Search

13 pages, 5 figures, supplementary information https://doi.org/10.1038/s41587-020-0718-6.-- Data availability: All available metagenomic data, bins and annotations are available through the IMG/M portal (https://img.jgi.doe.gov/). Bulk download for the 52,515 MAGs is available at https://genome.jgi.doe.gov/GEMs and https://portal.nersc.gov/GEM. Genome-scale metabolic models for the nonredundant, high-quality GEMs are summarized at https://doi.org/10.25982/53247.64/1670777 and available in KBase (https://narrative.kbase.us/#org/jgimags). IMG/M identifiers of all metagenomes binned, including detailed information for each metagenome, are available in Supplementary Table 1.-- The pipeline used to generate the metagenome bins is available at https://bitbucket.org/berkeleylab/metabat/src/master/, Publisher Correction: A genomic catalog of Earth’s microbiomes; Nature Biotechnology 39: 520 (2021); https://doi.org/10.1038/s41587-020-00769-4, The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes, This work was conducted by the US DOE Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02–05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US DOE (contract no. DE-AC02–05CH11231). This work was also supported as part of the Genomic Sciences Program DOE Systems Biology KBase (award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886).-- With the funding support of the ‘Severo Ochoa Centre of Excelle

Download ArticleExport citationTOTAL VIEWSSuggest a Research Topic >SHARE ONORIGINAL RESEARCH ARTICLEFront. Microbiol., 12 March 2020 | https://doi.org/10.3389/fmicb.2020.00376Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34fMichael L. Chen1,2, Eric D. Becraft1,3, Maria Pachiadaki1,4, Julia M. Brown1, Jessica K. Jarett5†, Josep M. Gasol6,7, Nikolai V. Ravin8, Duane P. Moser9, Takuro Nunoura10, Gerhard J. Herndl11,12, Tanja Woyke5 and Ramunas Stepanauskas1*1Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States2Department of Biology, Williams College, Williamstown, MA, United States3Department of Biology, University of North Alabama, Florence, AL, United States4Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States5U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States6Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain7Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia8Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia9Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States10Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan11Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria12Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, NetherlandsBacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.

© 2018 The Author(s). Background: Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity. Results: From 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs. Conclusions: This population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations.

© 2018 Waite, Vanwonterghem, Rinke, Parks, Zhang, Takai, Sievert, Simon, Campbell, Hanson, Woyke, Klotz and Hugenholtz. In our original publication, we proposed the phylum name Epsilonbacteraeota according to a proposal to modify Rule 8 of the International Code of Nomenclature of Prokaryotes, under which the suffix -aeota would be used to denote prokaryotic phyla (Oren et al., 2015). An addendum to this proposal was recently made whereby the shorter suffix -ota, instead of -aeota, be added to the stem of the name of one of the contained classes (Whitman et al., 2018). In accordance with this amendment, and the requirement that a class name is derived from a type genus (Oren et al., 2015), we propose to replace the name Epsilonbacteraeota with Campylobacterota. This change does not affect subordinate ranks of the phylum. Campylobacterota (Cam.py.lo.bac.ter.o'ta. N.L. neut. n. Campylobacter type genus of the type order of the type class of the phylum; suff. -ota, proposed ending to denote a phylum; N.L. neut. pl. n. Campylobacterota the phylum of the class Campylobacteria).

© 2018 Nature Publishing Group. All rights reserved. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen.

© 2018 Beukes, Palmer, Manyaka, Chan, Avontuur, van Zyl, Huntemann, Clum, Pillay, Palaniappan, Varghese, Mikhailova, Stamatis, Reddy, Daum, Shapiro, Markowitz, Ivanova, Kyrpides, Woyke, Blom, Whitman, Venter and Steenkamp. A corrigendum on Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato by Beukes, C. W., Palmer, M., Manyaka, P., Chan, W. Y., Avontuur, J. R., van Zyl, E., et al. (2017) Front. Microbiol. 8:1154. doi: 10.3389/fmicb.2017.01154. In the original article, there was a spelling mistake in a species name contained in Table 3 as published. As the information in this table is required for validation of the novel species combinations, this mistake has been corrected from "Caballeronia ptereocthonis comb. nov." to "Caballeronia ptereochthonis comb. nov." and "Burkholderia ptereocthonis" to "Burkholderia ptereochthonis". The corrected Table 3 appears below. TABLE 3: Table 3. Summary of the novel combinations proposed for 13 species of Caballeronia. Also, an additional section titled "Description of New Species Combinations" was added to the original article. The section contains a short protologue for each proposed novel combination to conform to the rules of the Bacterial Code of Nomenclature. The protologues appear below. The authors apologize for this error. The original article has been updated. Description of New Species Combinations. Description of Caballeronia arvi comb. nov. Caballeronia arvi (ar'vi. L. gen. n. arvi of a field). Basonym: Burkholderia arvi Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Analysis of 106 conserved protein-coding sequences have shown that this species is placed in the genus Caballeronia with very high support. The type strain is LMG 29317T (= CCUG 68412T = MAN34T). Description of Caballeronia arationis comb. nov. Caballeronia arationis (a.ra.ti.o'nis. L. gen. n. arationis from a field). Basonym: Burkholderia arationis Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Phylogenetic analysis of 106 conserved protein-coding loci clearly showed that there is high support for the placement of this species in Caballeronia. The type strain is LMG 29324T (=CCUG 68405T). Description of Caballeronia calidae comb. nov. Caballeronia calidae (ca'li.dae. L. gen. n. calidae from warm water, because this strain was isolated from pond water in a tropical garden). Basonym: Burkholderia calidae Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Phylogenetic analysis of 106 conserved protein-coding loci showed (with a high degree of certainty) that this species belongs in the genus Caballeronia. The type strain is LMG 29321T (=CCUG 68408T). Description of Caballeronia catudaia comb. nov. Caballeronia catudaia (ca.tu.da'ia. Gr. adj. catudaios subterraneous; N. L. fem. adj. catudaia, earth-born). Basonym: Burkholderia catudaia Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Our analyses of 106 conserved protein-coding loci clearly indicate that this species has high support for being included in Caballeronia. The type strain is LMG 29318T (=CCUG 68411T). Description of Caballeronia concitans comb. nov. Caballeronia concitans (con.ci'tans. L. fem. part. pres. concitans disturbing, upsetting; because the isolation of this bacterium from human sources, including blood, further disturbs the image of this lineage of Burkholderia species as benign bacteria). Basonym: Burkholderia concitans Peeters et al., 2016. The description is as provided in Peeters et al. (2016). Analysis of 106 conserved protein-coding loci showed that this species has high support for belonging to the genus Caballeronia. The type strain is LMG 29315T (=CCUG 68414T = AU12121T). Description of Caballeronia fortuita comb. nov. Caballeronia fortuita (for.tu.i'ta. L. fem. adj. fortuita accidental, unpremeditated; referring to its fortuitous isolation when searching for Burkholderia caledonica endophytes). Basonym: Burkholderia fortuita Peeters et al., 2016. The description is as described in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci clearly show this species is included in the genus Caballeronia. The type strain is LMG 29320T (=CCUG 68409T). Description of Caballeronia glebae comb. nov. Caballeronia glebae (gle'bae. L. gen. n. glebae from a lump or clod of earth, soil). Basonym: Burkholderia glebae Peeters et al., 2016. The description appears in Peeters et al. (2016). Analysis of 106 conserved protein-coding loci shows high support for the placement of this species in the genus Caballeronia. The type strain is LMG 29325T (=CCUG 68404T). Description of Caballeronia hypogeia comb. nov. Caballeronia hypogeia (hy.po.ge'ia. Gr. adj. hypogeios subterraneous; N. L. fem. adj. hypogeia, subterraneous, earth-born). Basonym: Burkholderia hypogeia Peeters et al., 2016. The description appears in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci supports the inclusion of this species into the genus Caballeronia. The type strain is LMG 29322T (=CCUG 68407T). Description of Caballeronia pedi comb. nov. Caballeronia pedi (pe'di. Gr. n. pedon soil, earth; N. L. gen. n. pedi, from soil). Basonym: Burkholderia pedi Peeters et al. 2016. The description is listed in Peeters et al. (2016). The analysis of 106 conserved protein-coding loci, showed that this species is placed in Caballeronia. The type strain is LMG 29323T (=CCUG 68406T). Description of Caballeronia peredens comb. nov. Caballeronia peredens (per.e'dens. L. fem. part. pres. peredens consuming, devouring; referring to the capacity of this bacterium to degrade fenitrothion). Basonym: Burkholderia peredens Peeters et al., 2016. The description is as discussed in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci clearly shows that this species should be included in the genus Caballeronia. The type strain is LMG 29314T (=CCUG 68415T = NF100T). Description of Caballeronia ptereochthonis comb. nov. Caballeronia ptereochthonis (pte.re.o.chtho'nis Gr. n. pteris fern; Gr. n. chthon soil; N. L. gen. n. ptereochthonis, from fern soil). Basonym: Burkholderia ptereochthonis Peeters et al., 2016. The description appears in Peeters et al. (2016). The analysis of 106 conserved protein-coding loci clearly shows that this species should be included in Caballeronia. The type strain is LMG 29326T (=CCUG 68403T). Description of Caballeronia temeraria comb. nov. Caballeronia temeraria (te.me.ra'ri.a. L. fem. adj. temeraria accidental, inconsiderate; referring to its accidental isolation when searching for Burkholderia caledonica endophytes). Basonym: Burkholderia temeraria Peeters et al., 2016. The description of this species appears in Peeters et al. (2016). The analysis of 106 conserved protein-coding loci here, shows that this species is included in Caballeronia with high support. The type strain is LMG 29319T (=CCUG 68410T). Description of Caballeronia turbans comb. nov. Caballeronia turbans (tur'bans. L. fem. part. pres. turbans disturbing, agitating, because the isolation of this bacterium from human pleural fluid further disturbs the image of this lineage of Burkholderia species as benign bacteria). Basonym: Burkholderia turbans Peeters et al., 2016. The original species description appears in Peeters et al. (2016). Our analysis of 106 conserved protein-coding loci shows that this species forms part of Caballeronia. The type strain is LMG 29316T (=CCUG 68413T = HI4065T). Conflict of Interest Statement. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

© 2018 Hahnke, Meier-Kolthoff, García-López, Mukherjee, Huntemann, Ivanova, Woyke, Kyrpides, Klenk and Göker. In the Taxonomic Consequences section of the Discussion chapter of the original article the type of the newly proposed class Saprospiria was incorrectly indicated (and in conflict with the etymology paragraph) within the description of the class. A correction has accordingly been made to Discussion, Taxonomic Consequences, Description of Saprospiria, class. nov.: Description of Saprospiria, class. nov. Sa.pros.pi'ri.a (N.L. fem. n. Saprospira, type genus of the type order of the class, -ia ending to denote a class; N.L. fem. pl. n. Saprospiria, the class of the order Saprospirales). The description is the same as for the order Saprospirales. This class is described on the basis of 16S rRNA gene and whole-genome phylogenetic analysis. The type and currently sole order of the class is Saprospirales. The authors apologize for this error and state that this does not change the scientific conclusions of the original article in any way. The original article has been updated.

© 2018 Pold et al. Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous forest in central Massachusetts. Here, we present the complete genome sequence of this phylogenetically novel organism, which consists of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and 3,273 predicted open reading frames.

© Springer Science+Business Media, LLC 2018. Sequencing of single bacterial and archaeal cells is an important methodology that provides access to the genetic makeup of uncultivated microorganisms. We here describe the high-throughput fluorescence-activated cell sorting-based isolation of single cells from the environment, their lysis and strand displacement-mediated whole genome amplification. We further outline 16S rRNA gene sequence-based screening of single-cell amplification products, their preparation for Illumina sequencing libraries, and finally propose computational methods for read and contig level quality control of the resulting sequence data.

There is a growing appreciation for the important roles microorganisms play in association with plants. Microorganisms are drawn to distinct plant surfaces by the nutrient-rich microenvironment, and in turn some of these colonizing microbes provide mutualistic benefits to their host. The development of plant probiotics to increase crop yield and provide plant resistance against biotic and abiotic stresses, while minimizing chemical inputs, would benefit from a deeper mechanistic understanding of plant-microbe interaction. Technological advances in molecular biology and high-throughput -omics provide stepping stones to the elucidation of critical microbiome gene functions that aid in improving plant performance. Here, we review -omics-based approaches that are propelling forward the current understanding of plant-associated bacterial gene functions, and describe how these technologies have helped unravel key bacterial genes and pathways that mediate pathogenic, beneficial, and commensal host interactions. Plants host large bacterial communities of importance to plant health and development. High-throughput -omics approaches have promoted elucidation of bacterial genes and pathways active at the plant-bacteria interface. We describe these methods and present functions performed by plant-associated bacterial genes that have been characterized by employing -omics methods.

© 2017 The Author(s). A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T(DSM 21565T= KCTC 5659T) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G+C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82Tgenome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.

© 2017 The Author(s). Paraburkholderiacaballeronis is a plant-associated bacterium. Strain TNe-841Twas isolated from the rhizosphere of tomato (Solanum lycopersicum L. var. lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was found to effectively nodulate Phaseolus vulgarisL. However, from an analysis of the genome of strain TNe-841Tand from repeat inoculation experiments, we found that this strain did not nodulate bean and also lacked nodulation genes, suggesting that the genes were lost. The genome consists of 7,115,141 bp with a G + C content of 67.01%. The sequence includes 6251 protein-coding genes and 87 RNA genes.

© 2017 The Author(s). Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0-3.0 μm × 0.5-1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis strain CT14-3T. The draft genome of P. extremaustralis strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%). We performed experimental analyses of the lipolytic activity and results showed activity mainly on short chain fatty acids. The genome analysis demonstrated the existence of two genes, lip515A and est515A, related to a triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes were also observed, mainly nitrate reductase genes. Genes related with synthesis of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were detected. The phaABC and phbABC operons also appeared complete in the genome. P. extremaustralis strain USBA-GBX-515 conserves the same gene organization of the type strain CT14-3T. We also thoroughly analyzed the potential for production of secondary metabolites finding close to 400 genes in 32 biosynthetic gene clusters involved in their production.

© 2017 The Author(s). The type strain of the prospective Bradyrhizobium shewensesp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina bruceinative to Ethiopia. The type strain Bradyrhizobium yuanmingenseCCBAU 10071T, was isolated from the nodules of Lespedeza cuneatain Beijing, China. The genomes of ERR11Tand CCBAU 10071Twere sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11Tis 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes. The CCBAU 10071Tgenome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiensUSDA110T. The genes encoding for nodulation and nitrogen fixation in ERR11Tshowed high sequence similarity with homologous genes found in the draft genome of peanut-nodulating Bradyrhizobium arachidisLMG 26795T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11Tand CCBAU 10071Tare organized in a similar way to the homologous genes identified in the genomes of USDA110T, Bradyrhizobium ottawaenseUSDA 4and Bradyrhizobium liaoningenseCCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11Talso contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaensebranch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11Tand closely related sequences revealed that strains belonging to B. ottawaensebranch (USDA4and CCBAU15615 ), were the closest strains to the strain ERR11Twith 95.2% ANI. Type strain ERR11Tshowed the highest DDH predicted value with CCBAU15615(58.5%), followed by USDA 4(53.1%). Nevertheless, the ANI and DDH values obtained between ERR11Tand CCBAU 15615or USDA 4were below the cutoff values (ANI ≥ 96.5%; DDH ≥ 70%) for strains belonging to the same species, suggesting that ERR11Tis a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewensesp. nov. with strain ERR11T(HAMBI 3532T=LMG 30162T) as the type strain.

© 2017 Yassin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The permanent draft genome sequence of Actinotignum schaalii DSM 15541Tis presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogen-sis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.

© 2017 The Author(s). The genus Marinobacterium belongs to the family Alteromonadaceae within the class Gammaproteobacteria and was reported in 1997. Currently the genus Marinobacterium contains 16 species. Marinobacterium rhizophilum CL-YJ9Twas isolated from sediment associated with the roots of a plant growing in a tidal flat of Youngjong Island, Korea. The genome of the strain CL-YJ9Twas sequenced through the Genomic Encyclopedia of Type Strains, Phase I: KMG project. Here we report the main features of the draft genome of the strain. The 5,364,574 bp long draft genome consists of 58 scaffolds with 4762 protein-coding and 91 RNA genes. Based on the genomic analyses, the strain seems to adapt to osmotic changes by intracellular production as well as extracellular uptake of compatible solutes, such as ectoine and betaine. In addition, the strain has a number of genes to defense against oxygen stresses such as reactive oxygen species and hypoxia.

© 2017 The Author(s). Dethiobacter alkaliphilus strain AHT1Tis an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1Twas sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

© 2017 The Author(s). Here we report the draft genome sequence of Chitinophaga costai A37T2T(=CIP 110584T, =LMG 27458T), which was isolated from the endophytic community of Pinus pinaster tree. The total genome size of C. costaii A37T2Tis 5.07 Mbp, containing 4204 coding sequences. Strain A37T2Tencoded multiple genes likely involved in cellulolytic, chitinolytic and lipolytic activities. This genome showed 1145 unique genes assigned into 109 Cluster of Orthologous Groups in comparison with the complete genome of C. pinensis DSM 2588T. The genomic information suggests the potential of the strain A37T2Tto interact with the plant metabolism. As there are only a few bacterial genomes related to Pine Wilt Disease, this work provides a contribution to the field.

© FEMS 2017. Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.

© 2017 The Author(s). Chryseobacterium bovis DSM 19482T(Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.

© 2017 Susanti et al. Desulfurococcus amylolyticus Z-533T, a hyperthermophilic crenarcheon, ferments peptide and starch, generating acetate, isobutyrate, isovalerate, CO2, and hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose and is inhibited by hydrogen. The reported draft genome sequence of D. amylolyticus Z-533T will help to understand the molecular basis for these differences.

© 2017 The Author(s). Bradyrhizobium elkanii USDA 76T(INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, B. elkanii USDA 76Twas selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of B. elkanii USDA 76Tare described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The B. elkanii USDA 76Tgenome contains a low GC content region with symbiotic nod and fix genes, indicating the presence of a symbiotic island integration. A comparison of five B. elkanii genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76Twere unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for Rj and/or rj soybean cultivars. Here we show that the USDA 76Tgenome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark (rj1), USDA 76Twas able to elicit nodules on Clark (rj1), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76Tto introduce various effector molecules into this host to enable nodulation.

© 2017 The Author(s). Anaerobium acetethylicum strain GluBS11Tbelongs to the family Lachnospiraceae within the order Clostridiales. It is a Gram-positive, non-motile and strictly anaerobic bacterium isolated from biogas slurry that was originally enriched with gluconate as carbon source (Patil, et al., Int J Syst Evol Microbiol 65:3289-3296, 2015). Here we describe the draft genome sequence of strain GluBS11Tand provide a detailed insight into its physiological and metabolic features. The draft genome sequence generated 4,609,043 bp, distributed among 105 scaffolds assembled using the SPAdes genome assembler method. It comprises in total 4,132 genes, of which 4,008 were predicted to be protein coding genes, 124 RNA genes and 867 pseudogenes. The content was 43.51 mol %. The annotated genome of strain GluBS11Tcontains putative genes coding for the pentose phosphate pathway, the Embden-Meyerhoff-Parnas pathway, the Entner-Doudoroff pathway and the tricarboxylic acid cycle. The genome revealed the presence of most of the necessary genes required for the fermentation of glucose and gluconate to acetate, ethanol, and hydrogen gas. However, a candidate gene for production of formate was not identified.

© 2017 The Author(s). Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the Genomic Encyclopedia of Bacteria and Archaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002T contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.