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

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

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

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

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Global diversity and geography of soil fungi

We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.

A new species

With the advancement of molecular techniques in the last two decades, cultures of marine fungi have been sequenced, and several new lineages of marine fungi have been revealed, suggesting multiple evolution of fungi into the marine environment. High-throughput sequencing has also allowed discovery of unculturable marine fungi, such as the Cryptomycota. Traditionally, marine fungi are known to belong mostly to the Ascomycota and asexual morphs with few basidiomycetes and chytrids. In this chapter, we will introduce the phylogenetic diversity of these groups with the emphasis on the ascomycetous classes Dothideomycetes and Sordariomycetes, where most marine ascomycetes are referred to. We will also summarize the current knowledge on the marine taxa at the basal lineages of fungi including the phyla Aphelida, Cryptomycota, and Microsporidia, currently classified in the superphylum Opisthosporidia.

Phylogenetic Diversity of Fungi in the Sea including the Opisthosporidia

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TAXONOMY AND PHYLOGENY OF DOTHIDEOMYCETES ( Title & copyright page)

Torpedospora yanbuensis sp. nov. (Torpedosporales, Sordariomycetes), a new marine fungus from the Red Sea mangroves, Saudi Arabia

Abstract This article revises the documented diversity of known marine fungi from nine phyla, 33 classes, 107 orders, 273 families, 767 genera and 1898 species reported worldwide. A member of the Aphelidiomycota, Pseudaphelidium drebesii, is reported for the first time from the marine environment, on a diatom. Likewise, the phylum Mortierellomycota is listed following taxonomic changes, as are six subclasses: Chaetothyriomycetidae, Savoryellomycetidae, Sclerococcomycetidae, Agaricostilbomycetidae, Auriculariomycetidae and Aphelidiomycotina. Thirty-three orders and 105 family names with marine species are added to the checklist, along with 641 species in 228 genera, bringing the total to 1898. New additions of species added to the list of marine fungi are highlighted. Four new combinations are proposed: Stigmatodiscus mangrovei, Diaporthe krabiensis and Diaporthe xylocarpi, while the hyphomycete Humicola alopallonella is referred to the genus Halosphaeriopsis, as Halosphaeriopsis alopallonella.

Updates on the classification and numbers of marine fungi

Abstract The fungal community associated with marine crabs is poorly known, except for the fungi causing diseases of marine animals of economic value. In this study we examined the diversity of fungi cultured from carapace and gut of the marine crab Portunus sanguinolentus, and the identification was based on nucleotide BLAST search results of the internal transcribed spacers of rDNA (ITS). A total of 256 fungal isolates representing 23 species were cultured from seven individuals of P. sanguinolentus including two unidentified species. The majority of the species belong to the Ascomycota, while three species of the Basidiomycota were isolated from the gut. Overall, Candida tropicalis (45.70 %, percentage occurrence), Apiotrichum lignicola (8.98 %) and Rhodotorula sp. (8.20 %) were the dominant fungi on the crab. The most dominant fungi on the carapace were C. tropicalis (66.95 %), Emericellopsis maritima (8.47 %), A. lignicola and Purpureocillium lilacinum (both 4.24 %). In the gut, C. tropicalis (27.54 %), A. lignicola (16.67 %), Rhodotorula sp. (15.22 %) and Fusarium solani (14.49 %) were dominant. The fungal diversity in the gut of P. sanguinolentus was higher than on the carapace according to the diversity indices. Although some of the isolated fungi were reported to be pathogenic, none were reported as pathogens of crabs, and no disease symptoms were noticed from the crab samples.

E. B. Gareth Jones

Papers

Phylogenetic Diversity of Fungi in the Sea including the Opisthosporidia

TAXONOMY AND PHYLOGENY OF DOTHIDEOMYCETES ( Title & copyright page)

Torpedospora yanbuensis sp. nov. (Torpedosporales, Sordariomycetes), a new marine fungus from the Red Sea mangroves, Saudi Arabia

Updates on the classification and numbers of marine fungi

Diversity of fungi isolated from carapace and gut of the marine crab Portunus sanguinolentus in northern waters of Taiwan