Dissecting the microbial community structure of internal organs during the early postmortem period in a murine corpse model.

BACKGROUND: Microorganisms distribute and proliferate both inside and outside the body, which are the main mediators of decomposition after death. However, limited information is available on the postmortem microbiota changes of extraintestinal body sites in the early decomposition stage of mammalian corpses. RESULTS: This study investigated microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition in male C57BL/6 J mice by 16S rRNA sequencing. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 h than that at 0.5 or 4 h. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific. CONCLUSION: The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 h in internal organs may inform a new direction for organ transplantation.

Gut-Thyroid axis: How gut microbial dysbiosis associated with euthyroid thyroid cancer.

Thyroid cancer in humans has a fast-growing prevalence, with the most common lethal endocrine malignancy for unknown reasons. The current study was aimed to perform qualitative and quantitative investigation and characterization of the gut bacterial composition of euthyroid thyroid cancer patients. The fecal samples were collected from sixteen euthyroid thyroid cancer patients and ten from healthy subjects. The PCR-DGGE was conducted by targetting the V3 region of 16S rRNA gene, as well as real-time PCR for Bacteroides vulgatus, E.coli Bifidobacterium, Clostridium leptum and Lactobacillus were carried. High-throughput sequencing of V3+V4 region of 16S rRNA gene was performed on Hiseq 2500 platform on 20 (10 healthy & 10 diseased subjects) randomly selected fecal samples. The richness indices and comparative diversity analysis showed significant gut microbial modification in euthyroid thyroid cancer than control. At phylum level, there was significant enrichment of Firmicutes, Verrucomicrobia, while a significant decrease in Bacteroidetes was detected in the experimental group. At family statistics, significant high levels of Ruminococcaceae and Verrucomicrobiaceae, while the significant lower abundance of Bacteroidaceae, Prevotellaceae, Porphyromonadaceae, and Alcaligenaceae was after observed. It also found that the significantly raised level of Escherichia-Shigella, Akkermansia [Eubacterium]_coprostanoligenes, Dorea, Subdoligranulum, and Ruminococcus_2 genera, while significantly lowered genera of the patient group were Prevotella_9, Bacteroides and Klebsiella. The species-level gut microbial composition showed a significantly raised level of Escherichia coli in euthyroid thyroid cancer. Thus, this study reveals that euthyroid thyroid cancer patients have significant gut microbial dysbiosis. Moreover, Statistics (P<0.05) of each gut microbial taxa were significantly changed in euthyroid thyroid cancer patients. Therefore, the current study may propose new approaches to understanding thyroid cancer patients' disease pathways, mechanisms, and treatment.

The Novel Interplay between Commensal Gut Bacteria and Metabolites in Diet-Induced Hyperlipidemic Rats Treated with Simvastatin.

Hyperlipidemia is one kind of metabolic syndrome for which the treatment commonly includes simvastatin (SV). Individuals vary widely in statin responses, and growing evidence implicates gut microbiome involvement in this variability. However, the associated molecular mechanisms between metabolic improvement and microbiota composition following SV treatment are still not fully understood. In this study, combinatory approaches using ultrahigh-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF MS/MS)-based metabolomic profiling, PCR-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR), and 16S rRNA gene sequencing-based gut microbiota profiling were performed to investigate the interplay of endogenous metabolites and the gut microbiota related to SV treatment. A total of 6 key differential endogenous metabolites were identified that affect the metabolism of amino acids (phenylalanine and tyrosine), unsaturated fatty acids (linoleic acid and 9-hydroxyoctadecadienoic acid (9-HODE)), and the functions of gut microbial metabolism. Moreover, a total of 22 differentially abundant taxa were obtained following SV treatment. Three bacterial taxa were identified to be involved in SV treatment, namely, Bacteroidaceae, Prevotellaceae, and Porphyromonadaceae. These findings suggested that the phenylalanine and tyrosine-associated amino acid metabolism pathways, as well as the linoleic acid and 9-HODE-associated unsaturated fatty acid metabolism pathways, which are involved in gut flora interactions, might be potential therapeutic targets for improvement in SV hypolipidemic efficacy. The mass spectrometric data have been deposited to MassIVE (https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp). Username: MSV000087842_reviewer. Password: hardworkingzsr.

Potential use of molecular and structural characterization of the gut bacterial community for postmortem interval estimation in Sprague Dawley rats.

Once the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.

Microbiota Analysis of Eggshells in Different Areas and During Different Storage Time by Non-cultural Methods.

This study is to investigate and characterize the microbiota composition on eggshells from 3 different areas of Shaanxi province (Yulin, Hanzhong and Xi'an). The eggs were stored at 25 °C for 56 days and bacterial samples were collected from eggshells on day 0, 14, 28, 42 and 56. Denaturing gradient gel electrophoresis and high-throughput sequencing of 16S rRNA hypervariable region V3-V4 were performed. Alpha diversity was applied for analyzing the diversity of samples through 6 indices, including Observed-species, Chao1, Shannon, Simpson, ACE and Good's-coverage. Beta diversity was used to study the similarities or differences in the community composition of the samples. Totally, 36 phyla and 595 genera were classified by 16S rRNA gene sequencing. The composition of the microbial communities of different regions was quite different. Firmicutes (33-38% of total phyla) and Actinobacteria (36-61% of total phyla) were the most abundant phyla in all three regions. Proteobacteria were relatively more abundant (about 18% of total phyla) on eggs from Hanzhong. During storage time, the microbial communities mainly changed from Firmicutes to Actinobacteria on eggs from Yulin and Xi'an. Lactobacillus, Kocuria and Streptomyces were much higher at the genus level. Spoilage bacteria Staphylococcus, Streptococcus, Pseudomonas and Enterococcus were detected at the genus level. Campylobacter jejuni (< 1% of total bacteria), which might be related to human illness, was also detected. In conclusion, the structure, abundance, and composition of microbiota on eggshells differ among areas. The microbiota changed regularly during storage time. The current study may offer a new insight into bacterial species on eggshells.

Molecular characterization of gut microbial shift in SD rats after death for 30 days.

To observe the temporal shifts of the intestinal microbial community structure and diversity in rats for 30 days after death. Rectal swabs were collected from rats before death (BD) and on day 1, 5, 10, 15, 20, 25, and 30 after death (AD). Bacteria genomic DNA was extracted and V3 + V4 regions of 16S rRNA gene were amplified by PCR. The amplicons were sequenced at Illumina MiSeq sequencing platform. The bacterial diversity and richness showed similar results from day 1 to 5 and day 10 to 25 all presenting downtrend, while from day 5 to 10 showed slightly increased. The relative abundance of Firmicutes and Proteobacteria displayed inverse variation in day 1, 5, 10 and that was the former decreased, the latter increased. Bacteroidetes, Spirochaete and TM7 in day 15, 20, 25, 30 was significantly decline comparing with BD. Enterococcus and Proteus displayed reduced trend over day 1, 5, 10 and day 10, 15, 20, 25, respectively, while Sporosarcina showed obvious elevation during day 15, 20, 25. Accordingly, there was a certain correlation between intestinal flora succession and the time of death. The results suggested that intestinal flora may be potential indicator to aid estimation of post-mortem interval (PMI).

Molecular characterization of gut microbiota in high­lipid diet­induced hyperlipidemic rats treated with simvastatin.

Hyperlipidemia is a major risk factor for cardiovascular diseases. Simvastatin (SV), a cholesterol­lowering agent, has been widely used in the treatment of hyperlipidemia. Gut microbiota is known to influence drug response, including that to statins. However, the effect of SV on the gut microbiota of hyperlipidemic rats is not fully understood. To investigate the influence of SV on gut microbiota in hyperlipidemic rats, the molecular characterization of gut microbiota and the potential functions of genes involved in the downstream metabolic pathways were analyzed using high­throughput sequencing technology and the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States approach. The results revealed that SV treatment could reduce the gut microbial diversity and drive marked remodeling of the fecal bacterial community composition. At the phylum level, the relative abundance of Firmicutes and Actinobacteria was decreased following SV therapy, whereas that of Bacteroidetes was elevated. At the genus level, the percentage of the genera Bacteroides, Sutterella and Phascolarctobacterium was significantly increased, but that of Bifidobacterium, Ruminococcaceae_NK4A214, Ruminococcaceae_UCG­009, Intestinimonas and Tyzzerella was significantly decreased. Additionally, functional prediction analysis indicated that in the SV­associated microbiota, genes involved in energy, carbohydrate, amino acid and nucleotide metabolism likely exhibited enrichment. Briefly, to the best of our knowledge, the present study was the first to establish a profound and comprehensive association between the SV­induced alterations of the gut flora and the consequent influences of downstream metabolic pathways by gut microbiota. These findings suggested that the gut microbiota may contribute to the SV hypolipidemic efficacy in the progression of hyperlipidemia, which could provide insights for the prevention and treatment of hyperlipidemia.

Predicting postmortem interval based on microbial community sequences and machine learning algorithms.

Microbes play an essential role in the decomposition process but were poorly understood in their succession and behaviour. Previous researches have shown that microbes show predictable behaviour that starts at death and changes during the decomposition process. Research of such behaviour enhances the understanding of decomposition and benefits estimating the postmortem interval (PMI) in forensic investigations, which is critical but faces multiple challenges. In this study, we combined microbial community characterization, microbiome sequencing from different organs (i.e. brain, heart and cecum) and machine learning algorithms [random forest (RF), support vector machine (SVM) and artificial neural network (ANN)] to investigate microbial succession pattern during corpse decomposition and estimate PMI in a mouse corpse system. Microbial communities exhibited significant differences between the death point and advanced decay stages. Enterococcus faecalis, Anaerosalibacter bizertensis, Lactobacillus reuteri, and so forth were identified as the most informative species in the decomposition process. Furthermore, the ANN model combined with the postmortem microbial data set from the cecum, which was the best combination among all candidates, yielded a mean absolute error of 1.5 ± 0.8 h within 24-h decomposition and 14.5 ± 4.4 h within 15-day decomposition. This integrated model can serve as a reliable and accurate technology in PMI estimation.

Molecular characterization of alterations in the intestinal microbiota of patients with grade 3 hypertension.

Hypertension has become a major risk factor for many diseases, including cardiovascular, cerebrovascular and kidney disorders. It has been reported that the composition of human gut microbiota is changed during the progression of cardiovascular and kidney diseases. The current study aimed to qualitatively and quantitatively compare the composition of gut microbiota between patients with hypertension and healthy controls. Fecal samples were collected from 50 patients diagnosed with grade 3 hypertension and 30 healthy controls. Touchdown PCR­denaturing gradient gel electrophoresis with primers specifically targeting the V3 region of 16S ribosomal RNA, and quantitative PCR, were performed to characterize all the samples. High­throughput sequencing of the V3­V4 regions was performed on 30 randomly selected samples. By comparing diversity and richness indices, the gut microbiome of the hypertensive individuals was found to be more diverse than that of the healthy controls. Among the main bacterial phlya that reside in the gut, Bacteroidetes, Firmicutes and Proteobacteria were dominant in all the samples; however the Firmicutes to Bacteroidetes ratio was variable, with a significant increase in the patients with hypertension compared with the healthy control group. In addition, at the genus level, there was an increased abundance of Prevotella_9, Megasphaera, Parasutterella and Escherichia­Shigella in patients with hypertension, while Bacteroides and Faecalibacterium were decreased. These results suggested that the human gut microbiota is altered in hypertension, and understanding the mechanism of these changes in microbial composition may open up new insights, and help to treat hypertension and other related diseases.

Calcium sulfate bone cements with nanoscaled silk fibroin as inducer.

Both nanostructures and conformations of different protein/polysaccharide additives have critical influence on the performance of calcium sulfate (CS) bone cements. Silk fibroin (SF) as matrix and additives has been introduced to develop bone scaffolds and cements. Here, ß-sheet-rich SF nanofibers (SFF) was used to tune the solidification of CS, achieving better mechanical and biological properties. The ratio of SFF was adjusted to further optimize CS functions. Compared to that regulated with natural silk fibers (NSF) and SF solutions (SFS), the SFF-induced CS showed smaller size and more filament structures. Better mechanical properties were achieved, suggesting the superiority of the SFF as the solidifying solution to combine with α-calcium sulfate hemihydrate (α-CSH) at the same liquid/solid (L/S) ratio. Scanning electron microscope, X-ray diffraction, Fourier transform infrared spectroscopy, setting time, porosity, mechanical performance test, degradation performance test, and water resistance test were used to demonstrate the properties of this bone repair cement. Cell culture experiments in vitro was used to evaluate the biocompatibility of this composited material. In conclusion, the results demonstrated that nanofibers was a better form of SF in the modification of CSH cement. And the research conducted in this article on improving the mechanical and biological properties of CSH would supported the reference for later clinical experiments. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B:2611-2619, 2019.

The influence of gut microbiota dysbiosis to the efficacy of 5-Fluorouracil treatment on colorectal cancer.

Colorectal cancer is one of the most frequently diagnosed cancers worldwide. Gut flora can modulate the host response to chemotherapeutic drugs. However, the understanding regarding the relationship between the gut microbiota and the antitumor efficacy of 5- Fluorouracil (5-FU) treatment is limited. Therefore, we compared the tumor size and profiled the gut microbiota of mice treated with 5-FU, combined with probiotics or ABX (an antibiotic cocktail of antibiotics) by using the Colorectal Cancer (CRC) mouse model and high-throughput sequencing. The results elucidated that ABX administration diminished the antitumor efficacy of 5-FU in mice and supplementation of probiotics upon 5-FU treatment could not significantly increase the efficacy of 5-FU treatment, despite improving mice body weight at day 33. There were significant differences in fecal bacteria community among the four groups (ANOSIM p < 0.05). ABX administration reduced microbiota biodiversity and altered microbiota community. The pathogenic bacteria included Escherichia shigella and Enterobacter significantly increased, while other commensal bacterial decreased unidentified Firmicutes increased and the opportunistic pathogens decreased after the administration of Probiotics. In addition, 5-FU treatment also changed the diversity and the community composition of the gut mirobiota. The relative abundance of genus Lachnospiracea_NK4 A136, Bacteroides, Odoribacter, Mucispirillum, and Blautia were significantly increased compared to the control group. Additionally, functional capacity analysis of gut microbiota using PICRUSt showed that genes involved in amino acid metabolism, replication and repair translation, nucleotide metabolism expressed much lower in FU.ABX group than the other groups. The current results suggest that ABX administration disrupted the gut microbiota in mice, which contributed to the reduction of antitumor efficacy of 5-FU.

A nano-micro dual-scale particulate-reinforced copper matrix composite with high strength, high electrical conductivity and superior wear resistance.

Due to the contradiction between mechanical properties and electrical conductivity, it is not easy to fabricate materials with both high strength and good wear resistance with favourable electrical conductivity for the application of electrical materials. In addition, strength and wear resistance do not always present a uniform growth trend at the same time. Herein, a novel copper matrix composite reinforced by in situ synthesized ZrB2 microparticles and nano Cu5Zr precipitates is successfully prepared by a casting method and sequential heat treatments. The Cu/dual-scale particulate composite possesses a desired trade-off of strength, electrical conductivity and wear resistance. ZrB2 microparticles form from Zr and B elements in copper melts, and nanoscale Cu5Zr precipitates form in the matrix after solid solution and aging treatments. The ZrB2 microparticles, nano Cu5Zr precipitates, and well-bonded interfaces contribute to a high tensile strength of 591 MPa and superior wear resistance, with a relative electrical conductivity of 83.7% International Annealed Copper Standard.

Active targeting theranostic iron oxide nanoparticles for MRI and magnetic resonance-guided focused ultrasound ablation of lung cancer.

Despite its great promise in non-invasive treatment of cancers, magnetic resonance-guided focused ultrasound surgery (MRgFUS) is currently limited by the insensitivity of magnetic resonance imaging (MRI) for visualization of small tumors, low efficiency of in vivo ultrasonic energy deposition, and damage to surrounding tissues. We hereby report the development of an active targeting nano-sized theranostic superparamagnetic iron oxide (SPIO) platform for significantly increasing the imaging sensitivity and energy deposition efficiency using a clinical MRgFUS system. The surfaces of these PEGylated SPIO nanoparticles (NPs) were decorated with anti-EGFR (epidermal growth factor receptor) monoclonal antibodies (mAb) for targeted delivery to lung cancer with EGFR overexpression. The potential of these targeted nano-theranostic agents for MRI and MRgFUS ablation was evaluated in vitro and in vivo in a rat xenograft model of human lung cancer (H460). Compared with nontargeting PEGylated SPIO NPs, the anti-EGFR mAb targeted PEGylated SPIO NPs demonstrated better targeting capability to H460 tumor cells and greatly improved the MRI contrast at the tumor site. Meanwhile, this study showed that the targeting NPs, as synergistic agents, could significantly enhance the efficiency for in vivo ultrasonic energy deposition in MRgFUS. Moreover, we demonstrated that a series of MR methods including T2-weighted image (T2WI), T1-weighted image (T1WI), diffusion-weighted imaging (DWI) and contrast-enhanced T1WI imaging, could be utilized to noninvasively and conveniently monitor the therapeutic efficacy in rat models by MRgFUS.

Safety and efficacy of a tCD25 preselective combination anti-HIV lentiviral vector in human hematopoietic stem and progenitor cells.

The successful suppression of human immunodeficiency virus (HIV) in the "Berlin Patient" has highlighted the ability of HIV-resistant hematopoietic stem cells to offer a potential functional cure for HIV-infected patients. HIV stem cell gene therapy can mimic this result by genetically modifying a patient's own cells with anti-HIV genes. Previous attempts of HIV gene therapy have been hampered by a low percentage of transplanted HIV-resistant cells which has led to minimal clinical efficacy. In our current study, we have evaluated the in vitro and in vivo safety and efficacy of a truncated/mutated form of human CD25 preselective anti-HIV lentiviral vector in human hematopoietic stem cells. This preselective vector allows us to purify vector-transduced cells prior to transplantation so an increased percentage of gene-modified cells can be delivered. Here, we demonstrate the safety of this strategy with successful engraftment and multilineage hematopoiesis of transduced cells in a humanized NOD-RAG1-/-IL-2rγ-/- knockout mouse model. Efficacy was also demonstrated with significant protection from HIV-1 infection including maintenance of human CD4+ cell levels and a decrease in HIV-1 plasma viremia. Collectively, these results establish the utility of this HIV stem cell gene therapy strategy and bring it closer to providing a functional cure for HIV-infected patients.

Determination of clenbuterol from pork samples using surface molecularly imprinted polymers as the selective sorbents for microextraction in packed syringe.

In this study, a selective sample pretreatment procedure combing surface molecularly imprinted polymers and microextraction in packed syringe (SMIPs-MEPS) was developed for the analysis of clenbuterol (CLB) from pork samples. SMIPs for CLB were synthesized on silica gel particles through a sol-gel process. A series of characterization and adsorption experiments revealed that the SMIPs exhibited porous structures, good thermal stability, high adsorption capacity and a fast mass transfer rate. The obtained SMIPs were employed as selective sorbents of SMIPs-MEPS for extraction of CLB from pork samples. Several parameters affecting the extraction efficiency were investigated, including the pH of sample solution, number of draw-eject cycles, volume of sample, type and volume of washing solution, and the type and volume of elution solution. Under the optimized conditions, a simple and rapid method for the determination of CLB from pork samples was established by coupling with high performance liquid chromatography (HPLC). The whole pretreatment process was rapid and it can be accomplished with 2min. The limit of quantitation and the limit of detection for CLB were 0.02 and 0.009µgkg(-1), respectively. The average recoveries of CLB at three spiked levels ranged from 86.5% to 91.2% with the relative standard deviations (RSD) ≤6.3%.

Combined solid-phase microextraction and high-performance liquid chromatography with ultroviolet detection for simultaneous analysis of clenbuterol, salbutamol and ractopamine in pig samples.

A simple and sensitive method based on the combination of solid-phase microextraction (SPME) and high-performance liquid chromatography with ultroviolet detection was developed for the simultaneous determination of clenbuterol, salbutamol and ractopamine in pig samples. Parameters of the SPME procedure affecting extraction efficiency, such as the type of fiber, extraction time, extraction temperature, ion strength, pH of sample and stirring rate, were optimized. The developed method was validated according to the International Conference on Harmonization guidelines. The calibration curves were linear over a range of 0.5-50 µg/L for clenbuterol and ractopamine, and 0.2-20 µg/L for salbutamol. The limits of detection were 0.1 µg/L for clenbuterol, 0.05 µg/L for salbutamol and 0.1 µg/L for ractopamine, respectively. The averages of intra- and inter-day accuracy ranged from 79.8 to 92.4%. The intra-day and inter-day precision were below 9.6% for the three analytes. This method exhibited the advantages of simplicity, rapidity and low solvent consumption, and was suitable for the monitoring of ß2 -agonists residue in pig samples.