Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles
Obesity and type 2 diabetes mellitus (T2DM) have become major public health issues globally. Recent research indicates that intestinal microbiota play roles in metabolic disorders. Though there are numerous studies focusing on gut microbiota of health and obesity states, those are primarily focused on Western countries. Comparatively, only a few investigations exist on gut microbiota of people from Asian countries. In this study, the fecal microbiota of 30 adult volunteers living in Chiang Rai Province, Thailand were examined using next-generation sequencing (NGS) in association with blood profiles and dietary habits. Subjects were categorized by body mass index (BMI) and health status as follows; lean (L) = 8, overweight (OV) = 8, obese (OB) = 7 and diagnosed T2DM = 7. Members of T2DM group showed differences in dietary consumption and fasting glucose level compared to BMI groups. A low level of high-density cholesterol (HDL) was observed in the OB group. Principal coordinate analysis (PCoA) revealed that microbial communities of T2DM subjects were clearly distinct from those of OB. An analogous pattern was additionally illustrated by multiple factor analysis (MFA) based on dietary habits, blood profiles, and fecal gut microbiota in BMI and T2DM groups. In all four groups, Bacteroidetes and Firmicutes were the predominant phyla. Abundance of Faecalibacterium prausnitzii, a butyrate-producing bacterium, was significantly higher in OB than that in other groups. This study is the first to examine the gut microbiota of adult Thais in association with dietary intake and blood profiles and will provide the platform for future investigations.
Gruneck et al. (2020) Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles. PeerJ 8:e9622 https://doi.org/10.7717/peerj.9622
Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine
Background Begomoviruses are widely distributed and causing devastating diseases in many crops. According to the number of genomic components, a begomovirus is known as either monopartite or bipartite begomovirus. Both the monopartite and bipartite begomoviruses have the DNA-A component which encodes all essential proteins for virus functions, while the bipartite begomoviruses still contain the DNA-B component. The satellite molecules, known as betasatellites, alphasatellites or deltasatellites, sometimes exist in the begomoviruses. So, the genomic components of begomoviruses are complex and varied. Different genomic components have different gene structures and functions. Classifying the components of begomoviruses is important for studying the virus origin and pathogenic mechanism. Methods We propose a model combining Subsequence Natural Vector (SNV) method with Support Vector Machine (SVM) algorithm, to classify the genomic components of begomoviruses and predict the genes of begomoviruses. First, the genome sequence is represented as a vector numerically by the SNV method. Then SVM is applied on the datasets to build the classification model. At last, recursive feature elimination (RFE) is used to select essential features of the subsequence natural vectors based on the importance of features. Results In the investigation, DNA-A, DNA-B, and different satellite DNAs are selected to build the model. To evaluate our model, the homology-based method BLAST and two machine learning algorithms Random Forest and Naive Bayes method are used to compare with our model. According to the results, our classification model can classify DNA-A, DNA-B, and different satellites with high accuracy. Especially, we can distinguish whether a DNA-A component is from a monopartite or a bipartite begomovirus. Then, based on the results of classification, we can also predict the genes of different genomic components. According to the selected features, we find that the content of four nucleotides in the second and tenth segments (approximately 150-350 bp and 1,450–1,650 bp) are the most different between DNA-A components of monopartite and bipartite begomoviruses, which may be related to the pre-coat protein (AV2) and the transcriptional activator protein (AC2) genes. Our results advance the understanding of the unique structures of the genomic components of begomoviruses.
Pei et al. (2020) Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine. PeerJ 8:e9625 https://doi.org/10.7717/peerj.9625
Molecular mechanism underlying the effect of illumination time on the growth performance of broilers via changes in the intestinal bacterial community
The circadian rhythms associated with light have important effects on the growth, metabolism, immunity and reproduction of broilers. However, there is a lack of systematic evaluations of the effect of the light cycle on intestinal microbes and the nutritional metabolism of these microbes in broilers. This study was designed to study the effects of the light cycle on the intestinal bacterial community structure and growth of broilers. In this study, Arbor Acre (AA) broilers were fed under a short photoperiod (1L:23D), a long photoperiod (23L:1D), and a normal photoperiod (16L:8D), respectively. The feed conversion ratio of the broilers was calculated, and the levels of endocrine hormones, such as melatonin, insulin and glucagon, were determined. Intestinal contents were collected from the small intestines of the broilers after slaughtering, and the V3+V4 region of the 16s rDNA gene was sequenced. The results demonstrated that changes in the light cycle could affect the synthetic rhythms of melatonin, insulin and glucagon. Compared to short and normal photoperiod, long photoperiod significantly increased the abundances of Barnesiella species in intestinal microbes and decreased the abundances of Bacteroides and Alistipes species. Cluster of Orthologous Groups of proteins analysis indicated that prolongation of the illumination increased the abundances of bacterial genes with glycometabolic and membrane transport functions in intestinal microorganisms. A model was established in this study, and our results showed that prolonged illumination altered the intestinal microbial community structures of broilers, increased the absorption and utilization of polysaccharides in broilers, and reduced the feed-to-meat ratios. To the best of our knowledge, this is also the first study to describe the molecular mechanism underlying the effects of the light cycle on the uptake and utilization of nutrients that occur via modification of the intestinal microbial community structure in broilers.
Wang et al. (2020) Molecular mechanism underlying the effect of illumination time on the growth performance of broilers via changes in the intestinal bacterial community. PeerJ 8:e9638 https://doi.org/10.7717/peerj.9638
Comparative transcriptomic analysis of Lactiplantibacillus plantarum RS66CD biofilm in high-salt conditions and planktonic cells
Background Lactiplantibacillus plantarum (L. plantarum), a dominant strain in traditional fermented foods, is widely used in fermentation industry because of its fast acid production. However, L. plantarum is easily inactivated due to acidity, high temperature and other factors. The formation of biofilm by bacteria can effectively increase environmental tolerance. Therefore, it is important to improve the environmental tolerance of L. plantarum by studying its biofilm formation conditions and regulatory mechanisms. Methods After determining a suitable NaCl concentration for promoting biofilm formation, L. plantarum was grown with 48 g L−1 NaCl. Differential gene expressions in L. plantarum biofilm vs. planktonic cells were analyzed using RNA sequencing and validated using qPCR. Result L. plantarum RS66CD biofilm formation formed highest amount of when grown at 48 g L−1 NaCl. Altogether 447 genes were up-regulated and 426 genes were down-regulated in the biofilm. KEGG pathway analysis showed that genes coding for D-Alanine metabolism, peptidoglycan biosynthesis, two-component system, carbon metabolism, bacterial secretion system, lysine biosynthesis and fatty acid metabolism were crucial for biofilm formation. In addition, eight other genes related to biofilm formation were differentially expressed. Our results provide insights into the differential gene expression involved in biofilm formation, which can help to reveal gene regulation during L. plantarum biofilm formation.
Ao et al. (2020) Comparative transcriptomic analysis of Lactiplantibacillus plantarum RS66CD biofilm in high-salt conditions and planktonic cells. PeerJ 8:e9639 https://doi.org/10.7717/peerj.9639
Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw
Background Chinese milk vetch (Astragalus sinicus L.) can improve paddy soil fertility and ecology through nitrogen fixation, but it can also increase greenhouse gas emissions. Our primary objective was to investigate how Chinese milk vetch, rice straw, and nitrogen fertilization affect the methane and microbial components of the rice rhizosphere. Methods We examined the rhizosphere’s methane emissions and microbial abundance and diversity after incorporating Chinese milk vetch and rice straw into paddy soil. We used high-throughput sequencing of the 16s rRNA and ITS1 genes to study changes in the bacterial and fungal communities, respectively. Over the course of our experiment, we applied seven different treatments to the paddy soil: conventional fertilization (the control treatment) for winter fallow crops, three levels of nitrogen in Chinese milk vetch, and three levels of nitrogen in Chinese milk vetch combined with rice straw. Results Rice yield and methane emissions increased during cultivation when the soil was treated with Chinese milk vetch with and without added straw. The nitrogen application also affected the methane fluxes. Alpha diversity measurements showed that Chinese milk vetch increased the diversity of the soil fungal community but did not significantly affect the bacterial community. Chinese milk vetch affected the rhizosphere microorganism communities by increasing the number of Methanomicrobia.
Ma et al. (2020) Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw. PeerJ 8:e9653 https://doi.org/10.7717/peerj.9653
Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis
Background Tumorigenesis is highly heterogeneous, and using clinicopathological signatures only is not enough to effectively distinguish clear cell renal cell carcinoma (ccRCC) and improve risk stratification of patients. DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis. Disorders of transcription and metabolism are also an important molecular mechanisms of tumorigenesis. Therefore, it is necessary to identify effective biomarkers involved in tumorigenesis through multi-omics analysis, and these biomarkers also provide new potential therapeutic targets. Method The discovery stage involved 160 pairs of ccRCC and matched normal tissues for investigation of DNAm and biomarkers as well as 318 cases of ccRCC including clinical signatures. Correlation analysis of epigenetic, transcriptomic and metabolomic data revealed the connection and discordance among multi-omics and the deregulated functional modules. Diagnostic or prognostic biomarkers were obtained by the correlation analysis, the Least Absolute Shrinkage and Selection Operator (LASSO) and the LASSO-Cox methods. Two classifiers were established based on random forest (RF) and LASSO-Cox algorithms in training datasets. Seven independent datasets were used to evaluate robustness and universality. The molecular biological function of biomarkers were investigated using DAVID and GeneMANIA. Results Based on multi-omics analysis, the epigenetic measurements uniquely identified DNAm dysregulation of cellular mechanisms resulting in transcriptomic alterations, including cell proliferation, immune response and inflammation. Combination of the gene co-expression network and metabolic network identified 134 CpG sites (CpGs) as potential biomarkers. Based on the LASSO and RF algorithms, five CpGs were obtained to build a diagnostic classifierwith better classification performance (AUC > 99%). A eight-CpG-based prognostic classifier was obtained to improve risk stratification (hazard ratio (HR) > 4; log-rank test, p-value < 0.01). Based on independent datasets and seven additional cancers, the diagnostic and prognostic classifiers also had better robustness and stability. The molecular biological function of genes with abnormal methylation were significantly associated with glycolysis/gluconeogenesis and signal transduction. Conclusion The present study provides a comprehensive analysis of ccRCC using multi-omics data. These findings indicated that multi-omics analysis could identify some novel epigenetic factors, which were the most important causes of advanced cancer and poor clinical prognosis. Diagnostic and prognostic biomarkers were identified, which provided a promising avenue to develop effective therapies for ccRCC.
Liu et al. (2020) Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis. PeerJ 8:e9654 https://doi.org/10.7717/peerj.9654
Characterization of two myostatin genes in pufferfish Takifugu bimaculatus: sequence, genomic structure, and expression
Myostatin (MSTN) is a negative regulator of muscle growth, which restrains the proliferation and differentiation of myoblasts. To understand the role of two mstn genes of Takifugu bimaculatus, the full-length cDNAs of 1131 bp Tbmstn1 and 1,080 bp Tbmstn2 were obtained from the T. bimaculatus’ genomic database, which encodes 376 and 359 amino acids, respectively. The results of qRT-PCR showed that Tbmstn1 was expressed in the eye, kidney, spleen, skeletal muscle, gill, and brain, and the expression level in the skeletal muscle was extremely significantly higher than in other examined tissues. Tbmstn2 was expressed in the skin, skeletal muscle, gill, and brain, and had the highest expression in the skeletal muscle, followed by expression in the brain. Meanwhile, in different stages of embryonic development, the expression of Tbmstn1 started from the gastrula stage. Its expression in the eye-pigment formation stage and hatching stage was significantly higher than that in other stages. The Tbmstn2 was expressed in all examined embryonic stages with different levels, and the highest expression was detected in the eye-pigment formation stage. These results suggested that Tbmstn1 and Tbmstn2 may involve in the development of skeletal muscle, and Tbmstn2 may be related to the formation of nervous system.
Sheng et al. (2020) Characterization of two myostatin genes in pufferfish Takifugu bimaculatus: sequence, genomic structure, and expression. PeerJ 8:e9655 https://doi.org/10.7717/peerj.9655
Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians
Background No Arabic or its dialect questionnaire is available to evaluate the anterior knee pain in the Saudi Arabian religious population. This study aims to translate, adapt, and psychometrically validate the Knee Injury and Osteoarthritis Outcome Score (KOOS-PF) Patellofemoral scale in the Arabic language in Saudi Arabic dialect. Method Translation has been done as per standard guidelines. The questionnaire was administered to 95 patients to determine the psychometric properties including on two different occasions, with a 48-hour gap in-between; to ensure that their answers were reliable; 84 patients (88.4% compliance rate) responded for test and retest reliability, ceiling-floor effects, validity and other psychometric criteria. Results Cronbach’s alpha (internal consistency) and test–retest reliability was good and excellent (∞ = 0.81; ICC > 0.95). None of the items showed >30% floor or ceiling effect and the minimal detectable change was within the acceptable range (<30%). The KOOS-PF subscale showed a moderate correlation (−0.568) with pain-visual analog scale for its construct validity. Conclusion The Arabic dialect of KOOS-PFis reliable and valid to be used to evaluate isolated knee pain of patellofemoral origin in Muslim patients in Saudi Arabia.
Ateef (2020) Measurement properties of the Knee Injury and Osteoarthritis Outcome Score Patello-Femoral questionnaire in Saudi Arabians. PeerJ 8:e9323 https://doi.org/10.7717/peerj.9323
Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage
In the Caribbean Basin the distribution and diversity patterns of deep-sea scleractinian corals and stylasterid hydrocorals are poorly known compared to their shallow-water relatives. In this study, we examined species distribution and community assembly patterns of scleractinian and stylasterid corals on three high-profile seamounts within the Anegada Passage, a deep-water throughway linking the Caribbean Sea and western North Atlantic. Using remotely operated vehicle surveys conducted on the E/V Nautilus by the ROV Hercules in 2014, we characterized coral assemblages and seawater environmental variables between 162 and 2,157 m on Dog Seamount, Conrad Seamount, and Noroît Seamount. In all, 13 morphospecies of scleractinian and stylasterid corals were identified from video with stylasterids being numerically more abundant than both colonial and solitary scleractinians. Cosmopolitan framework-forming species including Madrepora oculata and Solenosmilia variabilis were present but occurred in patchy distributions among the three seamounts. Framework-forming species occurred at or above the depth of the aragonite saturation horizon with stylasterid hydrocorals being the only coral taxon observed below Ωarag values of 1. Coral assemblage variation was found to be strongly associated with depth and aragonite saturation state, while other environmental variables exerted less influence. This study enhances our understanding of the factors that regulate scleractinian and stylasterid coral distribution in an underreported marginal sea and establishes a baseline for monitoring future environmental changes due to ocean acidification and deoxygenation in the tropical western Atlantic.
Auscavitch et al. (2020) Distribution of deep-water scleractinian and stylasterid corals across abiotic environmental gradients on three seamounts in the Anegada Passage. PeerJ 8:e9523 https://doi.org/10.7717/peerj.9523
Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight
Background Controversy exists on the relationship between iron metabolism and cardiometabolic risk. The aim of this study was to determine if there is a link between dysmetabolic iron and cardiometabolic markers in subjects with excess body weight. Methods Cross-sectional study with fifty participants presenting overweight or obesity and at least another metabolic syndrome factor. Determinations: anthropometry, body composition, blood pressure, lipids, glucose, insulin, leptin, areas under the curve (AUC) for glucose and insulin after an oral glucose tolerance test, hs-C reactive protein (hs-CRP), blood count, ferritin, transferrin, transferrin saturation (TSAT), soluble transferrin receptor (sTfR). Gender-adjusted linear correlations and two independent samples t tests were used. Results Ferritin was positively correlated with insulin-AUC (r = 0.547, p = 0.008) and TSAT was negatively correlated with waist-hip ratio (r = − 0.385, p = 0.008), insulin (r = − 0.551, p < 0.001), and insulin resistance (HOMA-IR, r = − 0.586, p < 0.001). Subjects with TSAT ≤ 20% had higher insulin (p = 0.012) and HOMA-IR (p = 0.003) compared to those with TSAT > 20%. In conclusion, the observed results suggest that iron transport and storage are altered in subjects with overweight/obesity, at the same time that they exhibit the characteristic features of insulin resistance. Nevertheless, this occurs without iron overload or deficiency. These results should be validated in wider cohorts since they suggest that iron transport and storage should be assessed when performing the clinical evaluation of subjects with excess body weight.
Vaquero et al. (2020) Relationship between iron status markers and insulin resistance: an exploratory study in subjects with excess body weight. PeerJ 8:e9528 https://doi.org/10.7717/peerj.9528