The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Sara C. Di Rienzi,Itai Sharon,Kelly C. Wrighton,Omry Koren,Laura A. Hug,Brian C. Thomas,Julia K. Goodrich,Jordana T. Bell,Tim D. Spector,Jillian F. Banfield,Ruth E. Ley +10 more
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TLDR
This article used whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which they propose the designation "Melainabacteria".Abstract:
Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation 'Melainabacteria'. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI:http://dx.doi.org/10.7554/eLife.01102.001.read more
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STAMP: statistical analysis of taxonomic and functional profiles
TL;DR: UNLABELLED STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles and a user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots.
Journal ArticleDOI
Human Genetics Shape the Gut Microbiome
Julia K. Goodrich,Jillian L. Waters,Angela C. Poole,Jessica L. Sutter,Omry Koren,Ran Blekhman,Michelle Beaumont,Will Van Treuren,Rob Knight,Rob Knight,Jordana T. Bell,Tim D. Spector,Andrew G. Clark,Ruth E. Ley +13 more
TL;DR: Compared microbiotas across >1,000 fecal samples obtained from the TwinsUK population, many microbial taxa whose abundances were influenced by host genetics were identified.
Journal ArticleDOI
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers,Nikos C. Kyrpides,Ramunas Stepanauskas,Miranda Harmon-Smith,Devin F. R. Doud,T. B. K. Reddy,Frederik Schulz,Jessica K. Jarett,Adam R. Rivers,Adam R. Rivers,Emiley A. Eloe-Fadrosh,Susannah G. Tringe,Susannah G. Tringe,Natalia Ivanova,Alex Copeland,Alicia Clum,Eric D. Becraft,Rex R. Malmstrom,Bruce W. Birren,Mircea Podar,Peer Bork,George M. Weinstock,George M. Garrity,Jeremy A. Dodsworth,Shibu Yooseph,Granger G. Sutton,Frank Oliver Gloeckner,Jack A. Gilbert,William C. Nelson,Steven J. Hallam,Sean P. Jungbluth,Sean P. Jungbluth,Thijs J. G. Ettema,Scott Tighe,Konstantinos T. Konstantinidis,Wen Tso Liu,Brett J. Baker,Thomas Rattei,Jonathan A. Eisen,Brian P. Hedlund,Katherine D. McMahon,Noah Fierer,Rob Knight,Robert D. Finn,Guy Cochrane,Ilene Karsch-Mizrachi,Gene W. Tyson,Christian Rinke,Alla Lapidus,Folker Meyer,Pelin Yilmaz,Donovan H. Parks,A. M. Eren,Lynn M. Schriml,Jillian F. Banfield,Philip Hugenholtz,Tanja Woyke +56 more
TL;DR: Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
Journal ArticleDOI
The first 1000 cultured species of the human gastrointestinal microbiota
TL;DR: This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya, Archaea and Bacteria based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences and unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms.
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Ecology and exploration of the rare biosphere
Michael D. Lynch,Josh D. Neufeld +1 more
TL;DR: The ecology of rare microbial populations is discussed, molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities are highlighted, and the value of studying the biogeography of microorganisms is highlighted.
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