Draft Genome Sequence of Coprobacter fastidiosus NSB1T

Bioinformatics in Russia: history and present-day landscape

Bioinformatics has become an interdisciplinary subject due to its universal role in molecular biology research. The current status of Russia's bioinformatics research in Russia is not known. Here, we review the history of bioinformatics in Russia, present the current landscape, and highlight future directions and challenges. Bioinformatics research in Russia is driven by four major industries: information technology, pharmaceuticals, biotechnology, and agriculture. Over the past three decades, despite a delayed start, the field has gained momentum, especially in protein and nucleic acid research. Dedicated and shared centers for genomics, proteomics, and bioinformatics are active in different regions of Russia. Present-day bioinformatics in Russia is characterized by research issues related to genetics, metagenomics, OMICs, medical informatics, computational biology, environmental informatics, and structural bioinformatics. Notable developments are in the fields of software (tools, algorithms, and pipelines), use of high computation power (e.g. by the Siberian Supercomputer Center), and large-scale sequencing projects (the sequencing of 100 000 human genomes). Government funding is increasing, policies are being changed, and a National Genomic Information Database is being established. An increased focus on eukaryotic genome sequencing, the development of a common place for developers and researchers to share tools and data, and the use of biological modeling, machine learning, and biostatistics are key areas for future focus. Universities and research institutes have started to implement bioinformatics modules. A critical mass of bioinformaticians is essential to catch up with the global pace in the discipline.

Heminiphilus faecis gen. nov., sp. nov., a member of the family Muribaculaceae, isolated from mouse faeces and emended description of the genus Muribaculum

The novel strain AM35^T was isolated from the faeces of C57BL/6 mice. These cells are strictly anaerobic, gram negative, oxidase negative, catalase positive, rod-shaped and non-motile. The strain produced creamy yellowish colonies on brain heart infusion (BHI) agar with hemin. Growth was investigated at 30-41 °C in the presence of 0.5-1.5% (w/v) NaCl at pH 6.5-8.5. Taxonomic analysis based on 16S rRNA gene sequencing revealed that strain AM35^T is affiliated with the family Muribaculaceae and closely related to the genus Muribaculum. The genomic DNA G + C content of strain AM35^T was 47.8 mol%. We detected the whole-cell sugars ribose and galactose; meso-2,6-diaminopimelic acid was absent. The major fatty acids (> 10%) were anteiso-C_15:0 and iso-C_15:0; the major polar lipid was phosphatidylethanolamine. The major respiratory quinones were MK-10 and MK-11. Based on our phylogenetic, phenotypic and chemotaxonomic analyses, strain AM35^T represents a novel genus within the family Muribaculaceae, for which we propose the name Heminiphilus faecis gen. nov., sp. nov. The type strain of Heminiphilus faecis gen. nov., sp. nov. is AM35^T (= KCTC 15907 ^T = DSM 110151 ^T).

Association analysis of dietary habits with gut microbiota of a native Chinese community

Environmental exposure, including a high-fat diet (HFD), contributes to the high prevalence of colorectal cancer by changing the composition of the intestinal microbiota. However, data examining the interaction between dietary habits and intestinal microbiota of the Chinese population is sparse. We assessed dietary habits using a food frequency questionnaire (FFQ) in native Chinese community volunteers. Based on the dietary fat content determined using the FFQ, the volunteers were divided into HFD group (≥40% of dietary calories came from fat) or low-fat diet (LFD) group (<40%). Fecal and colonic mucosal microbiota composition was determined using 16S rDNA based methods. In stool matter of HFD group, Prevotella and Abiotrophia showed significantly higher abundance, whereas unclassified genus of S24-7 (family level) of Bacteroidetes, Gemmiger, Akkermansia and Rothia were less abundant. On colonic mucosal tissue testing, unclassified genus of S24-7 showed significantly higher abundance while Bacteroides, Coprobacter, Abiotrophia, and Asteroleplasma were less abundant in HFD group. A high fat and low fiber diet in a native Chinese community may partially contribute to changes of intestinal microbiota composition that may potentially favor the onset and progression of gastrointestinal disorders including inflammatory, hyperplastic and neoplastic diseases.

Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces

Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism.The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C15 : 0 fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 (in a 1 : 1 ratio) and the predominant menaquinone was MK-11.The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627T and 177T placed these bacteria in the genera Alistipes(family Rikenellaceae) and Coprobacter (family Porphyromonadaceae), respectively.On the basis of the phenotypic and genotypic properties of strains 627T and 177T, we conclude that these strains from human faeces represent two novel bacterial species, for which the names Alistipes inops sp. nov. (type strain 627T5DSM 28863T5VKM B-2859T) and Coprobacter secundus sp. nov. (type strain 177T=DSM 28864T=VKM B-2857T) are proposed.