Clusters Of Orthologous Groups Database Research Articles

Complete Genome Sequence of Vibrio maritimus BH16, a Siderophore-Producing Mutualistic Bacterium Isolated from Diatom Skeletonema costatum.

Complete Genome Sequence of Vibrio maritimus BH16, a Siderophore-Producing Mutualistic Bacterium Isolated from Diatom Skeletonema costatum.

Comparative transcriptome analysis of leaf, stem, and root tissues of Semiliquidambar cathayensis reveals candidate genes involved in terpenoid biosynthesis.

Semiliquidambar cathayensis is a traditional medicinal plant and endemic species in China. Its roots, branches, leaves, bark, and nectar are known to have therapeutic effects against rheumatoid arthritis, lumbar muscle strain, and several other diseases. However, limited knowledge regarding the molecular properties of S. cathayensis highlights the need for further research in order to elucidate the underlying pathways governing the synthesis of its active ingredients and regulation of its accumulation processes. We conducted transcriptome sequencing of the leaf, stem and root epidermises, and stem and root xylems of S. cathayensis with three biological replicates. Moreover, candidate genes involved in terpenoid biosynthesis, such as IDI, FPPS, DXR, SQS, GPPS, and HMGR were selected for quantitative real-time PCR analysis. We identified 88,582 unigenes. Among which, 36,144 unigenes were annotated to the nr protein database, 21,981 to the Gene Ontology database, 11,565 to the Clusters of Orthologous Groups database, 24,209 to the Pfam database, 21,685 to the SWISS-PROT database, and 12,753 to the Kyoto Encyclopedia of Genes and Genomes (KEGG), with 5072 unigenes common to all six databases. Of those annotated using the KEGG database, 187 unigenes were related to the terpenoid metabolism pathway, and expression analysis of the related genes indicated that the mevalonate and methylerythritol 4-phosphate pathways play different roles in terpenoid biosynthesis in different tissues of S. cathayensis. These findings greatly expand gene resources of S. cathayensis and provide basic data for the study of the biosynthetic pathways and molecular mechanisms of terpenoids.

Isolation, identification, and whole-genome sequencing of high-yield protease bacteria from Daqu of ZhangGong Laojiu.

A total of 296 strains of protease-producing bacteria were isolated and purified from medium-temperature Daqu produced by ZhangGong LaoJiu Wine Co. Ltd. After calculating the ratio of transparent ring diameter to colony diameter and measuring the protease activities, a strain of high-yield protease bacteria, called DW-7, was screened out with a protease activity of 99.54 U/mL. Through morphological observation, 16S rDNA sequence analysis, and physiological and biochemical tests, the isolated bacteria DW-7 was determined to be Bacillus velezensis. In addition, whole-genome sequencing (WGS), using PacBio and the Illumina platform, was performed. Gene annotation was then conducted using the Clusters of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), Non-Redundant Protein Sequence Database (NR), and Gene Ontology (GO) databases. The results showed that the genome of DW-7 was 3,942,829 bp long with a GC content of 46.45%. A total of 3,662 protein-encoding genes were predicted, with a total length of 3,402,822 bp. Additionally, 2,283; 2,796; and 2,127 genes were annotated in the COG, KEGG, and GO databases, respectively. A total of 196 high-yield protease genes were mainly enriched in the metabolism of alanine, aspartic acid, glutamate, glycine, serine, and threonine, as well as ABC transporter and transporter pathways.

Organ-specific transcriptome sequencing and mining of genes involved in polyphyllin biosynthesis in Paris polyphylla

Paris polyphylla Smith is a perennial medicinal plant that is wildly distributed in China, and polyphyllin is the representative medicinal ingredient from the rhizome of this plant. To date, the mechanism of steroidal saponin biosynthesis in P. polyphylla is still unclear. In this study, comparative de novo transcriptome sequencing of the rhizomes, leaves and stems from P. polyphylla were performed with the Illumina HiSeq 2500 platform. A total of 53.71 Gb of transcriptomic data was obtained from the distinct organs, and 24,297 annotated unigenes out of 50,428 assembled unigenes were achieved by aligning with the nonredundant protein sequence database; evolutionary genealogy of genes: Nonsupervised Orthologous Groups; Pfam; Swiss-Prot; euKaryotic Orthologous Groups; Gene Ontology; Kyoto Encyclopedia of Genes and Genomes (KEGG); and the Clusters of Orthologous Groups databases, and 10,141 simple sequence repeat loci were identified based on their transcriptome profiles. KEGG pathway enrichment assigned 38, 32, and 7 unigenes to terpenoid backbone biosynthesis, steroid biosynthesis, and the sesquiterpenoid and triterpenoid biosynthesis pathway, respectively. A total of 25 unigenes that encoded 17 key enzymes were identified as being involved in steroidal saponin biosynthesis in P. polyphylla. CYP90B1 (4 unigenes) and CYP724B1 (2 unigenes) from the annotated cytochrome P450 s (36 unigenes) were inferred to play probable roles in steroidal saponin biosynthesis. The phylogenetic analysis of squalene monooxygenase and cycloartenol synthase from P. polyphylla indicated close homology with multiple monocots. Furthermore, the differentially expressed genes were identified by comparison of the transcriptome profiles of distinct organs in a pairwise fashion, and the expression patterns of the candidate unigenes that were potentially responsible for steroidal saponin biosynthesis were analyzed thoroughly and coupled with the determination of polyphyllin contents in the different organs. These findings offer abundant genetic resources and a molecular basis to further study polyphyllin biosynthesis in P. polyphylla and its closely related Paris species.

Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov.

This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5T, except for N2O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5T. Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5T. Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5T.

Transcriptome Landscape Variation in the Genus Thymus.

Among the Lamiaceae family, the genus Thymus is an economically important genera due to its medicinal and aromatic properties. Most Thymus molecular research has focused on the determining the phylogenetic relationships between different species, but no published work has focused on the evolution of the transcriptome across the genus to elucidate genes involved in terpenoid biosynthesis. Hence, in this study, the transcriptomes of five different Thymus species were generated and analyzed to mine putative genes involved in thymol and carvacrol biosynthesis. High-throughput sequencing produced ~43 million high-quality reads per sample, which were assembled de novo using several tools, then further subjected to a quality evaluation. The best assembly for each species was used as queries to search within the UniProt, KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (Clusters of Orthologous Groups) and TF (Transcription Factors) databases. Mining the transcriptomes resulted in the identification of 592 single-copy orthogroups used for phylogenetic analysis. The data showed strongly support a close genetic relationship between Thymus vulgaris and Thymus daenensis. Additionally, this study dates the speciation events between 1.5–2.1 and 9–10.2 MYA according to different methodologies. Our study provides a global overview of genes related to the terpenoid pathway in Thymus, and can help establish an understanding of the relationship that exists among Thymus species.

Identification of novel genes essential for Brucella abortus to establish infection by signature-tagged mutagenesis

Brucella is a facultative intracellular bacterium, causing brucellosis, an important zoonosis worldwide. Brucella has no classic virulence factors, thus virulence is dependent on invasion of host cells and subsequent intracellular replication. Identification of key genes involved in Brucella virulence is important to further elucidate its pathogenesis. In this study, signature-tagged mutagenesis was used to identify novel genes involved in B. abortus infection in a mouse model. In total 3600 mutants were obtained, of which 56 were identified as attenuated mutants. Furthermore, 53 genes were identified to be inactivated by transposon insertion, including 19 genes previously reported to be essential for Brucella virulence and 34 others that were newly identified in this study. These genes were catalogued into 16 functional classifications, except for three that were not cited in the Clusters of Orthologous Groups database. Bioinformatics analysis revealed that energy production and conversion, amino acid transport and metabolism, as well as inorganic ion transport and metabolism were predominant functional classifications, suggesting that genes involved in these functions were crucial for Brucella virulence. In addition, the function of the identified pyruvate carboxylase (pyc) gene in bacterial virulence was confirmed using an allelic replacement pyc mutant and a mouse model. These findings provide novel genetic information associated with Brucella infection.

De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana.

Dysphania schraderiana is widely distributed in Lhasa (Tibet, China) and used as a traditional medicine. However, the lack of genetic information hinders the understanding of its physiological processes, such as the biosynthesis of secondary metabolites. Herein, we used Illumina Hiseq4000 platform to sequence the transcriptome of flower and leaf tissues from D. schraderiana for the first time. Totally, 40,142 unigenes were assembled from approximately 5.2 million clean reads. All unigenes underwent gene prediction and were subsequently annotated in a NR (NCBI non-redundant protein) database, COG (Clusters of Orthologous Groups of proteins) database, and KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Among the 40,142 unigenes, 2,579 genes were identified as differentially expressed between flowers and leaves, and used in further enrichment analysis. Also, 2,156 unigenes were annotated as transcription factors. Furthermore, our transcriptome analysis resulted in the identification of candidate unigenes annotated to enzymes involved in terpenoid biosynthesis. Taken together, this work has laid the foundation for the investigation of secondary metabolite biosynthesis and other physiological processes of D. schraderiana.

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

BackgroundClematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the “Queen of the Vines”. However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C. finetiana obtained using the Illumina paired-end sequencing technology.ResultsSequences on a total of 71,900 high-quality unigenes with the mean length of 865 bp were produced in this study. There were 6192unigenes annotated and classified into 49 functional sub-groups in three main ontology categories in GO (Gen Ontology) database,14,022 unigenes mapped to COGs (Clusters of Orthologous Groups) database and classified into 25 functional categories, and 21,494 unigenes obtained and divided into 128 pathways of KEGG (Kyoto Encyclopedia of Genes) Database. A total of 7532 SSRs were discovered from 6337 unigenes. We randomly tested 210 primer pairs, of which 52 primer pairs were able to generate specific products, and 19 possessed polymorphism in the 13 wild populations of six species from Clematis, which were used as a test material.ConclusionsThe dataset of C. finetiana transcriptome and the identified new SSR markers will promote genetic research and breeding effort in Clematis.

Gene expression profiling of the unfed nymphal Dermacentor silvarum (Acari: Ixodidae) in response to low temperature

The tick Dermacentor silvarum is recognized as an emerging vector of marked medical and veterinary significance. The current study investigated the gene expression profiling of the unfed nymphal D. silvarum in response to low temperature using high-throughput transcriptome sequencing. A total of approximately 12-giga base pairs were produced, which yielded 87,500 unigenes, and among them, 29,815 unigenes were successfully annotated by all available databases (NCBI nonredundant, Swissprot, UniProtKB/TrEMBL, the clusters of orthologous groups databases, the Kyoto encyclopedia of genes and genomes database, and pfam database). After low temperature treatment (4°C for 10 days), 2,241 genes, including 1,160 up-regulated and 1,081 down-regulated genes, were differentially expressed. The differentially expressed genes were further enriched to GO terms and KEGG pathways, and our results showed that 133 genes were enriched in molecular function, 90 genes were enriched in cellular components, 107 genes were enriched in biological processes and 202 genes were assigned into different KEGG pathways. This study establishes a molecular basis for gene function analysis in the tick D. silvarum, and will provide theoretical information for mechanistic studies on the overwintering adaptations of ticks.

Modification of Flight and Locomotion Performances, Respiratory Metabolism, and Transcriptome Expression in the Lady Beetle Harmonia axyridis through Sublethal Pesticide Exposure.

Biological control is usually used in combination with chemical control for practical agricultural applications. Thus, the influence of insecticides on the natural predators used for biological control should be investigated for integrated pest management. The ladybird Harmonia axyridis is an effective predator on aphids and coccids. Beta-cypermethrin is a broad-spectrum insecticide used worldwide for controlling insect pests. H. axyridis is becoming increasingly threatened by this insecticide. Here, we investigated the effect of a sublethal dose of beta-cypermethrin on flight, locomotion, respiration, and detoxification system of H. axyridis. After exposure to beta-cypermethrin, succinic female adults flew more times, longer distances, and during longer time periods. Exposure to a sublethal dose of beta-cypermethrin also promoted an increase in walking rate, walking distance, walking duration, and also an increase in respiratory quotient and respiratory rate. To investigate the effects of beta-cypermethrin on H. axyridis detoxification system, we analyzed the transcriptome of H. axyridis adults, focusing on genes related to detoxification systems. De novo assembly generated 65,509 unigenes with a mean length of 799 bp. From these genes, 26,020 unigenes (40.91% of all unigenes) exhibited clear homology to known genes in the NCBI non-redundant database. In addition, 10,402 unigenes were annotated in the Cluster of Orthologous Groups database, 12,088 unigenes were assigned to the Gene Ontology database and 12,269 unigenes were in the Kyoto Encyclopedia of Genes and Genome (KEGG) database. Exposure to beta-cypermethrin had significant effects on the transcriptome profile of H. axyridis adult. Based on uniquely mapped reads, 3,296 unigenes were differentially expressed, 868 unigenes were up-regulated and 2,248 unigenes were down-regulated. We identified differentially-expressed unigenes related to general detoxification systems in H. axyridis. This assembled, annotated transcriptome provides a valuable genomic resource for further understanding the molecular basis of detoxification mechanisms in H. axyridis.

Sequencing and de novo assembly of visceral mass transcriptome of the critically endangered land snail Satsuma myomphala: Annotation and SSR discovery

Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis. We identified 103,774 unigenes of which 37,959, 12,890, and 17,699 were annotated in the PANM (Protostome DB), Unigene, and COG (Clusters of Orthologous Groups) databases, respectively. In addition, 14,451 unigenes were predicted under Gene Ontology functional categories, with 4581 assigned to a single category. Furthermore, 3369 sequences with 646 having Enzyme Commission (EC) numbers were mapped to 122 pathways in the Kyoto Encyclopedia of Genes and Genomes Pathway database. The prominent protein domains included the Zinc finger (C2H2-like), Reverse Transcriptase, Thioredoxin-like fold, and RNA recognition motif domain. Many unigenes with homology to immunity, defense, and reproduction-related genes were screened in the transcriptome. We also detected 3120 putative simple sequence repeats (SSRs) encompassing dinucleotide to hexanucleotide repeat motifs from >1kb unigene sequences. A list of PCR primers of SSR loci have been identified to study the genetic polymorphisms. The transcriptome data represents a valuable resource for further investigations on the species genome structure and biology. The unigenes information and microsatellites would provide an indispensable tool for conservation of the species in natural and adaptive environments.

Transcriptome analysis in the beet webworm, Spoladea recurvalis (Lepidoptera: Crambidae).

The beet webworm, Spoladea recurvalis Fabricius, is a destructive pest on vegetable crops in tropics and subtropics; its main host plant is amaranth. It has become imperative to develop non-chemical methods to control S. recurvalis on amaranth. However, the lack of molecular information about this species has hindered the development of novel pest management strategies. In this study, high-throughput RNA sequencing covering de novo sequence assemblies, functional annotation of transcripts, gene function classification and enrichment was performed on S. recurvalis. Illumina sequencing generated a total of 120435 transcript contigs ranging from 201 to 22729 bases with a mean length of 688 bases. The assembled transcripts were subjected to Basic Local Alignment Search Tool-X (BLASTX) to obtain the annotations against non-redundant, Swiss-Prot, Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases. A subset of 58225 transcript sequences returned hits from known proteins in the National Center for Biotechnology Information database, and the majority of the transcript sequences had the highest number of hits for Danaus plexippus (50.43%). A total of 1217 Gene Ontology-level 3 annotations were assigned to 51805 transcripts, while 39650 transcripts were predicted as functional protein-coding genes in the COG database and 20037 transcripts were enriched to KEGG pathways. We identified 40 putative genes related to pheromone production and reception in S. recurvalis, with the expression of one gene between 0.29 and 1141.79 fragments per kilo base per million (FPKM) reads. The transcriptome sequence of S. recurvalis is a first step toward offering a comprehensive genomic resource which would enable better understanding of molecular mechanisms to enable development of effective pest management practices for this species.

Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes.

Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.

Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants.

Bacillus subtilis XF-1 is a gram-positive, plant-associated bacterium that stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. In particular, it is especially highly efficient at controlling the clubroot disease of cruciferous crops. Its 4,061,186-bp genome contains an estimated 3853 protein-coding sequences and the 1155 genes of XF-1 are present in most genome-sequenced Bacillus strains: 3757 genes in B. subtilis 168, and 1164 in B. amyloliquefaciens FZB42. Analysis using the Cluster of Orthologous Groups database of proteins shows that 60 genes control bacterial mobility, 221 genes are related to cell wall and membrane biosynthesis, and more than 112 are genes associated with secondary metabolites. In addition, the genes contributed to the strain's plant colonization, bio-control and stimulation of plant growth. Sequencing of the genome is a fundamental step for developing a desired strain to serve as an efficient biological control agent and plant growth stimulator. Similar to other members of the taxon, XF-1 has a genome that contains giant gene clusters for the non-ribosomal synthesis of antifungal lipopeptides (surfactin and fengycin), the polyketides (macrolactin and bacillaene), the siderophore bacillibactin, and the dipeptide bacilysin. There are two synthesis pathways for volatile growth-promoting compounds. The expression of biosynthesized antibiotic peptides in XF-1 was revealed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

De novo assembly and characterization of the skeletal muscle transcriptome of sheep using Illumina paired-end sequencing

In order to enrich the ovine genome and provide a basis for future molecular genetics and functional genomics analyses in sheep, we used de novo assembly to establish transcriptomes of skeletal muscle tissues of Dorper and Small-tailed Han sheep. A total of 103,058,824 clean Illumina paired-end sequencing reads from the two libraries were assembled into 145,524 unigenes in a de novo project. There were 5718 unigenes showing differential expression between the two transcriptomes, and 7437 coding SSRs were exploited. After further assembly, we identified a total of 70,348 all-unigenes with an average length of 863bp; 35,201 of these all-unigenes could be annotated in the Nr database, and 12,219 were found in the clusters of orthologous groups database. Gene ontology searches indicated cell and binding as the main terms. Among 258 Kyoto Encyclopedia of Genes and Genomes database pathways, protein and amino acid metabolism pathways were the most commonly identified. We analyzed the ovine muscle transcriptome using high-throughput sequencing technology. Many unigenes were assembled and numerous molecular markers and differential expressed unigenes were identified.

Subtraction suppressive hybridisation analysis of differentially expressed genes associated with puberty in the goat hypothalamus.

The cost of developing replacement nanny goats could be reduced by decreasing the age at puberty because this way nanny goats could be brought into production at an earlier age. The aim of the present study was to screen genes related to puberty to investigate the molecular mechanisms of puberty. Subtracted cDNA libraries were constructed for hypothalami from juvenile (Group A), pubertal (Group B) and age-matched control pubertal (Group E) Jining grey (JG) and Liaoning cashmere (LC) goats using suppression subtractive hybridisation (SSH). Differentially expressed genes were analysed by bioinformatics methods. There were 203 expressed sequence tags (ESTs) in the subtracted cDNA libraries that were differentially expressed between JG and LC goats at the juvenile stage, 226 that were differentially expressed at puberty and 183 that were differentially expressed in the age-matched control group. The differentially expressed ESTs in each subtracted cDNA library were classified as known gene, known EST and unknown EST according to sequence homology in the GenBank non-redundant (NR) and EST database. According to gene function analysis in the COG (Cluster of Orthologous Groups) database, the known genes were grouped into 10 subdivisions in Group A, into seven subdivisions in Group E and into nine subdivisions in Group B under three categories: cellular processes and signalling, information storage and processing, and metabolism. Pathway analysis in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database of known genes revealed that the three pathways that most differentially expressed genes were involved in were metabolic pathways, Parkinson's disease and oxidative phosphorylation. Protein interaction analysis of the high homology genes revealed the most dominant network to be structure of ribosome/protein translation, oxidative phosphorylation and carbohydrate metabolism. The results reveal that the onset of puberty is a complex event involving multiple genes in multiple biological processes. The differentially expressed genes include genes related to both neuroendocrine and energy metabolism.

Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome

PurposeThe microbiome modulates numerous aspects of human physiology and is a crucial factor in the development of various human diseases. Vitamin D deficiency and downregulation of the vitamin D receptor (VDR) are also associated with the pathogenesis of diseases such as inflammatory bowel disease, cancers, obesity, diabetes, and asthma. VDR is a nuclear receptor that regulates the expression of antimicrobial peptides and autophagy regulator ATG16L1. Vitamin D may promote a balanced intestinal microbiome and improve glucose homeostasis in diabetes. However, how VDR regulates microbiome is not well known. In the current study, we hypothesize that VDR status regulates the composition and functions of the intestinal bacterial community. MethodsFecal and cecal stool samples were harvested from Vdr knockout (Vdr−/−) and wild-type mice for bacterial DNA and then sequenced with 454 pyrosequencing. The sequences were denoised and clustered into operational taxonomic units, then queried against the National Center for Biotechnology Information database. Metagenomics were analyzed, and the abundances of genes involved in metabolic pathways were compared by reference to the Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups databases. FindingsIn the Vdr−/− mice, Lactobacillus was depleted in the fecal stool, whereas Clostridium and Bacteroides were enriched. Bacterial taxa along the Sphingobacteria-to-Sphingobacteriaceae lineage were enriched, but no genera reached statistical significance. In the cecal stool, Alistipes and Odoribacter were depleted, and Eggerthella was enriched. Notably, all of the taxa upstream of Eggerthella remained unchanged. A comparison of Vdr−/− and wild-type samples revealed 40 (26 enriched, 14 depleted) and 72 (41 enriched, 31 depleted) functional modules that were significantly altered in the cecal and fecal microbiomes, respectively (both, P < 0.05), due to the loss of Vdr. In addition to phylogenetic differences in gut microbiome with different intestinal origins, we identify several important pathways, such as nucleotide-binding oligomerization domain–like receptor, affected by Vdr status, including amino acid, carbohydrate, and fatty acid synthesis and metabolism, detoxification, infections, signal transduction, and cancer and other diseases. ImplicationsOur study fills knowledge gaps by having investigated the microbial profile affected by VDR. Insights from our findings can be exploited to develop novel strategies to treat or prevent various diseases by restoring VDR function and healthy microbe–host interactions.

Lacking vitamin D receptor leads to intestinal dysbiosis

The microbiome modulates numerous aspects of human physiology and is critical in development of diseases. Vitamin D and its receptor VDR are associated with various diseases. We hypothesize that VDR status alters the composition and functions of microbiota. Fecal and cecal stool samples were harvested from VDR knockout mice and intestinal epithelial VDR conditional knockout (VDRΔIEC) mice. After 454 pyrosequencing, the sequences were clustered into OTUs. PICRUSt, together with HUMAnN were used to analyze the metagenomics and to compare abundances of genes involved in metabolic pathways by reference to KEGG and Clusters of Orthologous Groups databases. In VDR‐/‐ KO mice, Lactobacillus was depleted in fecal stool, whereas Clostridium and Bacteroides were enriched. In cecal stool, Alistipes and Odoribacter were depleted, and Eggerthella was enriched. A comparison between WT and VDR‐/‐ revealed 72 (41 enriched, 31 depleted) and 40 (26 enriched, 14 depleted) functional modules that were significantly altered in fecal and cecal microbiome, respectively. VDRΔIEC mice had enriched Eubacterium, Allobaculum, Prevotella, Limbacter, Anaplasma and depleted Akkermansia in fecal stool, and enriched Roseburia, Pseudoflavonifractor, Allobaculum, Prevotella, Alistipes and Eggerthella, and depleted Lactobacillus and Streptomyces in cecal stool. The numbers of functional modules significantly altered were 75 (33 enriched, 42 depleted) and 89 (47 enriched, 42 depleted) in fecal and cecal microbiome, respectively. Functional alterations regarded synthesis/metabolism of amino acids, carbohydrates and fatty acids, detoxification, infection, and cancer. Effects of VDR in maintaining host‐microbe interactions are critical for intestinal homeostasis. The insights can be exploited to develop novel strategies by restoring VDR in illness.

Transcriptome analysis for leaves of five chemical types in Cinnamomum camphora

Camphor tree (Cinnamomum camphora) is a representative species in Lauraceae family, and can be subdivided into five types: linalool, camphor, cineol, iso-nerolidol and borneol. In this paper, the leaves transcriptomes of Cinnamomum camphora were sequenced with the platform of Illumina HiSeq™ 2000. Based on the GO (Gene Ontology), COG (Clusters of Orthologous Groups), and KEGG (Kyoto Encyclopedia of Genes and Genomes) database, the function classification, pathway annotation, and the coding sequence prediction of all-Unigenes were carried out. 156 278 Unigenes with an average length of 584 bp and N50 (N50 value is defined as the Unigene length where half the assembly is represented by Unigenes of this size or longer) of 1 023 bp were generated by de novo assembly. A total of 5 5955 Unigenes (35.80%) were annotated through similarity comparison, in which 24 717 and 21 806 Unigenes were assigned into GO and COG, respectively. By searching KEGG database, 3 350 Unigenes were involved in biosynthesis of secondary metabolites, in which 424 Unigenes were involved in monoterpenoids, diterpenoids, sesquiterpenoids, and terpenoid backbone biosynthesis. The analysis of monoterpenoids biosynthesis pathway showed that 9 Unigenes likely encode (+)-linalool synthase, and their expression levels were higher in linalool type but lower in cineole type. This study provides a foundation for further characterizing the functional genes in C. camphora.