Microcella aerolata sp. nov., isolated from electronic waste-associated bioaerosols.

A Gram-positive, non-motile, non-spore-forming and short rod-shaped actinomycete strain, designated GA224T, was isolated from electronic waste-associated bioaerosols. The optimal growth conditions for this isolate, a facultatively anaerobic bacterium, were 37 °C and pH 8.0. The cell-wall peptidoglycan type was B2γ, with 2,4-diaminobutyric acid (DAB) as the diamino acids, while the major menaquinone was MK-12. The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and an unidentified lipid. The major cellular fatty acids were anteiso-C15:0 and iso-C16:0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GA224T fell within the genus Microcella. The draft genome of strain GA224T comprised 2,495,189 bp with a G + C content of 72.2 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain GA224T and the type strain of the type species of Microcella species were lower than 95% and 70%, respectively. Based on the phenotypic, chemotaxonomic and genomic data, strain GA224T represents a novel species, for which the name Microcella aerolata sp. nov. is proposed, with GA224T as the type strain (= GDMCC 1.2165 T = JCM 34462 T).

Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing.

Lactococcus petauri CF11 was originally isolated from the gut of healthy humans. To determine the underlying molecular and genetic mechanisms of the probiotic potential of CF11, we performed complete genome sequencing, annotation, and comparative genome analysis. The complete genome of L. petauri CF11 comprised of 1,997,720 bp, with a DNA G+C content of 38.21 mol% containing 1982 protein coding genes and 16 rRNA operons. We found that 1206 genes (56.05%) were assigned a putative function using the gene ontology (GO) resource. The gene products of CF11 were primarily concentrated in molecular function and biological processes, such as catalysis, binding, metabolism, and cellular processes. Furthermore, 1,365 (68.87%) genes were assigned an illative function using COGs. CF11 proteins were associated with carbohydrate transport and metabolism, and amino acid transport and metabolism. This indicates that CF11 bacteria can perform active energy exchange. We classified 1,111 (56.05%) genes into six KEGG functional categories; fructose-bisphosphate aldolase and the phosphoenol pyruvate:phosphotransferase system (PTS), which are necessary in producing short-chain fatty acids (SCFAs), were excited in the carbohydrate metabolic pathway. This suggests that L. petauri CF11 produces SCFAs via glycolysis. The genomic island revealed that some regions contain fragments of antibiotic resistance and bacteriostatic genes. In addition, ANI analysis showed that L. petauri CF11 had the closest relationship with L. petauri 159469T, with an average nucleotide consistency of 98.03%. Taken together, the present study offers further insights into the functional and potential role of L. petauri CF11 in health care.

ANTI-DIABETIC EFFECTS OF ZHUODUQING FORMULA, A CHINESE HERBAL DECOCTION, ON A RAT MODEL OF TYPE 2 DIABETES.

BACKGROUND: Zhuoduqing formula (ZDQ) is a Chinese herbal decoction and used to treat type 2 diabetes in clinical practice, but the potential evidence needs to be provided. MATERIALS AND METHODS: Type 2 diabetic model rats were induced by feeding high fat diet (HFD) and intraperitoneal injection of streptozotocin (STZ). The model rats were given ZDQ for 4 weeks. Insulin sensitivity was evaluated by homeostasis model assessment of basal insulin resistance (HOMA-IR) and intraperitoneal glucose tolerance test (IPGTT). Blood insulin and tumour necrosis factor-α (TNF-α) levels as well as SOCS-3 levels in skeletal muscles were analyzed by ELISA. RESULTS: ZDQ significantly decreased fasting blood glucose, ameliorated HOMA-IR and IPGTT, and reduced triglyceride and total cholesterol in type 2 diabetic rats. Moreover, ZDQ remarkably lowered blood TNF-α levels and inhibited SOCS-3 levels in skeletal muscles. CONCLUSION: The results display that ZDQ performs anti-diabetic functions in type 2 diabetic rats induced by feeding HFD and intraperitoneal injection of STZ. Abbreviations: ZDQ, zhuoduqing formula; ROS, rosiglitazone; HOMA-IR, homeostasis model assessment of basal insulin resistance; IPGTT, intraperitoneal glucose tolerance test; HFD, high fat diet; SOCS-3, suppressor of cytokine signaling-3; TNF-α, tumour necrosis factor-α.

Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD.

The changes in the microbial community structure during acute exacerbations of severe chronic obstructive pulmonary disease (COPD) in hospitalized patients remain largely uncharacterized. Therefore, further studies focused on the temporal dynamics and structure of sputum microbial communities during acute exacerbation of COPD (AECOPD) would still be necessary. In our study, the use of molecular microbiological techniques provided insight into both fungal and bacterial diversities in AECOPD patients during hospitalization. In particular, we examined the structure and varieties of lung microbial community in 6 patients with severe AECOPD by amplifying 16S rRNA V4 hyper-variable and internal transcribed spacer (ITS) DNA regions using barcoded primers and the Illumina sequencing platform. Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity. Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences. The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella. Our findings highlight that COPD patients have personalized structures and varieties in sputum microbial community during hospitalization periods.

Different Dynamic Patterns of ß-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity.

The adverse impact of antibiotics on the gut microbiota has attracted extensive interest, particularly due to the development of microbiome research techniques in recent years. However, a direct comparison of the dynamic effects of various types of antibiotics using the same animal model has not been available. In the present study, we selected six antibiotics from four categories with the broadest clinical usage, namely, ß-lactams (Ceftriaxone Sodium, Cefoperazone/Sulbactam and meropenem), quinolones (ofloxacin), glycopeptides (vancomycin), and macrolides (azithromycin), to treat BALB/c mice. Stool samples were collected during and after the administration of antibiotics, and microbial diversity was analyzed through Illumina sequencing and bioinformatics analyses using QIIME. Both α and ß diversity analyses showed that ceftriaxone sodium, cefoperazone/sulbactam, meropenem and vancomycin changed the gut microbiota dramatically by the second day of antibiotic administration whereas the influence of ofloxacin was trivial. Azithromycin clearly changed the gut microbiota but much less than vancomycin and the ß-lactams. In general, the community changes induced by the three ß-lactam antibiotics showed consistency in inhibiting Papillibacter, Prevotella and Alistipes while inducing massive growth of Clostridium. The low diversity and high Clostridium level might be an important cause of Clostridium difficile infection after usage of ß-lactams. Vancomycin was unique in that it inhibited Firmicutes, mainly the genus Clostridium. On the other hand, it induced the growth of Escherichia and effect lasted for months afterward. Azithromycin and meropenem induced the growth of Enterococcus. These findings will be useful for understanding the potential adverse effects of antibiotics on the gut microbiome and ensuring their better usage.

Lentivirus-mediated Persephin over-expression in Parkinson's disease rats.

Persephin, together with glial cell line-derived neurotrophic factor and neurturin, has a neurotrophic effect and promotes the survival of motor neurons cultured in vitro. In this study, dopaminergic neurons in the substantia nigra of rats were transfected with the Persephin gene. One week later 6-hydroxydopamine was injected into the anterior medial bundle to establish a Parkinson's disease model in the rats. Results found that the number of dopaminergic neurons in the substantia nigra increased, tyrosine hydroxylase expression was upregulated and concentrations of dopamine and its metabolites in corpus striatum were increased after pretreatment with Persephin gene. In addition, the rotating effect of the induced Parkinson's disease rats was much less in the group pretreated with the Persephin gene. Persephin has a neuroprotective effect on the 6-hydroxydopamine-induced Parkinson's disease through protecting dopaminergic neurons.

HCN channels modulate the activity of the subthalamic nucleus in vivo.

The subthalamic nucleus is a key component in the indirect pathway of the basal ganglia, which mediates a variety of motor functions. The subthalamic nucleus neurons have intrinsic pacemaking properties. Hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels are expressed in the central nervous system, including the subthalamic nucleus. However, the in vivo modulation of HCN channels in the subthalamic nucleus remains relatively obscure. To investigate the direct effects of HCN channels in the subthalamic nucleus, multi-barrel extracellular recordings and behavioral tests were performed in the present study. In 42 out of the 89 subthalamic nucleus neurons, micropressure ejection of HCN channel inhibitor, ZD7288 (0.05 mM), decreased the spontaneous firing rate from 11.6 ± 1.8 to 5.7 ± 1.3 Hz (P < 0.001). The average decrease was 56.7 ± 5.3 %. In another 47 out of the 89 subthalamic nucleus neurons, micropressure ejection of ZD7288 increased the spontaneous firing rate from 9.5 ± 1.6 to 16.3 ± 2.4 Hz (P < 0.001), with the average increase of 142.2 ± 29.8 %. Activation of HCN channels by 8-Br-cAMP also produced bidirectional modulation on the firing rate of the subthalamic nucleus neurons. Furthermore, unilateral microinjection of ZD7288 or 8-Br-cAMP produced postural behavior in awake rats. The present electrophysiological and behavioral findings demonstrated that the pharmacological blockade or activation of HCN channels produces bidirectional modulation on the excitability of the subthalamic nucleus.

Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags.

Low cost and high throughput capacity are major advantages of using next generation sequencing (NGS) techniques to determine metagenomic 16S rRNA tag sequences. These methods have significantly changed our view of microorganisms in the fields of human health and environmental science. However, DNA extraction using commercial kits has shortcomings of high cost and time constraint. In the present study, we evaluated the determination of fecal microbiomes using a direct boiling method compared with 5 different commercial extraction methods, e.g., Qiagen and MO BIO kits. Principal coordinate analysis (PCoA) using UniFrac distances and clustering showed that direct boiling of a wide range of feces concentrations gave a similar pattern of bacterial communities as those obtained from most of the commercial kits, with the exception of the MO BIO method. Fecal concentration by boiling method affected the estimation of α-diversity indices, otherwise results were generally comparable between boiling and commercial methods. The operational taxonomic units (OTUs) determined through direct boiling showed highly consistent frequencies with those determined through most of the commercial methods. Even those for the MO BIO kit were also obtained by the direct boiling method with high confidence. The present study suggested that direct boiling could be used to determine the fecal microbiome and using this method would significantly reduce the cost and improve the efficiency of the sample preparation for studying gut microbiome diversity.

Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags.

Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with Acidobacteria, Nitrospira, Verrucomicrobia, Alphaproteobacteria, and Betaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such as Chloroflexi, Bacillariophyta, Gammaproteobacteria, and Epsilonproteobacteria) as well as saprophytic microbes (such as Actinomycetales, Bacteroidetes, and Firmicutes). The marine sediment had a higher abundance of Gammaproteobacteria and Deltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.

Unusual CT hyperattenuating dermoid cyst of cerebellum: a new case report and literature review.

Almost all intracranial dermoid cysts typically display low-density lesions on plain computerized tomography (CT) scans due to abundant lipids content. CT hyperattenuating dermoid cyst (CHADC) is very uncommon with only nine case reports in the literature update, which occurs exclusively in the posterior fossa. Moreover, CHADC with mural nodule is exceptionally rare, and only one such case was documented previously. Here, we report a new case of cerebellar CHADC with mural nodule in a 14-year-old male patient who presented with a 4-week history of dull headache and 5-day history of gait disturbance. With an average attenuation value of 89.9 Hounsfield units on CT scans, the lesion mainly displayed T1 hyperintensity, T2 hypointensity, and FLAIR hypointensity on magnetic resonance imaging. The patient underwent lesion gross total resection and symptomatic improvement, and final pathology was consistent with dermoid cyst. For further clarifying the mechanism of unusual CT hyperdensity, we sampled the cystic content and quantified its protein, calcium, and cholesterol, and our result suggested the high protein, high calcium, and low lipids in contents was the main mechanism of increased CT attenuation for CHADC.

Integrated lysis procedures reduce extraction biases of microbial DNA from mangrove sediment.

Sufficient lysis of soil or sediment microbes is a critical step for analyzing microbial community structures and for preparing metagenomic DNA libraries. The present study compared lysis methods for recovering archaeal, bacterial, actinomycete, and fungal DNAs from a mangrove sediment sample. PCR results showed that individual procedures using SDS, lysozyme, sonication, freeze-thaw, microwave, and vigorous shaking could extract archaeal or bacterial DNA but failed for actinomycetes or fungi cells. In comparison, an integrated lysis procedure using SDS, lysozyme, and vigorous shaking successfully obtained fungal DNA, and a combination of SDS, lysozyme, vigorous shaking, and microwave treatments recovered DNA from actinomycetes. Denaturing gradient gel electrophoresis (DGGE) results showed that although single lysis procedures can lyse bacterial DNA, all of them assessed the indigenous bacterial community structure with significant biases. The integrated lysis protocols described in the present study could be useful for extracting DNA from various types of sediments.

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method.

BACKGROUND: The primer and amplicon length have been found to affect PCR based estimates of microbial diversity by pyrosequencing, while other PCR conditions have not been addressed using any deep sequencing method. The present study determined the effects of polymerase, template dilution and PCR cycle number using the Solexa platform. RESULTS: The PfuUltra II Fusion HS DNA Polymerase (Stratagene) with higher fidelity showed lower amount of PCR artifacts and determined lower taxa richness than the Ex Taq (Takara). More importantly, the two polymerases showed different efficiencies for amplifying some of very abundant sequences, and determined significantly different community structures. As expected, the dilution of the DNA template resulted in a reduced estimation of taxa richness, particularly at the 200 fold dilution level, but the community structures were similar for all dilution levels. The 30 cycle group increased the PCR artifacts while comparing to the 25 cycle group, but the determined taxa richness was lower than that of the 25 cycle group. The PCR cycle number did not changed the microbial community structure significantly. CONCLUSIONS: These results highlight the PCR conditions, particularly the polymerase, have significant effect on the analysis of microbial diversity with next generation sequencing methods.

[Comparison of two kinds of cationic vectors-mediated gene delivery].

In order to study the important factors involved in cationic liposome-mediated gene transfer, Lipofectamine 2000 or DOTAP was evaluated using three types of cells (Hep-2, MCF-7 and SW-480) in vitro transfection efficiencies. Different properties of the two reagents were analyzed and compared by DNA arrearage assay and MTT assay. Both Lipofectamine 2000 and DOTAP had strong capability to combine with DNA; Lipofectamine 2000 can get higher transfection efficiency of the three cells by using GFP as report gene, meanwhile, DOTAP can also get higher transfection efficiency against Hep-2 cell. However, DOTAP showed lower transfection efficiency against MCF-7 and SW-480 cell. On the other hand, the cytotoxicity assay showed that over 85% cell viability of MCF-7 cell could be achieved both by Lipofectamine 2000 and DOTAP under the optimal transfection condition. Relatively speaking, Lipofectamine 2000 has very high transfection efficiency in a broad range of cell lines, but because of the special selectivity of cell type on liposome, DOTAP also has a broad application prospect.

[Main bottleneck and developments of metagenomic technology].

This review analyzed the main bottleneck of metagenomic technology on construction and screening of environmental library, discussed the recent developments towards overcoming the main bottleneck. Finally, the enormous scope and potential for both fundamental microbial ecology and biotechnological development of metagenomics was highlighted.

[Construction of large fragment metagenome library of natural mangrove soil].

Applying our optimized direct extraction method, the percentage of large fragment DNA in the total extracted mangrove soil DNA was significant increased. The large fragment metagenome library derived from natural mangrove soil over four seasons was successfully constructed by the optimized DNA extraction and electro elution purification method. All of the clones had recombinant Cosmids and each differed in their fragment profiles when Cosmid DNA was extracted from 12 randomly picked colonies and digested with BamHI. The average insert size for this library was larger than 35 kbp. This culturing-independent library at least encompassed 335 Mbp valuable genetic information of mangrove soil microbes. It allowed mining of valuable intertidal microbial resource to become a reality. It is a recommended method for those researchers who have still not circumvented the large insert environmental libraries or for those beginning research in this field, so as to avoid them attempting repetitive, fussy work.

[Research on mangrove soil microorganisms: past, present and future].

Special Mangrove soil niches possesses valuable microbial resources. Unfortunately, up to the present, so far there is very little knowledge on the mangrove soil microbial communities. It mainly due to the limitations of research methods. Cultureindependent approaches based on 16S rRNA, 18S rRNA gene analysis open the window to study microbial diversity in mangrove soil. The progress had achieved about studying on mangrove soil microbial species diversity, metabolic diversity and treating environmental pollutions was summarized in the paper. In addition, the bright future of mangrove soil microorganisms was described.