Metagenomics articles within Nature

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  • Article
    | Open Access

    Two Prevotella copri metagenome-assembled genomes that are positively associated with ponderal growth are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2—a microbiome-directed complementary food.

    • Matthew C. Hibberd
    • , Daniel M. Webber
    •  & Jeffrey I. Gordon

  • Article
    | Open Access

    Faecal carbohydrates, particularly host-accessible monosaccharides, are increased in individuals with insulin resistance and are associated with microbial carbohydrate metabolisms and host inflammatory cytokines.

    • Tadashi Takeuchi
    • , Tetsuya Kubota
    •  & Hiroshi Ohno

  • Article
    | Open Access

    Analyses of multiple phylogenetic marker datasets of Asgard archaea provide insight into the transition from prokaryotes to eukaryotes, specifically placing eukaryotes within Asgard archaea and as a sister lineage to Hodarchaeales.

    • Laura Eme
    • , Daniel Tamarit
    •  & Thijs J. G. Ettema

  • Article
    | Open Access

    A phylogeny-guided genome-resolved metagenomic analysis of DNA viruses in the ocean reveals atypical plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota.

    • Morgan Gaïa
    • , Lingjie Meng
    •  & Tom O. Delmont

  • Article
    | Open Access

    Data from more than 9,700 human stool and oral metagenomes has been used to decipher the strain transmission patterns of the human microbiome from mother to infant, within households and within populations.

    • Mireia Valles-Colomer
    • , Aitor Blanco-Míguez
    •  & Nicola Segata

  • Article
    | Open Access

    Cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera, and the majority of respiration was found to be performed by minority members of prokaryoplankton, whereas cells of the most prevalent lineages had extremely low respiration rates.

    • Jacob H. Munson-McGee
    • , Melody R. Lindsay
    •  & Ramunas Stepanauskas

  • Article |

    A computational system termed MetaWIBELE (workflow to identify novel bioactive elements in the microbiome) is used to identify microbial gene products that are potentially bioactive and have a functional role in the pathogenesis of inflammatory bowel disease.

    • Yancong Zhang
    • , Amrisha Bhosle
    •  & Eric A. Franzosa

  • Article |

    Serratus, an open-source cloud-computing infrastructure, can be used to screen millions of nucleic acid sequencing libraries at the petabase scale, and has enabled many new RNA viruses to be identified efficiently.

    • Robert C. Edgar
    • , Brie Taylor
    •  & Artem Babaian

  • Article
    | Open Access

    A large-scale metagenomic analysis of plant and mammal environmental DNA reveals complex ecological changes across the circumpolar region over the past 50,000 years, as biota responded to changing climates, culminating in the postglacial extinction of large mammals and emergence of modern ecosystems.

    • Yucheng Wang
    • , Mikkel Winther Pedersen
    •  & Eske Willerslev

  • Article
    | Open Access

    Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.

    • Marsha C. Wibowo
    • , Zhen Yang
    •  & Aleksandar D. Kostic

  • Article |

    Analyses of microbial communities that live 10–750 m below the seafloor at Atlantis Bank, Indian Ocean, provide insights into how these microorganisms survive by coupling energy sources to organic and inorganic carbon resources.

    • Jiangtao Li
    • , Paraskevi Mara
    •  & Virginia P. Edgcomb

  • Article |

    Microbial nucleic acids are detected in samples of tissues and blood from more than 10,000 patients with cancer, and machine learning is used to show that these can be used to discriminate between and among different types of cancer, suggesting a new microbiome-based diagnostic approach.

    • Gregory D. Poore
    • , Evguenia Kopylova
    •  & Rob Knight

  • Article
    | Open Access

    Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.

    • Basem Al-Shayeb
    • , Rohan Sachdeva
    •  & Jillian F. Banfield

  • Article |

    The human placenta does not have a microbiota, suggesting that bacterial infection of the placenta is not a common cause of adverse pregnancy outcome, but group B Streptococcus is found in approximately 5% of placental samples.

    • Marcus C. de Goffau
    • , Susanne Lager
    •  & Gordon C. S. Smith

  • Article
    | Open Access

    The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.

    • Alexandre Almeida
    • , Alex L. Mitchell
    •  & Robert D. Finn

  • Letter
    | Open Access

    An analysis of more than 10,000 metagenomes from the TEDDY study provides a detailed functional profile of the gut microbiome in relation to islet autoimmunity, and supports the protective effects of short-chain fatty acids in early-onset type 1 diabetes.

    • Tommi Vatanen
    • , Eric A. Franzosa
    •  & Ramnik J. Xavier

  • Letter |

    Metagenomic and soil microcosm analyses identify abundant biosynthetic gene clusters in genomes of microorganisms from a northern Californian grassland ecosystem that provide a potential source for the future development of bacterial natural products.

    • Alexander Crits-Christoph
    • , Spencer Diamond
    •  & Jillian F. Banfield

  • Letter |

    Genome data for thirteen alphaproteobacteria-related clades expand the coverage of alphaproteobacterial diversity and suggest that mitochondria diverged from Alphaproteobacteria before the diversification of all currently known alphaproteobacterial lineages.

    • Joran Martijn
    • , Julian Vosseberg
    •  & Thijs J. G. Ettema

  • Article |

    Commensal bacteria have N-acyl amide synthase genes that encode signalling molecules (N-acyl amides) that can interact with G-protein-coupled receptors and elicit host cellular responses similar to eukaryotic N-acyl amides.

    • Louis J. Cohen
    • , Daria Esterhazy
    •  & Sean F. Brady

  • Article |

    This work describes the Asgard superphylum, an assemblage of diverse archaea that comprises Odinarchaeota, Heimdallarchaeota, Lokiarchaeota and Thorarchaeota, offering insights into the earliest days of eukaryotic cells and their complex features.

    • Katarzyna Zaremba-Niedzwiedzka
    • , Eva F. Caceres
    •  & Thijs J. G. Ettema

  • Article |

    An analysis of bacterial community structure and antibiotic resistance gene content of interconnected human faecal and environmental samples from two low-income communities in Latin America was carried out using a combination of functional metagenomics, 16S sequencing and shotgun sequencing; resistomes across habitats are generally structured along ecological gradients, but key resistance genes can cross these boundaries, and the authors assessed the usefulness of excreta management protocols in the prevention of resistance gene dissemination.

    • Erica C. Pehrsson
    • , Pablo Tsukayama
    •  & Gautam Dantas

  • Letter |

    Until now, the oxidation steps necessary for complete nitrification had always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by Daims et al., van Kessel et al. report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as ‘comammox’ (for complete ammonia oxidation).

    • Maartje A. H. J. van Kessel
    • , Daan R. Speth
    •  & Sebastian Lücker

  • Letter |

    More than 15% of the bacterial domain consists of a radiation of phyla about which very little is known; here, metagenomics is used to reconstruct 8 complete and 789 draft genomes from more than 35 of these phyla, revealing a shared evolutionary history, metabolic limitations, and unusual ribosome compositions.

    • Christopher T. Brown
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Article |

    This study identifies a clade of archaea that is the immediate sister group of eukaryotes in phylogenetic analyses, and that also has a repertoire of proteins otherwise characteristic of eukaryotes—proteins that would have provided the first eukaryotes with a ‘starter kit’ for the genomic and cellular complexity characteristic of the eukaryotic cell.

    • Anja Spang
    • , Jimmy H. Saw
    •  & Thijs J. G. Ettema

  • Article |

    The physical size of the commonly used Cas9 from Streptococcus pyogenes poses challenges for CRISPR-Cas genome editing systems that use the adeno-associated virus as a delivery vehicle; here, smaller Cas9 orthologues are characterized, and Cas9 from Staphylococcus aureus allowed targeting of the cholesterol regulatory gene Pcsk9 in the mouse liver.

    • F. Ann Ran
    • , Le Cong
    •  & Feng Zhang

  • Article |

    Previous work has shown that human skin is home to a rich and varied microbiota; here a metagenomic approach for samples from physiologically diverse body sites illuminates that the skin microbiota, including bacterial, fungal and viral members, is shaped by the local biogeography and yet marked by strong individuality.

    • Julia Oh
    • , Allyson L. Byrd
    •  & Julia A. Segre

  • Article |

    Non-caloric artificial sweeteners (NAS), widely used food additives considered to be safe and beneficial alternatives to sugars, are shown here to lead to the development of glucose intolerance through compositional and functional changes in the gut microbiota of mice, and the deleterious metabolic effects are transferred to germ-free mice by faecal transplant; NAS-induced dysbiosis and glucose intolerance are also demonstrated in healthy human subjects.

    • Jotham Suez
    • , Tal Korem
    •  & Eran Elinav

  • Letter |

    The metagenome of uncultured, Pacific Ocean viruses linked to a ubiquitous cyanobacteria is characterized using viral-tagging, revealing discrete populations in viral sequence space that includes previously cultivated populations and new populations missed in isolate-based studies.

    • Li Deng
    • , J. Cesar Ignacio-Espinoza
    •  & Matthew B. Sullivan

  • Letter |

    Functional metagenomic selections for resistance to 18 antibiotics in 18 different soils reveal that bacterial community composition is the primary determinant of soil antibiotic resistance gene content.

    • Kevin J. Forsberg
    • , Sanket Patel
    •  & Gautam Dantas

  • Letter |

    Viruses are isolated from the SAR11 bacterial clade, the most abundant group of bacteria in the ocean, that were thought to be resistant to viral infection; because of the essential role of SAR11 in carbon cycling these viruses are also an important factor in biogeochemical cycling.

    • Yanlin Zhao
    • , Ben Temperton
    •  & Stephen J. Giovannoni

  • Article |

    A framework for metagenomic variation analysis to explore variation in the human microbiome is developed; the study describes SNPs, short indels and structural variants in 252 faecal metagenomes of 207 individuals from Europe and North America.

    • Siegfried Schloissnig
    • , Manimozhiyan Arumugam
    •  & Peer Bork

  • News & Views |

    An innovative method for probing the genomes of the vast community of microorganisms that inhabit the human gut provides an alternative approach to identifying risk factors for type 2 diabetes. See Letter p.55

    • Julia Oh
    •  & Julia A. Segre

  • Article |

    The authors have developed a new method, metagenome-wide association study (MGWAS), to compare the combined genetic content of the faecal microbiota of healthy people versus patients with type 2 diabetes; they identify multiple microbial species and metabolic pathways that are associated with either cohort and show that some of these may be used as biomarkers.

    • Junjie Qin
    • , Yingrui Li
    •  & Jun Wang

  • News & Views |

    Microbial inhabitants outnumber our body's own cells by about ten to one. These residents have become the subject of intensive research, which is beginning to elucidate their roles in health and disease. See Articles p.207 & p.215

    • David A. Relman

  • Article
    | Open Access

    The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

    • Curtis Huttenhower
    • , Dirk Gevers
    •  & Owen White

  • Article
    | Open Access

    The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.

    • Barbara A. Methé
    • , Karen E. Nelson
    •  & Owen White

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