The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

Bacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2 . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.Phages-viruses that infect bacteria-are considered distinct from cellular life owing to their inability to carry out most biological processes required for reproduction. They are agents of ecosystem change because they prey on specific bacterial populations, mediate lateral gene transfer, alter host metabolism and redistribute bacterially derived compounds through cell lysis 2-4 . They spread antibiotic resistance 5 and disperse pathogenicity factors that cause disease in humans and animals 6,7 . Most knowledge about phages is based on laboratorystudied examples, the vast majority of which have genomes that are a few tens of kb in length. Widely used isolation-based methods select against large phage particles, and they can be excluded from phage concentrates obtained by passage through 100-nm or 200-nm filters 1 . In 2017, only 93 isolated phages with genomes that were more than 200 kb in length were published 1 . Sequencing of whole-community DNA can uncover phage-derived fragments; however, large genomes can still escape detection owing to fragmentation 8 . A new clade of human-and animal-associated megaphages was recently described on the basis of genomes that were manually curated to completion from metagenomic datasets 9 . This finding prompted us to carry out a more-comprehensive analysis of microbial communities to evaluate the prevalence, diversity and ecosystem distribution of phages with large genomes. Previously, phages with genomes of more than 200 kb have been referred to as 'jumbophages' 1 or, in the case of phages with genomes of more than 500 kb, as megaphages 9 . As the set reconstructed here span both size ranges we refer to them simply as 'huge phage...

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration.

In vitro fabrication of vascularized three-dimensional (3D) human cardiomyocyte (CM) tissues derived from human induced pluripotent stem cells (iPSCs) has attracted much attention owing to their requirement of much amount of nutrition and oxygen, but not yet published. In this manuscript, we report construction of vascularized 3D-iPSC-CM tissues by a newly-discovered filtration-Layer-by-Layer (LbL) technique. The filtration-LbL fabricates nanometer-sized fibronectin and gelatin (FN-G) films onto iPSC-CM surfaces. The FN-G nanofilms induce cell-cell interactions via integrin molecules on cell surfaces, leading to construction of 3D-tissues. The constructed vascularized 3D-iPSC-CM tissues would be a promising tool for tissue regeneration and drug development. We believe that this manuscript has a strong impact and offers important suggestions to researchers concerned with biomaterials and tissue engineering.

Objective: To examine the correlation between dietary glycemic index (GI) and cardiovascular disease (CVD) risk factors among subjects who consume white rice as a staple food. Design: A cross-sectional study was conducted to explore the associations between dietary GI, dietary glycemic load (GL) and dietary intakes, and CVD risk factors. Dietary GI and GL were calculated from a 3-day (including two consecutive weekdays and one holiday) dietary records. Setting: A weight-reduction program at a municipal health center in Tokyo, Japan. Subjects: A total of 32 women aged 52.577.2 y participated in the weight-reduction program. Result: The GI food list made for the current study calculated for 91% of carbohydrate intakes measured. The mean dietary GI was 6476, and the mean dietary GL was 150737. Individuals in the highest tertile of GI consumed more carbohydrate, mostly from white rice (Po0.001), and less fat (Po0.01). Individuals in all three groups by tertile of GL showed similar tendencies. In the lowest GI tertile, the highest concentration of HDL-cholesterol and lowest concentration of triacylglycerol and immunoreactive insulin were observed (Po0.01). In the lowest GL tertile, the highest concentration of HDL-cholesterol and the lowest concentration of triacylglycerol were observed (Po0.05). Conclusion: Calculated dietary GI and GL were positively associated with CVD risk factors among the Japanese women who consumed white rice as a staple food.