2 and TNF-α) decreased in the high group, while the anti-inflammatory factor IL-10 increased. Of course, except IL-2, these differences were not significant (P > 0.05). Finally, the correlation analysis showed that Escherichia-Shigella was significantly positively correlated with IL-1β (P < 0.05). These findings may provide fundamental data for the development of next-generation probiotics and assist the development of strategies for changing the gut microbiota to promote the growth performance in the duck industry.