Overall and individual associations between per- and polyfluoroalkyl substances and liver function indices and the metabolic mechanism.

Per- and polyfluoroalkyl substances (PFAS) can disrupt liver homeostasis. Studies have shown that a single exposure to PFAS may provoke abnormal liver function; however, few studies have investigated the overall effect of PFAS mixtures. We aimed to investigate associations between exposure to PFAS mixtures and liver function indices and explore the relevant mechanisms. This study included 278 adult males from Guangzhou, China. Serum metabolite profiles were analyzed using untargeted metabolomics. We applied weighted quantile sum (WQS) regression as well as Bayesian kernel machine regression (BKMR) to analyze the association of nine PFAS mixtures with 14 liver function indices. PFAS mixtures were positively associated with apolipoprotein B (APOB) and gamma-glutamyltransferase (GGT) and negatively associated with direct bilirubin (DBIL) and total bilirubin (TBIL) in both the WQS and BKMR analyses. In addition, Spearman's correlation test showed individual PFAS correlated with APOB, GGT, TBIL, and DBIL, while there's little correlation between individual PFAS and other liver function indices. In linear regression analysis, PFHxS, PFOS, PFHpS, PFNA, PFDA, and PFUdA were associated with APOB; PFOA, PFDA, PFOS, PFNA, and PFUdA were associated with GGT. Subsequently, a metabolome-wide association study and mediation analysis were combined to explore metabolites that mediate these associations. The mechanisms linking PFAS to APOB and GGT are mainly related with amino acid and glycerophospholipid metabolism. High-dimensional mediation analysis showed that glycerophospholipids are the main markers of the association between PFAS and APOB, and that (R)-dihydromaleimide, Ile Leu, (R)-(+)-2-pyrrolidone-5-carboxylic acid, and L-glutamate are the main markers of the association between PFAS and GGT. In summary, overall associations between PFAS and specific indices of liver function were found using two statistical methods; the metabolic pathways and markers identified here may serve to prompt more detailed study in animal-based systems, as well as a similar detailed analysis in other populations.

Seasonal variations of airborne microbial diversity in waste transfer stations and preventive effect on Streptococcus pneumoniae induced pulmonary inflammation.

Environment, location, and season are important factors that influence the microbiological community, yet, little research on airborne microorganisms in waste transfer stations (WTSs). Here, the airborne bacterial and fungal communities at four WTSs during different seasons were analyzed by high-throughput sequencing. The bacteria were isolated by cultural method and screened bacterium alleviate inflammation induced by Streptococcus pneumoniae (Spn) by regulating gut microbiome. The results revealed that collected bioaerosols from the WTSs varied significantly by location and season. Proteobacteria and Pseudomonadota are prevalent in summer and winter, respectively. Ascomycota was predominant in two seasons. Hazard quotients for adults from four WTSs were below one. Three selected potential probiotics were formulated into a microbial preparation with a carrier that effectively prevented inflammation in bacterial and animal experiments. The expression levels of interleukin-1ß, interleukin-6, and tumor necrosis factor-α in Pre group (0.11, 0.17, and 0.48-fold) were significantly lower than Spn group (2.75, 1.71, and 5.01-fold). These mechanisms are associated with changes in gut microbiota composition and short-chain fatty acids (SCFAs) levels, such as affecting Lachnospiraceae lachnospira abundance and acetic acid content. This study provides insights into the potential application of probiotics derived from WTSs as an alternative approach to preventing respiratory infections.

Effects of tris (2-chloroethyl) phosphate exposure on gut microbiome using the simulator of the human intestinal microbial ecosystem (SHIME).

Tris (2-chloroethyl) phosphate (TCEP) has been widely used, and its health risk has received increasing attention. However, the rare research has been conducted on the effects of TCEP exposure on changes in the structure of the human gut microbiome and metabolic functions. In this experiment, Simulator of the human intestinal microbial ecosystem (SHIME) was applied to explore the influences of TCEP on the human gut bacteria community and structure. The results obtained from high-throughput sequencing of 16S rRNA gene have clearly revealed differences among control and exposure groups. High-dose TCEP exposure increased the Shannon and Simpson indexes in the results of α-diversity of the gut microbiome. At phylum level, Firmicutes occupied a higher proportion of gut microbiota, while the proportion of Bacteroidetes decreased. In the genus-level analysis, the relative abundance of Bacteroides descended with the TCEP exposure dose increased in the ascending colon, while the abundances of Roseburia, Lachnospira, Coprococcus and Lachnoclostridium were obviously correlated with exposure dose in each colon. The results of short chain fatty acids (SCFAs) showed a remarkable effect on the distribution after TCEP exposure. In the ascending colon, the control group had the highest acetate concentration (1.666 ± 0.085 mg⋅mL-1), while acetate concentrations in lose-dose medium-dose and high-doseTCEP exposure groups were 1.119 ± 0.084 mg⋅mL-1, 0.437 ± 0.053 mg⋅mL-1 and 0.548 ± 0.106 mg⋅mL-1, respectively. TCEP exposure resulted in a decrease in acetate and propionate concentrations, while increasing butyrate concentrations in each colon. Dorea, Fusicatenibacter, Kineothrix, Lachnospira, and Roseburia showed an increasing tendency in abundance under TCEP exposure, while they had a negatively correlation with acetate and propionate concentrations and positively related with butyrate concentrations. Overall, this study confirms that TCEP exposure alters both the composition and metabolic function of intestinal microbial communities, to arouse public concern about its negative health effects.

Dosimetric comparison of two dose expansion methods in intensity modulated radiotherapy for breast cancer.

BACKGROUND: To explore the dosimetric difference between IMRT-VB plan based on the establishment of external expansion structure and virtual bolus (VB) and IMRT-SF based on the skin flash (SF) tool of the Eclipse treatment planning system in postoperative chest wall target intensity modulation radiotherapy plan of breast cancer. METHODS: Twenty patients with breast cancer were randomly selected as subjects to develop IMRT-VB plan based on virtual bolus and IMRT-SF plan based on skin flash tool of Eclipse treatment planning system. The planning target volume, monitor unit (MU) of every single treatment and the dosimetric parameters of organ at risk (OARs) were recorded. Paired t-test was used for normal distribution data while nonparametric paired Wilcoxon rank sum test was used for non-normal distribution data. RESULTS: Both IMRT-VB and IMRT-SF plan can expand outward to the chest wall skin and meet the dose requirements of clinical prescription. The conformal index, the homogeneity index, D2%, D98% and D50% were significantly better in IMRT-SF plan than those in IMRT-VB plan (P < 0.05). The average MU of the IMRT-SF plan was much higher than that of the IMRT-VB plan (866.0 ± 68.1 MU vs. 760.9 ± 50.4 MU, P < 0.05). In terms of organ at risk protection, IMRT-SF plan had more advantages in the protection of ipsilateral lung and spinal cord than IMRT-VB plan (P < 0.05). CONCLUSION: Our study indicated that IMRT-SF plan displayed clinical application superiority compared to IMRT-VB plan, and the operation steps of which are simpler and faster. Besides, IMRT-SF plan took advantages in achieve effective external expansion of skin dose intensity and OARs protection.

Deep learning predicts immune checkpoint inhibitor-related pneumonitis from pretreatment computed tomography images.

Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of lung cancer, including both non-small cell lung cancer and small cell lung cancer. Despite the promising results of immunotherapies, ICI-related pneumonitis (ICIP) is a potentially fatal adverse event. Therefore, early detection of patients at risk for developing ICIP before the initiation of immunotherapy is critical for alleviating future complications with early interventions and improving treatment outcomes. In this study, we present the first reported work that explores the potential of deep learning to predict patients who are at risk for developing ICIP. To this end, we collected the pretreatment baseline CT images and clinical information of 24 patients who developed ICIP after immunotherapy and 24 control patients who did not. A multimodal deep learning model was constructed based on 3D CT images and clinical data. To enhance performance, we employed two-stage transfer learning by pre-training the model sequentially on a large natural image dataset and a large CT image dataset, as well as transfer learning. Extensive experiments were conducted to verify the effectiveness of the key components used in our method. Using five-fold cross-validation, our method accurately distinguished ICIP patients from non-ICIP patients, with area under the receiver operating characteristic curve of 0.918 and accuracy of 0.920. This study demonstrates the promising potential of deep learning to identify patients at risk for developing ICIP. The proposed deep learning model enables efficient risk stratification, close monitoring, and prompt management of ICIP, ultimately leading to better treatment outcomes.

Performance of ImproGene cfDNA blood collection tubes for mutation analysis in cancer patients.

With the widely application of liquid biopsy and the development of detection technology, the standardization of pre-analysis procedures is necessary. For controlling pre-analysis variation of circulating tumor DNA (ctDNA) in blood samples, the blood collection tubes for ctDNA preservation particularly contribute a lot. The objective of this study was to investigate whether ImproGene® Cell Free DNA Tube (ImproGene tube) can be used in sample collection, preservation and NGS based mutation detection for ctDNA. We investigated hemolysis and cell free DNA (cfDNA) concentration of blood samples stored in ImproGene tubes and detected ß-actin, LINE1 and exogenous gene level by qPCR. We compared cfDNA and RNA quantity between samples in ImproGene tube and Streck Cell-Free DNA BCT® (Streck tube). And 10 gene mutations and three fusion mutations analysis were compared by sequencing. When stored at room temperature within 7 days in ImproGene tubes, blood samples had no visible hemolysis and the cfDNA concentration, levels of ß-actin, LINE1 and exogenous gene remained stable which means no genomic DNA release and cfDNA was protected. There was no significant difference in cfDNA and RNA quantity between ImproGene tubes and Streck tubes. Furthermore, based on this limited data set, ImproGene tubes showed increased detection rates of low-level mutations. Therefore, ImproGene Cell Free DNA Tubes may have promising applications in sample collection, preservation and NGS based mutation detection for ctDNA by its good preservation performance.

Survival outcomes, hematologic complications and growth impairment after sequential chemoradiotherapy in intracranial NGGCTs: a retrospective study.

PURPOSE: This study aimed to evaluate the clinical features, prognostic factors, and survival outcomes for patients with intracranial nongerminomatous germ cell tumors (NGGCTs), with a particular focus on treatment toxicity for long-term survivors. METHODS: Intracranial NGGCTs treated with platinum-based chemotherapy and craniospinal irradiation (CSI) in our institution were retrospectively analyzed. Hematological complications following sequential chemoradiotherapy as well as height and weight in childhood survivors were evaluated. Plasma growth hormone (GH) concentrations prior to and after radiotherapy were obtained for the comparisons. RESULTS: A total of 111 intracranial NGGCTs were included. The 3­year overall survival (OS) and event-free survival (EFS) rates were 83.5% ± 3.9% and 71.0% ± 4.8%, respectively. A combined treatment modality consisting of ≥ 4 cycles of platinum-based chemotherapy and CSI was associated with an improved OS (P = 0.003) and EFS (P < 0.001). Thrombocytopenia of any grade occurred in 35.4% (34/96) of patients, and the threshold age for an increased risk of thrombocytopenia was 14 years (area under the curve AUC = 0.752, P < 0.0001) as derived from receiver operating characteristic (ROC) analysis. Growth impediment was found in 8 of 56 (14%) patients. The age for receiving radiotherapy was found to inversely correlate with height development, revealing a cut-off age of 11.5 years for risking growth impairment (AUC = 0.806, P = 0.004). Consistently, a significant decline in plasma growth hormone after radiotherapy was observed in patients ≤ 11.5 years (P < 0.01) but not patients > 11.5 years. (P > 0.05). CONCLUSION: Our study suggested that a combined treatment modality with at least four cycles of chemotherapy and CSI was safe and effective for patients with intracranial NGGCTs. Radiotherapy should be used with caution for patients < 11.5 years due to growth impairment.

Performance of ImproGene Cell-Free DNA Tubes for Stabilization and Analysis of cfDNA in Blood Samples.

BACKGROUND: With the development of liquid biopsy technology, the demand for noninvasive prenatal testing (NIPT) is increasing rapidly. The aim of the study is to evaluate the effects of different blood collection tubes on plasma cfDNA and NIPT quality control. METHODS: We investigated hemolysis, cfDNA concentration, and fragment distribution within blood samples stored in EDTA, ImproGene, and Streck tubes. The effects of ImproGene and Streck tubes on NIPT quality control were evaluated. RESULTS: The ImproGene tubes prevented the time-dependent increase of cfDNA concentration and preserved the cfDNA fragment size distribution. For NIPT quality control, there is no significant difference in cfDNA, library concentration, and fetal fraction between ImproGene and Streck tubes samples. GC content of the samples in ImproGene tubes was closer to the human genome. CONCLUSION: The ImproGene cfDNA tube has excellent performance and is an effective choice for storing blood samples for NIPT testing or other cfDNA analysis.

Individualized Nomogram for Predicting Survival in Patients with Brain Metastases After Stereotactic Radiosurgery Utilizing Driver Gene Mutations and Volumetric Surrogates.

It is well-known that genomic mutational analysis plays a significant role in patients with NSCLC for personalized treatment. Given the increasing use of stereotactic radiosurgery (SRS) for brain metastases (BM), there is an emerging need for more precise assessment of survival outcomes after SRS. Patients with BM and treated by SRS were eligible in this study. The primary endpoint was overall survival (OS). Cox regression models were used to identify independent prognostic factors. A survival predictive nomogram was developed and evaluated by Concordance-index (C-index), area under the curve (AUC), and calibration curve. From January 2016 to December 2019, a total of 356 BM patients were eligible. The median OS was 17.7 months [95% confidence interval (CI) 15.5-19.9] and the actual OS at 1- and 2-years measured 63.2 and 37.6%, respectively. A nomogram for OS was developed by incorporating four independent prognostic factors: Karnofsky Performance Score, cumulative tumor volume, gene mutation status, and serum lactate dehydrogenase. The nomogram was validated in a separate cohort and demonstrated good calibration and good discriminative ability (C-index = 0.780, AUC = 0.784). The prognostic accuracy of the nomogram (0.792) was considerably enhanced when compared with classical prognostic indices, including the Graded Prognostic Assessment (0.708), recursive partitioning analysis (0.587), and the SRS (0.536). Kaplan-Meier curves showed significant differences in OS among the stratified low-, median- and high-risk groups (P < 0.001). In conclusion, we developed and validated an individualized prognostic nomogram by integrating physiological, volumetric, clinical chemistry, and molecular biological surrogates. Although this nomogram should be validated by independent external study, it has a potential to facilitate more precise risk-stratifications to guide personalized treatment for BM.

Reliable Method for Fabricating Tissue-Mimicking Materials With Designated Relative Permittivity and Conductivity at 128 MHz.

Artificial materials that can simultaneously mimic the relative permittivity and conductivity of various human tissues are usually used in medical applications. However, the method of precisely designing these materials with designated values of both relative permittivity and conductivity at 3 T MRI resonance frequency is lacking. In this study, a reliable method is established to determine the compositions of artificial dielectric materials with designated relative permittivity and conductivity at 128 MHz. Sixty dielectric materials were produced using oil, sodium chloride, gelatin, and deionized water as the main raw materials. The dielectric properties of these dielectric materials were measured using the open-ended coaxial line method at 128 MHz. Nonlinear least-squares Marquardt-Levenberg algorithm was used to obtain the formula, establishing the relationship between the compositions of the dielectric materials and their dielectric properties at 128 MHz. The dielectric properties of the blood, gall bladder, muscle, skin, lung, and bone at 128 MHz were selected to verify the reliability of the obtained formula. For the obtained formula, the coefficient of determination and the expanded uncertainties with a coverage factor of k = 2 were 0.991% and 4.9% for relative permittivity and 0.992% and 6.4% for conductivity. For the obtained artificial materials measured using the open-ended coaxial line method, the maximal difference of relative permittivity and conductivity were 1.0 and 0.02 S/m, respectively, with respect to the designated values. In conclusion, the compositions of tissue-mimicking material can be quickly determined after the establishment of the formulas with the expanded uncertainties of less than 10%. Bioelectromagnetics. 2021;42:86-94. © 2020 Bioelectromagnetics Society.

Variation in the dielectric properties of freshly excised colorectal cancerous tissues at different tumor stages.

The study was designed to identify differences in the dielectric properties of ex vivo colorectal cancerous tissues at different tumor stages. To date, 130 freshly excised colorectal cancerous specimens underwent measurement of both relative permittivity and conductivity on the serosal and mucosal surfaces of the carcinoma nidus, and the mucosa of the surgical resection margin ranging from 50 to 500 MHz at the Larmor frequencies. Tumor node metastasis staging was determined according to pathological reports for each patient. There were statistically significant differences in the relative permittivity of both colorectal cancerous serosa and mucosa among stages ≤I, II, III, and IV and between stages ≤II and ≥III (P < 0.05) at most frequencies under 300 MHz; statistically significant differences in conductivity were also observed for most of the measured frequencies (P < 0.05). The significant differences in dielectric characteristics among tumor stages, especially between early and advanced stages, have value for selecting appropriate surgical strategies. The presented ex vivo data provide important information for magnetic resonance electrical properties tomography in vivo system because the frequencies of 64 MHz (1.5T) and 128 MHz (3T) are usually used in clinical settings. Bioelectromagnetics. 38:522-532, 2017. © 2017 Wiley Periodicals, Inc.

A large-scale measurement of dielectric properties of normal and malignant colorectal tissues obtained from cancer surgeries at Larmor frequencies.

PURPOSE: Knowledge of dielectric properties of malignant human tissues is necessary for the recently developed magnetic resonance (MR) technique called MR electrical property tomography. This technique may be used in early tumor detection based on the obvious differentiation of the dielectric properties between normal and malignant tissues. However, the dielectric properties of malignant human tissues in the scale of the Larmor frequencies are not completely available in the literature. In this study, the authors focused only on the dielectric properties of colorectal tumor tissue. METHODS: The dielectric properties of 504 colorectal malignant samples excised from 85 patients in the scale of the Larmor frequencies were measured using the precision open-ended coaxial probe method. The obtained complex-permittivity data were fitted to the single-pole Cole-Cole model. RESULTS: The median permittivity and conductivity for the malignant tissue sample were 79.3 and 0.881 S/m at 128 MHz, which were 14.6% and 17.0% higher, respectively, than those of normal tissue samples. Significant differences between normal and malignant tissues were found for the dielectric properties (p < 0.05). CONCLUSIONS: Experimental results indicated that the dielectric properties were significantly different between normal and malignant tissues for colorectal tissue. This large-scale clinical measurement provides more subtle base data to validate the technique of MR electrical property tomography.

Quantitative analysis of the reconstruction errors of the currently popular algorithm of magnetic resonance electrical property tomography at the interfaces of adjacent tissues.

This work quantitatively analyzed the reconstruction errors (REs) of electrical property (EP) images using a currently popular algorithm of magnetic resonance electrical property tomography (MREPT), which occurred along the tissue interfaces. Transmitted magnetic fields B1+ were acquired at 3 T using a birdcage coil loaded with a phantom consisting of various adjacent tissues. Homogeneous Helmholtz was employed to calculate the EP maps by Laplacian computation of central differences. The maps of absolute REs (aREs) and relative REs (rREs) were calculated. The maximum and mean rREs, in addition to rRE distributions at the interfaces, were presented. Reconstructed EP maps showed various REs along different interface boundaries. Among all the investigated tissue interfaces, the kidney-fat interface presented the maximum mean rREs for both conductivity and relative permittivity. The minimum mean rRE of conductivity was observed at the spleen-muscle interface, and the minimum mean rRE of relative permittivity was detected along the lung-heart interface. The mean rREs ranged from 0.3986 to 36.11 for conductivity and 0.2218 to 11.96 for relative permittivity. Overall, this research indicates that different REs occur at various tissue boundaries, as shown by the currently popular algorithm of MREPT. Thus, REs should be considered when applying MREPT to reconstruct the EP distributions inside the human body. Copyright © 2016 John Wiley & Sons, Ltd.

[Experimental Research on Detection of Breast Carcinoma and Adjacent Tissues Based on Open-ended Coaxial Probe Tumor Sensor with Radio Frequencies].

This study aimed to verify whether the open-ended coaxial line tumor sensor with radio frequency was effective or not in detecting the differences in permittivity and conductivity between the breast malignant tissues and adjacent tissues.Sixteen breast infiltrating ductal carcinoma samples were freshly obtained from the department of general surgery in Zhujiang Hospital.The permittivity and conductivity of cancerous nidus points of breast samples,3cm adjacent tissue points and 5cm adjacent tissue points were detected respectively by the open-ended coaxial line tumor sensor with radio frequency noninvasively in conjunction with vector network analyzer at the frequency ranging from 42.85~500 MHz.All the detected points were marked.After finishing the detection,we conducted postoperative pathological examinations on all the marked points.According to the statistics,there were statistically significant differences between the breast cancerous tissues and the 3cm adjacent tissues for the dielectric properties(P<0.01).There were statistically significant differences between the breast cancerous tissues and the 5cm adjacent tissues for the dielectric properties(P<0.01).There was no statistically significant difference in the dielectric properties between the 3cm adjacent tissues and 5cm adjacent tissues(P>0.05).Both the 3cm adjacent tissues and5 cm adjacent tissues were found no breast cancer cell infiltration.The results indicated that the open-ended coaxial line tumor sensor at radio frequency could be effective in detecting the differences in permittivity and conductivity between breast cancerous tissues and adjacent tissues and,therefore,it may have a potential prospect in making a final diagnosis to confirm whether the detected breast tissue is malignant or not.

Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis.

Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases, and there are controversial reports regarding the diversity of the associated vaginal microbiota. We determined the vaginal microbial community in patients with VVC, bacterial vaginosis (BV), and mixed infection of VVC and BV using Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed the following order: normal control < VVC only < mixed BV and VVC infection < BV only. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV samples. A detailed comparison showed that, although the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern, with a relatively higher abundance of Lactobacillus than the BV group and higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. In contrast, the VVC-only group could not be described by any single profile, ranging from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC resulted in inconsistent changes of the vaginal microbiota, with four BV/VVC samples recovering to a higher Lactobacillus level, whereas many VVC-only patients did not. These results will be useful for future studies on the role of vaginal microbiota in VVC and related infectious diseases.

Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons.

BACKGROUND: Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally. RESULTS: We amplified a group of fecal samples using both V4F-V6R and V6F-V6R primer sets, excised the same V6 fragment from the two sets of Illumina sequencing data, and compared the resulting data in terms of the α-diversity, ß-diversity, and community structure. Principal component analysis (PCA) comparing the microbial community structures of different datasets, including those with simulated sequencing errors, was very reliable. Procrustes analysis showed a high degree of concordance between the different datasets for both abundance-weighted and binary Jaccard distances (P < 0.05), and a meta-analysis of individual datasets resulted in similar conclusions. The Shannon's diversity index was consistent as well, with comparable values obtained for the different datasets and for the meta-analysis of different datasets. In contrast, richness estimators (OTU and Chao) varied significantly, and the meta-analysis of richness estimators was also biased. The community structures of the two datasets were obviously different and led to significant changes in the biomarkers identified by the LEfSe statistical tool. CONCLUSIONS: Our results suggest that beta-diversity analysis and Shannon's diversity are relatively reliable for meta-analysis, while community structures and biomarkers are less consistent. These results should be useful for future meta-analyses of microbiomes from different data sources.

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.

Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland.

The microbial community plays an essential role in the high productivity in mangrove wetlands. A proper understanding of the spatial variations of microbial communities will provide clues about the underline mechanisms that structure microbial groups and the isolation of bacterial strains of interest. In the present study, the diversity and composition of the bacterial community in sediments collected from four locations, namely mudflat, edge, bulk, and rhizosphere, within the Mai Po Ramsar Wetland in Hong Kong, SAR, China were compared using the barcoded Illumina paired-end sequencing technique. Rarefaction results showed that the bulk sediment inside the mature mangrove forest had the highest bacterial α-diversity, while the mudflat sediment without vegetation had the lowest. The comparison of ß-diversity using principal component analysis and principal coordinate analysis with UniFrac metrics both showed that the spatial effects on bacterial communities were significant. All sediment samples could be clustered into two major groups, inner (bulk and rhizosphere sediments collected inside the mangrove forest) and outer mangrove sediments (the sediments collected at the mudflat and the edge of the mangrove forest). With the linear discriminate analysis scores larger than 3, four phyla, namely Actinobacteria, Acidobacteria, Nitrospirae, and Verrucomicrobia, were enriched in the nutrient-rich inner mangrove sediments, while abundances of Proteobacteria and Deferribacterias were higher in outer mangrove sediments. The rhizosphere effect of mangrove plants was also significant, which had a lower α-diversity, a higher amount of Nitrospirae, and a lower abundance of Proteobacteria than the bulk sediment nearby.