Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
Project description:Changjiang (Yangtze River) Estuary has experienced severe hypoxia since the 1950s. In order to investigate potential ecological functions of key microorganisms in relation to hypoxia, we performed 16S rRNA-based Illumina Miseq sequencing to explore the bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea (ECS). The results showed that numerous Proteobacteria-affiliated sequences in the sediments of the inner continental shelf were related to both sulfate-reducing and sulfur-oxidizing bacteria, suggesting an active sulfur cycle in this area. Many sequences retrieved from the hypoxic zone were also related to Planctomycetes from two marine upwelling systems, which may be involved in the initial breakdown of sulfated heteropolysaccharides. Bacteroidetes, which is expected to degrade high-molecular-weight organic matter, was abundant in all the studied stations except for station A8, which was the deepest and possessed the largest grain size. In addition, dissolved organic carbon, water depth, percentage ratio of clay to silt, salinity, and sedimentary grain size were environmental effectors that shaped the sedimentary microbial community structure. Our results showed that putative Gammaproteobacteria-affiliated sulfur-oxidizing bacteria may not only detoxify hydrogen sulfide produced by sulfate-reducing prokaryotes, but also serve as the primary producers in the marine sediments. Specific groups of aerobic Bacteroidetes and Planctomycetes participated in degrading organic matter, which might contribute to the oxygen depletion in the hypoxic zones.
Project description:Marine algal toxins, highly toxic secondary metabolites, have significant influences on coastal ecosystem health and mariculture safety. The occurrence and environmental control factors of lipophilic marine algal toxins (LMATs) in the surface seawater of the Changjiang estuary (CJE) and the adjacent East China Sea (ECS) were investigated. Pectenotoxin-2 (PTX2), okadaic acid (OA), dinophysistoxin-1(DTX1), and gymnodimine (GYM) were detected in the CJE surface seawater in summer, with concentration ranges of not detected (ND)-105.54 ng/L, ND-13.24 ng/L, ND-5.48 ng/L, and ND-12.95 ng/L, respectively. DTX1 (ND-316.15 ng/L), OA (ND-16.13 ng/L), and PTX2 (ND-4.97 ng/L) were detected in the ECS during spring. LMATs formed a unique low-concentration band in the Changjiang diluted water (CJDW) coverage area in the typical large river estuary. PTX2, OA, and DTX1 in seawater were mainly derived from Dinophysis caudate and Dinophysis rotundata, while GYM was suspected to be from Karenia selliformis. Correlation analyses showed that LMAT levels in seawater were positively correlated with dissolved oxygen and salinity, but negatively correlated with temperature and nutrients, indicating that the hydrological condition and nutritional status of seawater and climatic factors exert significant effects on the distribution of LMATs.
Project description:Amino acids (AAs) constitute the largest reservoir of organic nitrogen in most marine organisms and are a major fraction of characterized carbon in marine particulate matter. AAs are also useful indicators of degradation in the marine environment. This article reports original content data of 17 individual amino acids on 47 surface sediment samples and 18 suspended particulate samples in the water column in Changjiang Estuary. Contents of amino acids in suspended particulates were much higher than that in the surface sediments. The data are supplemental to our research paper, entitled "Organic matter degradation in surface sediments of the Changjiang Estuary: Evidence from amino acids" (Wang et al., 2018) [1]. The data are very useful to researchers and policy makers on estuarine benthic environment and ecology.
Project description:The northwestern Pacific, characterized by unique tectonic and hydrological settings, has greatly intrigued marine phylogeographers. However, current studies mostly focus on the influence of Pleistocene isolation of sea basins in population structure of species in the region, leaving the contribution of other factors (such as freshwater outflow and environmental gradients) largely unexploited. Here we shed light on the question by investigating phylogeography of the surf clam Mactra chinensis in the East China Sea (ECS). Genetic information was acquired from 501 specimens collected from its main distribution in the region, represented by mitochondrial cytochrome oxidase I (COI) and nine polymorphic microsatellite loci. A shallow and star-like phylogeny was revealed for all COI haplotypes, indicating the origin of populations from a single refugium. Although no divergent lineages existed, population subdivision was detected in both data sets. The most striking pattern was the significant differentiation between populations north and south of a biogeographic boundary-the Changjiang Estuary, suggesting a barrier effect of the freshwater outflow to gene flow. For the northern group, substructure was revealed by COI result as one southernmost population was significant different from other ones. Clear latitude gradations in allele frequencies were revealed by microsatellite analyses, likely influenced by environmental gradient factors such as temperature. Our results demonstrate that genetic subdivision can arise for populations within the ECS despite they have a single origin, and multiple mechanisms including Changjiang River outflow, environmental gradient factors and life-history traits may act in combination in the process.
Project description:Here we report metagenomic sequencing data in gut microbiota of autism spectrum disorders (ASD) compared with healthy volunteers (30 for ASD children and 30 for healthy controls, respectively). The genes changed in autistic subjects involved 1,312,364 analytes that compare to 1,335,835 analytes in healthy controls. The number of taxa in autistic subjects were significantly increased as compared to the healthy controls based on the phylum and genus level (P = 0.001). However, the number of species were significantly decreased in autistic subjects (P = 0.001).