Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

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Diet rapidly and reproducibly alters the human gut microbiome

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Evolution of Protein Molecules

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

http://web.stanford.edu/~kpeay/papers/Koljalg_2013_MEC.pdf

Towards a unified paradigm for sequence-based identification of fungi

A method employing tissue culture techniques for growth of mosses is described. This method allows for the completion of the sexual life cycle of the mossPhyscomitrella patens (Hedw.) BSG under controlled conditions in a two month period. The moss system is useful for class demonstration or for research in the areas of development, genetics and plant physiology.

Life cycle of the moss,Physcomitrella patens, in culture

The stipitate pore-bearing fungus Polyporus tricholoma (Polyporus infrageneric group Polyporellus) is commonly reported from Mesoamerica and more rarely from the palaeotropics. Collections from Puerto Rico, Mexico, and Costa Rica did not differ morphologically, but their monokaryotic cultures revealed the existence of three interINcompatibility groups. These putative cryptic species exist sympatrically in Costa Rica. Sequencing, restriction enzyme digestion, and specific primers targeting the ITS region of nuclear ribosomal DNA (ITS 1-5.8S-ITS2) could only partly be used for detecting intercompatibility groups. Heterogeneity within the rDNA repeat was observed. Molecular evidence supports the existence of a close relative in Australia.

The tropical Polyporus tricholoma (Polyporaceae) — Taxonomy, phylogeny, and the development of methods to detect cryptic species

Multivariate morphometric analyses of micromorphological characters measured on 35 specimens of Flammulina fennae and related species show that only a combination of spore dimensions and ixohyphidia characters are suitable for delimitation of this species. In order to confirm species identifications based on micromorphology, ribosomal ITS DNA sequences were obtained and compared with those previously deposited in GenBank, and phylogenetic analyses were performed using an ITS dataset of all known Flammulina species. All six specimens morphologically determined as F. fennae were identified by molecular data. Two of twelve specimens morphologically assigned to F. velutipes had F. elastica sequences. One ITS sequence of F. velutipes appears to be a hybrid: the ITS1 region is homologous to F. velutipes and ITS2 is homologous to another Flammulina species, F. rossica. Variability of morphocharacters observed for F. fennae and related species is discussed and compared with the data from previous studies. A key is provided to European taxa of the genus Flammulina together with a full description of F. fennae.

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The delimitation of Flammulina fennae

Tetraploid tobacco plants (Nicotiana tabacum) derived from cultured cell lines (TC) are partially cross-incompatible with their diploid progenitors (C). C x TC crosses (TC-derived tetraploids as the pollen parent) yield only 2% viable seed. The remaining seeds are normal size but lack an embryo (apoembryonic seeds). Apoembryonic seeds do not occur in the reciprocal TC x C crosses. Sections of ovules from C x TC crosses revealed that an embryo formed but that embryo growth slowed at 5 days postpollination and that by the 12th day following pollination, the embryo had disappeared although the ovule continued to develop. Endosperm degeneration occurred concurrently with embryo death. Culturing ovules from C x TC crosses has increased the yield of F1 plants from 2% to as much as 25% indicating that embryo rescue is possible. Surviving F1 plants from TC x C crosses have close to triploid chromosome numbers and are fertile. WHEN PLANT TISSUES are placed in culture, there is sometimes an increase in point mutations and chromosomal aberrations (Scowcroft and Larkin, 1982). In previous studies, tobacco plants (Nicotiana tabacum var. Wis. 38) were regenerated from both herbicide (paraquat)resistant and wild type cell lines (Miller and

Reciprocal differences in intraspecific crosses of tobacco result from embryo death

Ability of several populations of theMimulus luteas complex to intercross was compared with an estimate of genetic divergence of the populations derived from a Prim network based on 134 traits. On the average we find that low levels of genetic differentiation result in heterosis or partial interference with ability to intercross and that with increasing genetic divergence, these are replaced with increasingly strong barriers to gene exchange.

Karen W. Hughes

Papers

Life cycle of the moss,Physcomitrella patens, in culture

The tropical Polyporus tricholoma (Polyporaceae) — Taxonomy, phylogeny, and the development of methods to detect cryptic species

The delimitation of Flammulina fennae

Reciprocal differences in intraspecific crosses of tobacco result from embryo death

Patterns of heterosis and crossing barriers resulting from increasing genetic distance between populations of theMimulus luteus complex