Publications by authors named "Markus Göker"

289 Publications

High-quality draft genome sequences of DSM 14164, DSM 17497, DSM 15088, DSM 21245 and DSM 16006: taxonomic considerations.

Access Microbiol 2019 29;1(10):e000067. Epub 2019 Oct 29.

Department of Biology-Microbiology, Universitat de les Illes Balears, Palma de, Mallorca, Spain.

is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: (DSM 14164), (DSM 17497), (DSM 15088) (DSM 21245) and (DSM 16006). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the phylogenetic group of species.
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http://dx.doi.org/10.1099/acmi.0.000067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7491935PMC
October 2019

Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates.

Proc Natl Acad Sci U S A 2020 08 3;117(32):19544-19555. Epub 2020 Aug 3.

Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9RT, United Kingdom;

Corresponding attributes of neural development and function suggest arthropod and vertebrate brains may have an evolutionarily conserved organization. However, the underlying mechanisms have remained elusive. Here, we identify a gene regulatory and character identity network defining the deutocerebral-tritocerebral boundary (DTB) in This network comprises genes homologous to those directing midbrain-hindbrain boundary (MHB) formation in vertebrates and their closest chordate relatives. Genetic tracing reveals that the embryonic DTB gives rise to adult midbrain circuits that in flies control auditory and vestibular information processing and motor coordination, as do MHB-derived circuits in vertebrates. DTB-specific gene expression and function are directed by -regulatory elements of developmental control genes that include homologs of mammalian and DTB-specific -regulatory elements correspond to regulatory sequences of human , and that direct MHB-specific expression in the embryonic mouse brain. We show that -regulatory elements and the gene networks they regulate direct the formation and function of midbrain circuits for balance and motor coordination in insects and mammals. Regulatory mechanisms mediating the genetic specification of cephalic neural circuits in arthropods correspond to those in chordates, thereby implying their origin before the divergence of deuterostomes and ecdysozoans.
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http://dx.doi.org/10.1073/pnas.1918797117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431035PMC
August 2020

A publicly accessible database for genome sequences supports tracing of transmission chains and epidemics.

Microb Genom 2020 08 29;6(8). Epub 2020 Jul 29.

Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany.

is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (<10) or single wards (=0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with -mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by .
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http://dx.doi.org/10.1099/mgen.0.000410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641423PMC
August 2020

List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.

Int J Syst Evol Microbiol 2020 Nov 23;70(11):5607-5612. Epub 2020 Jul 23.

Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7 B, 38124 Braunschweig, Germany.

The List of Prokaryotic names with Standing in Nomenclature (LPSN) was acquired in November 2019 by the DSMZ and was relaunched using an entirely new production system in February 2020. This article describes in detail the structure of the new site, navigation, page layout, search facilities and new features.
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http://dx.doi.org/10.1099/ijsem.0.004332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723251PMC
November 2020

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of .

Front Microbiol 2020 7;11:468. Epub 2020 Apr 7.

Department of Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Brunswick, Germany.

The class is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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http://dx.doi.org/10.3389/fmicb.2020.00468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179689PMC
April 2020

Draft Genome Sequences of Six Type Strains of the Genus .

Microbiol Resour Announc 2020 Apr 30;9(18). Epub 2020 Apr 30.

Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany

High-quality draft genome sequences were determined for 6 sp. type strains. The genomes of these strains show considerable biosynthetic potential for producing secondary metabolites.
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http://dx.doi.org/10.1128/MRA.00226-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193931PMC
April 2020

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species.

BMC Genomics 2020 Jan 8;21(1):24. Epub 2020 Jan 8.

Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.

Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus.

Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains.

Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094), is able to grow on glycerol with the production of 1,3-propanediol.
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http://dx.doi.org/10.1186/s12864-019-6410-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950789PMC
January 2020

Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species.

Arch Microbiol 2020 May 16;202(4):815-824. Epub 2019 Dec 16.

GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Düsternbrooker Weg 20, 24105, Kiel, Germany.

Kiloniella laminariae is a true marine bacterium and the first member of the family and order, the Kiloniellaceae and Kiloniellales. K. laminariae LD81 (= DSM 19542) was isolated from the marine macroalga Saccharina latissima and is a mesophilic, typical marine chemoheterotrophic aerobic bacterium with antifungal activity. Phylogenetic analysis of 16S rRNA gene sequence revealed the similarity of K. laminariae LD81 not only with three validly described species of the genus Kiloniella, but also with undescribed isolates and clone sequences from marine samples in the range of 93.6-96.7%. We report on the analysis of the draft genome of this alphaproteobacterium and describe some selected features. The 4.4 Mb genome has a G + C content of 51.4%, contains 4213 coding sequences including 51 RNA genes as well as 4162 protein-coding genes, and is a part of the Genomic Encyclopaedia of Bacteria and Archaea (GEBA) project. The genome provides insights into a number of metabolic properties, such as carbon and sulfur metabolism, and indicates the potential for denitrification and the biosynthesis of secondary metabolites. Comparative genome analysis was performed with K. laminariae LD81 and the animal-associated species Kiloniella majae M56.1 from a spider crab, Kiloniella spongiae MEBiC09566 from a sponge as well as Kiloniella litopenai P1-1 from a white shrimp, which all inhabit quite different marine habitats. The analysis revealed that the K. laminariae LD81 contains 1397 unique genes, more than twice the amount of the other species. Unique among others is a mixed PKS/NRPS biosynthetic gene cluster with similarity to the biosynthetic gene cluster responsible for the production of syringomycin.
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http://dx.doi.org/10.1007/s00203-019-01791-0DOI Listing
May 2020

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Sci Data 2019 11 26;6(1):285. Epub 2019 Nov 26.

DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel.
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http://dx.doi.org/10.1038/s41597-019-0287-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879543PMC
November 2019

100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii.

Environ Microbiol 2020 01 11;22(1):198-211. Epub 2019 Nov 11.

Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater bacterium is a rare example of as-yet-uncultivated prokaryotes with validly published names and unknown identity. We report the results of molecular identification of this elusive bacterium, which was detected in a eutrophic boreal lake in Northern Russia. By using high-performance cell sorting, P. bekefii-like cell rosettes were selectively enriched from lake water. The retrieved 16S rRNA gene sequence was nearly identical to those in dozens of metagenomes assembled from freshwater lakes during cyanobacterial blooms and was phylogenetically placed within a large group of environmental sequences originating from various freshwater habitats worldwide. In contrast, 16S rRNA gene sequence similarity to all currently described members of the order Planctomycetales was only 83%-92%. The metagenome assembled for P. bekefii reached 43% genome coverage and showed the potential for degradation of peptides, pectins, and sulfated polysaccharides. Tracing the seasonal dynamics of P. bekefii by Illumina paired-end sequencing of 16S rRNA gene fragments and by fluorescence in situ hybridization revealed that these bacteria only transiently surpass the detection limit, with a characteristic population peak of up to 10 cells ml following cyanobacterial blooms.
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http://dx.doi.org/10.1111/1462-2920.14838DOI Listing
January 2020

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of .

Front Microbiol 2019 23;10:2083. Epub 2019 Sep 23.

Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum , there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as , and but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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http://dx.doi.org/10.3389/fmicb.2019.02083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767994PMC
September 2019

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy.

Nat Commun 2019 05 16;10(1):2182. Epub 2019 May 16.

Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Braunschweig, Germany.

Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.
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http://dx.doi.org/10.1038/s41467-019-10210-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522516PMC
May 2019

Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems.

ISME J 2019 06 4;13(6):1404-1421. Epub 2019 Feb 4.

Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl-von-Ossietzky-Str. 9 -11, D-26111, Oldenburg, Germany.

Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, affiliated with the marine Roseobacter group, and retrieved similar phage genomes from publicly available metagenomics databases. Phylogenetic analysis placed the new phages within the Cobavirus group, in the here newly proposed genus Siovirus and subfamily Riovirinae of the Podoviridae. Gene composition and presence of direct terminal repeats in cultivated cobaviruses point toward a genome replication and packaging strategy similar to the T7 phage. Investigation of the genomes suggests that viral lysis of the cell proceeds via the canonical holin-endolysin pathway. Cobaviral hosts include members of the genera Lentibacter, Sulfitobacter and Celeribacter of the Roseobacter group within the family Rhodobacteraceae (Alphaproteobacteria). Screening more than 5,000 marine metagenomes, we found cobaviruses worldwide from temperate to tropical waters, in the euphotic zone, mainly in bays and estuaries, but also in the open ocean. The presence of cobaviruses in protist metagenomes as well as the phylogenetic neighborhood of cobaviruses in glutaredoxin and ribonucleotide reductase trees suggest that cobaviruses could infect bacteria associated with phototrophic or grazing protists. With this study, we expand the understanding of the phylogeny, classification, genomic organization, biogeography and ecology of this phage group infecting marine Rhodobacteraceae.
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http://dx.doi.org/10.1038/s41396-019-0362-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775973PMC
June 2019

Genome-Based Taxonomic Classification of the Phylum .

Front Microbiol 2018 22;9:2007. Epub 2018 Aug 22.

Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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http://dx.doi.org/10.3389/fmicb.2018.02007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6113628PMC
August 2018

Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae.

ISME J 2018 08 24;12(8):1994-2010. Epub 2018 May 24.

Department of Protists and Cyanobacteria (PuC), Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA-like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae.
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http://dx.doi.org/10.1038/s41396-018-0150-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052148PMC
August 2018

Corrigendum: Genome-Based Taxonomic Classification of .

Front Microbiol 2018 21;9:304. Epub 2018 Feb 21.

Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

[This corrects the article on p. 2003 in vol. 7, PMID: 28066339.].
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http://dx.doi.org/10.3389/fmicb.2018.00304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826396PMC
February 2018

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.

Sci Rep 2018 01 11;8(1):525. Epub 2018 Jan 11.

School of Biology, Newcastle University, Newcastle upon Tyne, UK.

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.
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http://dx.doi.org/10.1038/s41598-017-17392-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765111PMC
January 2018

Genome-Scale Data Call for a Taxonomic Rearrangement of .

Front Microbiol 2017 19;8:2501. Epub 2017 Dec 19.

Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

(order , class ) form a comparatively isolated family within the phylum and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156 and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, , is not monophyletic, hence the arrangement of the genera of must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within . In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, , with the type species sp. nov. and harboring four species formerly assigned to , and . Emended descriptions of all species of are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.
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http://dx.doi.org/10.3389/fmicb.2017.02501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5742155PMC
December 2017

Draft genome sequence of CL-YJ9 (DSM 18822), isolated from the rhizosphere of the coastal tidal-flat plant .

Stand Genomic Sci 2017 30;12:65. Epub 2017 Oct 30.

Microbial Oceanography Laboratory, School of Earth and Environmental Sciences, and Research Institute of Oceanography, Seoul National University, Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea.

The genus belongs to the family within the class and was reported in 1997. Currently the genus contains 16 species. CL-YJ9 was 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-YJ9 was 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.
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http://dx.doi.org/10.1186/s40793-017-0275-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663061PMC
October 2017

VICTOR: genome-based phylogeny and classification of prokaryotic viruses.

Bioinformatics 2017 Nov;33(21):3396-3404

Department of Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany.

Motivation: Bacterial and archaeal viruses are crucial for global biogeochemical cycles and might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is still unclear how to best use genome sequence data for a fast, universal and accurate taxonomic classification of such viruses.

Results: We here present a novel in silico framework for phylogeny and classification of prokaryotic viruses, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses. The resulting trees revealed a high agreement with the classification. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clusters obtained with distance thresholds chosen for maximizing taxonomic agreement appeared phylogenetically reasonable, too. Analysis of an expanded dataset, containing >4000 genomes from public databases, revealed a large number of novel species, genera, subfamilies and families.

Availability And Implementation: The selected methods are available as the easy-to-use web service 'VICTOR' at https://victor.dsmz.de.

Contact: jan.meier-kolthoff@dsmz.de.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btx440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860169PMC
November 2017

The Composite 259-kb Plasmid of DSM 17316-A Natural Replicon with Functional RepABC Modules from and .

Front Microbiol 2017 21;8:1787. Epub 2017 Sep 21.

Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweig, Germany.

A multipartite genome organization with a chromosome and many extrachromosomal replicons (ECRs) is characteristic for . The best investigated ECRs of terrestrial rhizobia are the symbiotic plasmids for legume root nodulation and the tumor-inducing (Ti) plasmid of . RepABC plasmids represent the most abundant alphaproteobacterial replicon type. The currently known homologous replication modules of rhizobia and are phylogenetically distinct. In this study, we surveyed type-strain genomes from the One Thousand Microbial Genomes (KMG-I) project and identified a roseobacter-specific RepABC-type operon in the draft genome of the marine rhizobium DSM 17316. PacBio genome sequencing demonstrated the presence of three circular ECRs with sizes of 593, 259, and 170-kb. The rhodobacteral RepABC module is located together with a rhizobial equivalent on the intermediate sized plasmid pMM259, which likely originated in the fusion of a pre-existing rhizobial ECR with a conjugated roseobacter plasmid. Further evidence for horizontal gene transfer (HGT) is given by the presence of a roseobacter-specific type IV secretion system on the 259-kb plasmid and the rhodobacteracean origin of 62% of the genes on this plasmid. Functionality tests documented that the genuine rhizobial RepABC module from the 259-kb plasmid is only maintained in C58 () but not in DSM 17395 (). Unexpectedly, the roseobacter-like replication system is functional and stably maintained in both host strains, thus providing evidence for a broader host range than previously proposed. In conclusion, pMM259 is the first example of a natural plasmid that likely mediates genetic exchange between roseobacters and rhizobia.
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http://dx.doi.org/10.3389/fmicb.2017.01787DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613091PMC
September 2017

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Nat Methods 2017 Nov 2;14(11):1063-1071. Epub 2017 Oct 2.

Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
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http://dx.doi.org/10.1038/nmeth.4458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5903868PMC
November 2017

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Nat Biotechnol 2017 Jul 12;35(7):676-683. Epub 2017 Jun 12.

Department of Energy, Joint Genome Institute, Walnut Creek, California, USA.

We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
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http://dx.doi.org/10.1038/nbt.3886DOI Listing
July 2017

High quality permanent draft genome sequence of DSM 19482, isolated from raw cow milk.

Stand Genomic Sci 2017 8;12:31. Epub 2017 May 8.

Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.

DSM 19482 (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. is a member of the , a family within the phylum . 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 genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.
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http://dx.doi.org/10.1186/s40793-017-0242-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422911PMC
May 2017

Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens.

Sci Rep 2017 04 7;7(1):730. Epub 2017 Apr 7.

Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, 26129, Oldenburg, Germany.

Antibiotics are typically regarded as microbial weapons, but whereas their function at concentrations lethal for bacteria is often well characterized, the role of antibiotics at much lower concentrations as possibly found under natural conditions remains poorly understood. By using whole-transcriptome analyses and phenotypic screenings of the marine bacterium Phaeobacter inhibens we found that the broad-spectrum antibiotic tropodithietic acid (TDA) causes the same regulatory effects in quorum sensing (QS) as the common signaling molecule N-acyl-homoserine lactone (AHL) at concentrations 100-fold lower than the minimal inhibitory concentration against bacteria. Our results show that TDA has a significant impact on the expression of ~10% of the total genes of P. inhibens, in the same manner as the AHL. Furthermore, TDA needs the AHL associated LuxR-type transcriptional regulator, just as the AHL molecule. Low concentrations of antibiotics can obviously have a strong influence on the global gene expression of the bacterium that produces it and drastically change the metabolism and behaviour of the bacterium. For P. inhibens this includes motility, biofilm formation and antibiotic production, all important for settlement on new host-associated surfaces. Our results demonstrate that bacteria can produce antibiotics not only to antagonise other bacteria, but also to mediate QS like endogenous AHL molecules.
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http://dx.doi.org/10.1038/s41598-017-00784-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429656PMC
April 2017

Genomic Analysis of , the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum .

Front Microbiol 2017 20;8:195. Epub 2017 Feb 20.

Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia.

The genome of , the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of : starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum .
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http://dx.doi.org/10.3389/fmicb.2017.00195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5317091PMC
February 2017

Complete genome sequence of strain YIM 002 (DSM 44835), the type species of the genus and source of new antibiotic compounds.

Stand Genomic Sci 2017 3;12:21. Epub 2017 Feb 3.

State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Life Science, Sun Yat-Sen University, Guangzhou, China.

strain YIM 002 is the type strain of the type species of the genus , 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 project, and here we describe the complete genome sequence and annotation of this taxon. The genome of strain YIM 002 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 species, 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.
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http://dx.doi.org/10.1186/s40793-017-0226-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5292007PMC
February 2017

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats.

ISME J 2017 06 20;11(6):1483-1499. Epub 2017 Jan 20.

Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% of bacterial communities in pelagic environments and are often mutualists of eukaryotes. As 'Roseobacter clade', these 'roseobacters' are assumed to be monophyletic, but non-marine Rhodobacteraceae have not yet been included in phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling and its effect on phylogenetic stability, and investigated relationships between marine versus non-marine habitat, evolutionary origin and genomic adaptations. Our analyses, providing no unequivocal evidence for the monophyly of roseobacters, indicate several shifts between marine and non-marine habitats that occurred independently and were accompanied by characteristic changes in genomic content of orthologs, enzymes and metabolic pathways. Non-marine Rhodobacteraceae gained high-affinity transporters to cope with much lower sulphate concentrations and lost genes related to the reduced sodium chloride and organohalogen concentrations in their habitats. Marine Rhodobacteraceae gained genes required for fucoidan desulphonation and synthesis of the plant hormone indole 3-acetic acid and the compatible solutes ectoin and carnitin. However, neither plasmid composition, even though typical for the family, nor the degree of oligotrophy shows a systematic difference between marine and non-marine Rhodobacteraceae. We suggest the operational term 'Roseobacter group' for the marine Rhodobacteraceae strains.
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http://dx.doi.org/10.1038/ismej.2016.198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437341PMC
June 2017

High quality draft genome of type strain a rock actinobacterium, and emended description of .

Stand Genomic Sci 2017 6;12. Epub 2017 Jan 6.

School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RY UK.

DLS-10 isolated from rock in Korea, is one of the four type strains of the genus In this study, we describe the high quality draft genome of DLS-10 and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10 presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of in terms of G + C content was also proposed.
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http://dx.doi.org/10.1186/s40793-016-0216-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217420PMC
January 2017

Genome-Based Taxonomic Classification of .

Front Microbiol 2016 20;7:2003. Epub 2016 Dec 20.

Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.

The bacterial phylum , characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of as new phylum from and of as new class from . is nested within the older genus and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, is proposed to be included in . is confirmed as being heterogeneous and dissected, yielding six distinct genera. is a later heterotypic synonym of . Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
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http://dx.doi.org/10.3389/fmicb.2016.02003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167729PMC
December 2016