Genomic and Applied Microbiology

List of Publications (2024 - 2020)

( 2024   -   2023   -   2022   -   2021   -   2020 )


2024

Baum C, Zeldes B, Poehlein A, Daniel R, Müller V, Basen M (2024) The energy-converting hydrogenase Ech2 is important for the growth of the thermophilic acetogen Thermoanaerobacter kivui on ferredoxin-dependent substrates. Microbiol Spectr 22:e0338023 (DOI:10.1128/spectrum.03380-23).

Böer T, Bengelsdorf FR, Daniel R, Poehlein A (2024) Complete genome sequences of Blautia hydrogenotrophica DSM 10507T isolated from human feces and Blautia coccoides DSM 935T isolated from mouse feces. Microbiol Resour Announc 13(4):e00016-24 (DOI:10.1128/mra.00016-24).

Böer T, Schüler MA, Lüschen A, Eysell L, Dröge J, Heinemann M, Engelhardt L, Basen M, Daniel R, Poehlein A (2024) Isolation and characterization of novel acetogenic strains of the genera Terrisporobacter and Acetoanaerobium. Front Microbiol 15:1426882 (DOI:10.3389/fmicb.2024.1426882).

Böer T, Lüschen A, Daniel R, Poehlein A (2024) Complete genome sequence of Sporomusa sphaeroides DSM 2875T isolated from mud of the Leine river and Sporomusa ovata DSM 2662T isolated from sugar beet leaf silage. Microbiol Resour Announc 13(9):e0037224 (DOI:10.1128/mra.00372-24).

Böer T, Engelhardt L, Lüschen A, Eysell L, Yoshida H, Schneider D, Angenent LT, Basen M, Daniel R, Poehlein A (2024) Isolation and characterization of novel acetogenic Moorella strains for employment as potential thermophilic biocatalysts. FEMS Microbiol Ecol 100(9):fiae109 (DOI:10.1093/femsec/fiae109).

Brønnum Bjerg CS, Poehlein A, Bömeke M, Himmelbach A, Schramm A, Brüggemann H (2024) Increased biofilm formation in dual-strain compared to single-strain communities of Cutibacterium acnes. Sci Rep 14:14547 (DOI:10.1038/s41598-024-65348-y).

Flaiz M, Poehlein A, Wilhelm W, Mook A, Daniel R, Dürre P, Bengelsdorf FR (2024) Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering. Microb Cell Fact 23:24 (DOI:10.1186/s12934-024-02301-8).

Funkner K, Poehlein A, Jehmlich N, Egelkamp R, Daniel R, von Bergen M, Rother M0 (2024) Proteomic and transcriptomic analysis of selenium utilization in Methanococcus maripaludis. mSystems e01338-23 (DOI:10.1128/mSystems.01338-23).

Hahnke S, Berger M, Schlingloff A, Athale I, Wolf J, Neumann-Schaal M, Adenaya A, Poehlein A, Daniel R, Petersen J, Brinkhoff T (2024) Roseobacter fucihabitans sp. nov., isolated from the brown alga Fucus spiralis. Int J Syst Evol Microbiol 74(6):006403 (DOI:10.1099/ijsem.0.006403).

Holert J, Borker A, Nübel LL, Daniel R, Poehlein A, Philipp B (2024) Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS. ISME J 18(1): (DOI:10.1093/ismejo/wrad023).

Moon J, Poehlein A, Daniel R, Müller V (2024) Redirecting electron flow in Acetobacterium woodii enables growth on CO and improves growth on formate. Nat Commun 15:5424 (DOI:10.1038/s41467-024-49680-5).

Ravagnan G, Lesemann J, Müller M-F, Poehlein A, Daniel R, Noack S, Kabisch J, Schmid J (2024) Genome reduction in Paenibacillus polymyxa DSM 365 for chassis development. Front Bioeng Biotechnol 12:1378873 (DOI:10.3389/fbioe.2024.1378873).

Regalado L, Appelhans MS, Poehlein A, Himmelbach A, Schmidt AR (2024) Plastome phylogenomics and new fossil evidence from Dominican amber shed light on the evolutionary history of the Neotropical fern genus Pecluma. AJ Botany e16410 (DOI:10.1002/ajb2.16410).

Riedel R, Commichau FM, Benndorf D, Hertel R, Holzer K, Hoelzle LE, Mardoukhi MSY, Noack LE, Martienssen M (2024) Biodegradation of selected aminophosphonates by the bacterial isolate Ochrobactrum sp. BTU1. Microbiol Res 280:127600 (DOI:10.1016/j.micres.2024.127600).

Rosiak M, Hosang L, Hollensteiner J, Gregor KM, Beythien G, Hülskötter K, Schreiner T, Lockow S, Pätz-Warncke C, Felmy F, Daniel R, Flügel A, Baumgärtner W, Odoardi F (2024) Role of the lung microbiome in SARS-CoV-2 infection – The effect of intranasal antibiotic treatment on the type I interferon response and microglial morphology in the CNS. Tierarztl Prax Ausg K Kleintiere Heimtiere 52:201 (DOI:10.1055/s-0044-1787354).

Schüler MA, Schneider D, Poehlein A, Daniel R (2024) Culture-independent detection of low-abundant Clostridioides difficile in environmental DNA via PCR. Appl Environ Microbiol 9:e01278-23 (DOI:10.1128/aem.01278-23).

Schüler MA, Daniel R, Poehlein A (2024) Novel insights into phage biology of the pathogen Clostridioides difficile based on the active virome. Front Microbiol 15:1374708 (DOI:10.3389/fmicb.2024.1374708).

Schüler MA, Riedel T, Overmann J, Daniel R, Poehlein A (2024) Comparative genome analyses of clinical and non-clinical Clostridioides difficile strains. Front Microbiol 15:1404491 (DOI:10.3389/fmicb.2024.1404491).

Schüler MA, Poehlein A, Daniel R (2024) Detektions-PCR und Amplikon- Sequenzierung: ein Power-Paar. BIOspektrum 30:533-535 (DOI:10.1007/s12268-024-2282-y).

Trischler R, Rustler SM, Poehlein A, Daniel R, Breitenbach M, Helfrich EJN, Müller V (2024) 3-Hydroxypropionate production from myo-inositol by the gut acetogen Blautia schinkii. Environ Microbiol 26(9):e16692 (DOI:10.1111/1462-2920.16692).

Wang S, Schneider D, Hartke TR, Ballauff J, de Melo Moura CC, Schulz G, Li Z, Polle A, Daniel R, Gailing O, Irawan B, Scheu S, Krashevska V (2024) Optimising highthroughput sequencing data analysis, from gene database selection to the analysis of compositional data: a case study on tropical soil nematodes. Front Ecol Evol 12:1168288 (DOI:10.3389/fevo.2024.1168288).

Wenzel A, Westphal C, Ballauff J, Berkelmann D, Brambach F, Buchori D, Camarretta N, Corre MD, Daniel R, Darras K, Erasmi S, Formaglio G, Hölscher D, Iddris NA, Irawan B, Knohl A, Kotowska MM, Krashevska V, Kreft H, Mulyani Y, Muβhoff O, Paterno GB, Polle A, Potapov A, Röll A, Scheu S, Schlund M, Schneider D, Sibhatu KT, Stiegler C, Sundawati L, Tjoa A, Tscharntke T, Veldkamp E, Waite PA, Wollni M, Zemp DC, Grass I (2024) Balancing economic and ecological functions in smallholder and industrial oil palm plantations. PNAS 121(17):e2307220121 (DOI:10.1073/pnas.2307220121).

Wicke D, Neumann P, Gößringer M, Chernev A, Davydov S, Poehlein A, Daniel R, Urlaub H, Hartmann RK, Ficner R, Stülke J (2024) The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in Bacillus subtilis in vitro. Nucleic Acids Res 52:1404-1419 (DOI:10.1093/nar/gkad1171).


2023

Alberti L, König P, Zeidler S, Poehlein A, Daniel R, Averhoff B, Müller V (2023) Identification and characterization of a novel pathway for aldopentose degradation in Acinetobacter baumannii. Appl Environ Microbiol 25(11):2416-2430 (DOI:10.1111/1462-2920.16471).

Anzà S, Schneider D, Daniel R, Heistermann M, Sangmaneedet S, Ostner J, Schülke O (2023) The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels. Microbiome 11(1):165 (DOI:10.1186/s40168-023-01596-w).

Böer T, Bengelsdorf FR, Bömeke M, Daniel R, Poehlein A (2023) Genome-based metabolic and phylogenomic analysis of three Terrisporobacter species. PLoS One 18(10):e0290128 (DOI:10.1371/journal.pone.0290128).

Burrascano S, Chianucci F, Trentanovi G, Kepfer-Rojas S, Sitzia T, et al. (2023) Where are we now with European forest multi-taxon biodiversity and where can we head to?. Biol Conserv 284:110176 (DOI:10.1016/j.biocon.2023.110176).

Castillo Villamizar GA, Nacke H, Daniel R (2023) Functional metagenomics approach for the discovery of novel genes encoding phosphatase activity. Methods Mol Biol 2555:103-114 (DOI:10.1007/978-1-0716-2795-2_7).

Chibani CM, Hertel R, Neumann-Schaal M, Goehlich H, Wagner K, Bunk B, Spröer C, Overmann J, Hoppert M, Marten M, Roth O, Liesegang H, Wendling CC (2023) Vibrio syngnathi sp.nov., a fish pathogen, isolated from the Kiel fjord. Int J Syst Evol Microbiol 73(6):005951 (DOI:10.1099/ijsem.0.005951).

Commichau FM, Hertel R, Stülke J (2023) Projekt im Wandel: von iGEM zu neuen Ufern. BIOspektrum 29:698

Friedrich I, Hertel R (2023) Isolation of a host-confined phage metagenome allows the detection of phages both capable and incapable of plaque formation. Methods Mol Biol 2555:195-203 (DOI:10.1007/978-1-0716-2795-2_14).

Friedrich I, Kuritsyn A, Hertel R, Daniel R (2023) Luteibacter flocculans sp. nov., isolated from a eutrophic pond and isolation and characterization of Luteibacter phage vB_LflM‐Pluto. Microorganisms 11:307 (DOI:10.3390/ microorganisms11020307).

Friedrich I, Neubauer H, Kuritsyn A, Bodenberger B, Tskhay F, Hartmann S, Poehlein A, Bömeke M, Hoppert M, Schneider D, Hertel R, Daniel R (2023) Brevundimonas and Serratia as host systems for assessing associated environmental viromes and phage diversity by complementary approaches. Front Microbiol 14:1095850 (DOI:10.3389/fmicb.2023.1095850).

Goehlich H, Roth O, Sieber M, Chibani CM, Poehlein A, Rajkov J, Liesegang H, Wendling CC (2023) Suboptimal environmental conditions prolong phage epidemics in bacterial populations. Mol Ecol (DOI:10.1111/mec.17050).

Guzman J, Won M, Poehlein A, Sombolestani AS, Mayorga-Ch D, Laureys D, Clippeleer J, Kämpfer P, Daniel R, Vilcinskas A, Vandamme P, Kwon SW (2023) Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants. Int J Syst Evol Microbiol 73(2):005699 (DOI:10.1099/ijsem.0.005699).

Guzman J, Poehlein A, Daniel R, Kämpfer P, Vilcinskas A (2023) Vagococcus luciliae sp. nov., isolated from the common green bottle fly Lucilia sericata. Int J Syst Evol Microbiol 73(3):005787 (DOI:10.1099/ijsem.0.005787).

Guzman J, Raval D, Hauck D, Titz A, Poehlein A, Degenkolb T, Daniel R, Vilcinskas A (2023) The resuscitation-promoting factor (Rpf) from Micrococcus luteus and its putative reaction product 1,6-anhydro-MurNAc increase culturability of environmental bacteria. Access Microbiol 5:000647.v4 (DOI:10.1099/acmi.0.000647.v4).

Heffner T, Brami SA, Mendes LW, Kaupper T, Hannula ES, Poehlein A, Horn MA, Ho A (2023) Interkingdom interaction: the soil isopod Porcellio scaber stimulates the methane-driven bacterial and fungal interaction. ISME COMMUN 3(1):62 (DOI:10.1038/s43705-023-00271-3).

Hollensteiner J, Wemheuer F, Schneider D, Pfeiffer B, Wemheuer B (2023) Extraction of total DNA and RNA from marine filter samples and generation of a universal cDNA as universal template for marker gene studies. Methods Mol Biol 2555:13-21 (DOI:10.1007/978-1-0716-2795-2_2).

Hollensteiner J, Schneider D, Poehlein A, Himmelbach A, Daniel R (2023) Metagenome-assembled genomes from particle-associated microbial communities in the mesopelagic zone of the Pacific Ocean. Microbiol Resour Announc 12(12):e0061423 (DOI:10.1128/MRA.00614-23).

Hollensteiner J, Schneider D, Poehlein A, Brinkhoff T, Daniel R (2023) Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits. PLoS One 18(12):e0287947 (DOI:10.1371/journal.pone.0287947).

Iddris NA-A, Formaglio G, Paul C, von Groß V, Chen G, Angulo-Rubiano A, Berkelmann D, Brambach F, Darras KFA, Krashevska V , Potapov A, Wenzel A, Irawan B, Damris M, Daniel R, Grass I, Kreft H, Scheu S, Tscharntke T, Tjoa A, Veldkamp E, Corre MD (2023) Mechanical weeding enhances ecosystem multifunctionality and profit in industrial oil palm. Nat Sustain 6:683-695 (DOI:10.1038/s41893-023-01076-x).

Jensen MG, Svraka L, Baez E, Lund M, Poehlein A, Brüggemann H (2023) Species- and strain-level diversity of Corynebacteria isolated from human facial skin. BMC Microbiol 23:366 (DOI: 10.1186/s12866-023-03129-9).

Kohm K, Lutz VT, Friedrich I, Hertel R (2023) CRISPR-Cas9 shaped viral metagenomes associated with Bacillus subtilis. Methods Mol Biol 2555:205-212 (DOI:10.1007/978-1-0716-2795-2_15).

Kohm K, Jalomo-Khayrova E, Krüger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau FM, Czech L (2023) Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ. Nucleic Acids Res 51(17):9452-9474 (DOI:10.1093/nar/gkad675).

König P, Wilhelm A, Schaudinn C, Poehlein A, Daniel R, Widera M, Averhoff B, Müller V (2023) The VBNC state: a fundamental survival strategy of Acinetobacter baumannii. mBio 28:e0213923 (DOI:10.1128/mbio.02139-23).

Lehmann M, Prohaska C, Zeldes B, Poehlein A, Daniel R, Basen M (2023) Adaptive laboratory evolution of a thermophile toward a reduced growth temperature optimum. Front Microbiol 14:1265216 (DOI:10.3389/fmicb.2023.1265216).

Liu Y, Brinkhoff T, Berger M, Poehlein A, Voget S, Paoli L, Sunagawa S, Amann R, Simon M (2023) Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster. Microbiome 11:265 (DOI:10.1186/s40168-023-01644-5).

Moon J, Schubert A, Poehlein A, Daniel R, Müller V (2023) A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii. Environ Microbiol Rep 15(5):339-351 (DOI:10.1111/1758-2229.13160).

Ponraj DS, Lund M, Lange J, Poehlein A, Himmelbach A, Falstie-Jensen T, Jørgensen NP, Ravn C, Brüggemann H (2023) Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent. Front Cell Infect Microbiol 13:1165017 (DOI:10.3389/fcimb.2023.1165017).

Protasov E, Nonoh JO, Kästle Silva JM, Mies US, Hervé V, Dietrich C, Lang K, Mikulski L, Platt K, Poehlein A, Köhler-Ramm T, Miambi E, Boga HI, Feldewert C, Ngugi DK, Plarre R, Sillam-Dussès D, Šobotník J, Daniel R, Brune A (2023) Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods. Front Microbiol 14:1281628 (DOI:10.3389/fmicb.2023.1281628).

Rao S, Esvaran M, Chen L, Kok C, Keil AD, Gollow I, Simmer K, Wemheuer B, Conway P, Patole S (2023) Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: guidelines for future research. Pediatr Res 93:49–55 (DOI:10.1038/s41390-022-02087-8).

Schneider D, Ganbarzade A, Post S, Zühlke D, Hinzke T, Hollensteiner J, Poehlein A, Riedel K, Daniel R (2023) Complete genome sequence of Citrobacter braakii GW-Imi-1b1, isolated from hospital wastewater in Greifswald, Germany. Microbiol Resour Announc 12(5):e0014323 (DOI:10.1128/mra.00143-23).

Schöne C, Poehlein A, Rother M (2023) Genetic and physiological probing of cytoplasmic bypasses for the energy-converting methyltransferase Mtr in Methanosarcina acetivorans. Appl Environ Microbiol 89(7):e0216122 (DOI:10.1128/aem.02161-22).

Schüler M, Daniel R, Poehlein A (2023) Complete genome sequence of a Clostridioides difficile cryptic C-III strain isolated from horse feces. Microbiol Resour Announc 12(12):00781-23 (DOI:10.1128/MRA.00781-23).

Schwedt I, Collignon M, Mittelstädt C, Giudici F, Rapp J, Meißner J, Link H, Hertel R, Commichau FM (2023) Genomic adaptation of Burkholderia anthina to glyphosate uncovers a novel herbicide resistance mechanism. Environ Microbiol Rep 15(6):727-739 (DOI:10.1111/1758-2229.13184).

Schwedt I, Schöne K, Eckert M, Pizzinato M, Winkler L, Knotkova B, Richts B, Hau JL, Steuber J, Mireles R, Noda-Garcia L, Fritz G, Mittelstädt C, Hertel R, Commichau FM (2023) The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates. Environ Microbiol 25(12):3604-3622 (DOI:10.1111/1462-2920.16518).

Simon C, Daniel R (2023) Construction of small-insert and large-insert metagenomic libraries. Methods Mol Biol 2555:1-12 (DOI:10.1007/978-1-0716-2795-2_1).

Strittmatter CS, Poehlein A, Himmelbach A, Daniel R, Steinbüchel A (2023) Medium-chain-length fatty acid catabolism in Cupriavidus necator H16: Transcriptome sequencing reveals differences from long-chain-length fatty acid β-oxidation and involvement of several homologous genes. Appl Environ Microbiol 89(1):e0142822 (DOI:10.1128/aem.01428-22).

Trischler R, Poehlein A, Daniel R, Müller V (2023) Ethanologenesis from glycerol by the gut acetogen Blautia schinkii. Environ Microbiol 25(12):3577-3591 (DOI:10.1111/1462-2920.16517).

Zeldes B, Poehlein A, Jain S, Baum C, Daniel R, Müller V, Basen M (2023) DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component. ISME COMMUN 3:2 (DOI:10.1038/s43705-022-00211-7).

Zemp DC, Guerrero-Ramirez N, Brambach F, Darras K, Grass I, Potapov A, Röll A, Arimond I, Ballauff J, Behling H, Berkelmann D, Biagioni S, Buchori D, Craven D, Daniel R, Gailing O, Ellsäßer F, Fardiansah R, Hennings N, Irawan B, Khokthong W, Krashevska V, Krause A, Kückes J, Li K, Lorenz H, Maraun M, Merk MS, Moura CCM, Mulyani YA, Paterno GB, Pebrianti HD, Polle A, Prameswari DA, Sachsenmaier L, Scheu S, Schneider D, Setiajiati F, Setyaningsih CA, Sundawati L, Tscharntke T, Wollni M, Hölscher D, Kreft H (2023) Tree islands enhance biodiversity and functioning in oil palm landscapes. Nature 618:316-321 (DOI:10.1038/s41586-023-06086-5).


2022

Afshar M, Møllebjerg A, Minero GA, Hollensteiner J, Poehlein A, Himmelbach A, Lange J, Meyer RL, Brüggemann H (2022) Biofilm formation and inflammatory potential of Staphylococcus saccharolyticus: A possible cause of orthopedic implant-associated infections. Front Microbiol 13:1070201 (DOI:10.3389/fmicb.2022.1070201).

Aguilar-Cruz Y, Milke F, Leinberger J, Poehlein A, Zotz G, Brinkhoff T (2022) Diversity and putative metabolic function of prokaryotic communities in tank bromeliads along an elevation gradient in tropical Mexico. Front Microbiol 13:945488 (DOI:10.3389/fmicb.2022.945488).

Ahle CM, Stødkilde C, Poehlein A, Bömeke M, Streit WR, Wenck H,Reuter JH, Hüpeden J, Brüggemann H (2022) Interference and co-existence of staphylococci and Cutibacterium acnes within the healthy human skin microbiome. Commun Biol 5:923 (DOI:10.1038/s42003-022-03897-6).

Baur ST, Markussen S, Di Bartolomeo F, Poehlein A, Baker A, Jenkinson ER, Daniel R, Wentzel A, Dürre P (2022) Increased butyrate production in Clostridium saccharoperbutylacetonicum from lignocellulose-derived sugars. Appl Environ Microbiol 21:e0241921 (DOI:10.1128/aem.02419-21).

Baur ST, Poehlein A, Renz NJ, Hollitzer SK, Montoya Solano JD, Schiel-Bengelsdorf B, Daniel R, Dürre P (2022) Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation. Front Genet 13:966643 (DOI:10.3389/fgene.2022.966643).

Breidenbach A, Schleuss P-M, Liu S, Schneider D, Dippold MA, de la Haye T, Miehe G, Heitkamp F, Seeber E, Mason-Jones K, Xu X, Huanming Y, Xu J, Dorji T, Gube M, Norf H, Meier J, Guggenberger G, Kuzyakov Y, Spielvogel S (2022) Microbial functional changes mark irreversible course of Tibetan grassland degradation. Nat Commun 13:2681 (DOI:10.1038/s41467-022-30047-7).

Breisch J, Schumm C, Poehlein A, Daniel R, Averhoff B (2022) The carnitine degradation pathway of Acinetobacter baumannii and its role in virulence. Environ Microbiol 24(9):4437-4448 (DOI:10.1111/1462-2920.16075).

Chacón FI, Sineli PE, Mansilla FI, Pereyra MM, Diaz MA, Volentini SI, Poehlein A, Meinhardt F, Daniel R, Dib JR (2022) Native cultivable bacteria from the blueberry microbiome as novel potential biocontrol agents. Microorganisms 10(5):969 (DOI:10.3390/microorganisms10050969).

Dlugosch L, Poehlein A, Wemheuer B, Pfeiffer B, Badewien TH, Daniel R, Simon M (2022) Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. Nat Commun 11:1186 (DOI:10.1038/s41467-022-28128-8).

Eze MO, Thiel V, Hose GC, George SC, Daniel R (2022) Enhancing rhizoremediation of petroleum hydrocarbons through bioaugmentation with a plant growth-promoting bacterial consortium. Chemosphere 289:133143 (DOI:10.1016/j.chemosphere.2021.133143).

Eze MO, Thiel V, Hose GC, George SC, Daniel R (2022) Bacteria-plant interactions synergistically enhance biodegradation of diesel fuel hydrocarbons. Commun Earth Environ 3:192 (DOI:10.1038/s43247-022-00526-2).

Fussmann D, von Hoyningen-Huene AJE, Reimer A, Schneider D, Karius V, Riechelmann S, Pederson CH, Swart PK, Daniel R, Arp G (2022) Decoupling of pore water chemistry, bacterial community profiles, and carbonate mud diagenesis in a land-locked pool on Aldabra (Seychelles, Indian Ocean). Geomicrobiol J 39(9):731-749 (DOI:10.1080/01490451.2022.2070689).

Gudzuhn M, Alio I, Moll R, de Vries J, Boehlich J, Assmann M, Janneschütz J, Schützenmeister N, Himmelbach A, Poehlein A, Daniel R, Streit WR (2022) Molecular insight into gene response of diorcinol- and rubrolide-treated biofilms of the emerging pathogen Stenotrophomonas maltophilia. Microbiol Spectr 26:e0258221 (DOI:10.1128/spectrum.02582-21).

Guzman J, Ortúzar M, Poehlein A, Daniel R, Trujillo ME, Vilcinskas A (2022) Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata. Int J Syst Evol Microbiol 72(3):005283 (DOI:10.1099/ijsem.0.005283).

Guzman J, Poehlein A, Glaeser SP, Schwengers O, Blom J, Hollensteiner J, Kämpfer P, Vilcinskas A (2022) Pseudocitrobacter corydidari sp. nov., isolated from the Asian emerald cockroach Corydidarum magnifica. Int J Syst Evol Microbiol 72:005497 (DOI:10.1099/ijsem.0.005497).

Hertel R, Schöne K, Mittelstädt C, Meißner J, Zschoche N, Collignon M, Kohler C, Friedrich I, Schneider D, Hoppert M, Kuhn R, Schwedt I, Scholz P, Poehlein A, Martienssen M, Ischebeck T, Daniel R, Commichau FM (2022) Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution. Environ Microbiol Rep 14(1):70-84 (DOI:10.1111/1758-2229.13022).

Hertel R, Gibhardt J, Martienssen M, Kuhn R, Commichau FM (2022) Molecular mechanisms underlying glyphosate resistance in bacteria. Environ Microbiol 23(6):2891-2905 (DOI:10.1111/1462-2920.15534).

Hosang L, Canals RC, van der Flier FJ, Hollensteiner J, Daniel R, Flügel A, Odoardi F (2022) The lung microbiome regulates brain autoimmunity. Nature 603:138-144 (DOI:10.1038/s41586-022-04427-4).

Kaupper T, Mendes LW, Poehlein A, Frohloff D, Rohrbach S, Horn MA, Ho A (2022) The methane-driven interaction network in terrestrial methane hotspots. Environ Microbiome 17:15 (DOI:10.1186/s40793-022-00409-1).

Kipnyargis A, Mwirichia R, Pfeiffer B, Daniel R (2022) Complete genome sequence of Alkalihalobacillus sp. strain LMS39, a haloalkaliphilic bacterium isolated from a hypersaline lake. Microbiol Resour Announc 11:e0032522 (DOI:10.1128/mra.00325-22).

Kohm K, Floccari VA, Lutz VT, Nordmann B, Mittelstädt C, Poehlein A, Dragoš A, Commichau FM, Hertel R (2022) The Bacillus phage SPβ and its relatives: a temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components. Environ Microbiol 24(4):2098-2118 (DOI:10.1111/1462-2920.15964).

Leinberger J, Milke F, Christodoulou M, Poehlein A, Caraveo‐Patiño J, Teske A, Brinkhoff T (2022) Microbial epibiotic community of the deep‐sea galatheid squat lobster Munidopsis alvisca. Sci Rep 12:2675 (DOI:10.1038/s41598-022-06666-x).

Lewkowski O, Poehlein A, Daniel R, Erler S (2022) In the battle of the disease: a transcriptomic analysis of European foulbrood-diseased larvae of the Western honey bee (Apis mellifera). BMC Genomics 23(1):837 (DOI:10.1186/s12864-022-09075-6).

Lu M, Schneider D, Daniel R (2022) Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern. Front Microbiol 13:851969 (DOI:10.3389/fmicb.2022.851969).

Murillo T, Schneider D, Fichtel C, Daniel R (2022) Dietary shifts and social interactions drive temporal fluctuations of the gut microbiome from wild redfronted lemurs. ISME COMMUN 2:3 (DOI:10.1038/s43705-021-00086-0).

Murillo T, Schneider D, Heistermann M, Daniel R, Fichtel C (2022) Assessing the drivers of gut microbiome composition in wild redfronted lemurs via longitudinal metacommunity analysis. Sci Rep 12:21462 (DOI:10.1038/s41598-022-25733-x).

Papaioannou KK, Hollensteiner J, Witte JKH, Poehlein A, Daniel R (2022) Complete genome sequence of the type strain Aliivibrio fischeri DSM 507. Microbiol Resour Announc 11(12):e00801-22 (DOI:10.1128/mra.00801-22).

Pérez CAR, Janz D, Schneider D, Daniel R, Polle A (2022) Transcriptional landscape of ectomycorrhizal fungi and their host provides insight into N uptake from forest soil. mSystems 7(1):e00957-21 (DOI:10.1128/mSystems.00957-21).

Rao S, Esvaran M, Chen L, Keil AD, Gollow I, Simmer K, Wemheuer B, Conway P, Patole S (2022) Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: a pilot randomised controlled trial. Pediatr Res 92:1122–1131 (DOI:10.1038/s41390-021-01884-x).

Rosenbaum FP, Poehlein A, Daniel R, Müller V (2022) Energy-conserving dimethyl sulfoxide reduction in the acetogenic bacterium Moorella thermoacetica. Environ Microbiol 24:2000-2012 (DOI:10.1111/1462-2920.15971).

Rudolph K, Schneider D, Fichtel C, Daniel R, Heistermann M, Kappeler PM (2022) Drivers of gut microbiome variation within and between groups of a wild Malagasy primate. Microbiome 10:28 (DOI:10.1186/s40168-021-01223-6).

Ryadin AR, Janz D, Schneider D, Tjoa A, Irawan B, Daniel R, Polle A (2022) Early effects of fertilizer and herbicide reduction on root-associated biota in oil palm plantations. Agronomy 12(1):199 (DOI:10.3390/agronomy12010199).

Sadoughi B, Schneider D, Daniel R, Schülke O, Ostner J (2022) Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized. Microbiome 10:95 (DOI:10.1186/s40168-022-01283-2).

Schmitt M, Jarosch KA, Hertel R, Spielvogel S, Dippold MA, Loeppmann S (2022) Manufacturing triple-isotopically labeled microbial necromass to track C, N and P cycles in terrestrial ecosystems. Appl Soil Ecol 171:104322 (DOI:10.1016/j.apsoil.2021.104322).

Schoch T, Höfele F, Odeh H, Winter L-M, Stöferle S, Karl M, Bengelsdorf F, Poehlein A, Daniel R, Dürre P (2022) Reclassification of Clostridium aurantibutyricum Hellinger 1944 and Clostridium roseum (ex McCoy and McClung 1935) Cato et al. 1988. Int J Syst Evol Microbiol 72:005589 (DOI:10.1099/ijsem.0.005589).

Schöne C, Poehlein A, Jehmlich N, Adlung N, Daniel R, von Bergen M, Scheller S, Rother M (2022) Deconstructing Methanosarcina acetivorans into an acetogenic archaeon. PNAS 119(2):e2113853119 (DOI:10.1073/pnas.2113853119).

Shin JH, Bömeke M, Poehlein A, Hollensteiner J (2022) Complete genome sequence of Bacillus frigoritolerans JHS1. Microbiol Resour Announc 11(6):e0018422 (DOI:10.1128/mra.00184-22).

Tebbe DA, Geihser S, Wemheuer B, Daniel R, Schäfer H, Engelen B (2022) Seasonal and zonal succession of bacterial communities in North Sea salt marsh sediments. Microorganisms 10:859 (DOI:10.3390/ microorganisms10050859).

Varaljay VA, Charles TC, Daniel R (2022) Editorial: Functional Metagenomics for Enzyme Discovery. Front Microbiol 13:956106 (DOI:10.3389/fmicb.2022.956106).

von Hoyningen‑Huene AJE, Schneider D, Fussmann D, Reimer A, Arp G, Daniel R (2022) DNA‑ and RNA‑based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll. Sci Rep 12:4257 (DOI:10.1038/s41598-022-07980-0).

Wang S, Schneider D, Hartke TR, Ballauff J, de Melo Moura CC, Schulz G, Li Z, Polle A, Daniel R, Gailing O, Irawan B, Scheu S, Krashevska V (2022) Optimising High-throughput sequencing data analysis, from gene database selection to the analysis of compositional data: A case study on tropical soil nematodes. SSRN preprint (DOI:10.2139/ssrn.4078698).

Wendling CC, Lange J, Liesegang H, Sieber M, Poehlein A, Bunk B, Rajkov J, Goehlich H, Roth O, Brockhurst MA (2022) Higher phage virulence accelerates the evolution of host resistance. Proc R Soc B 289(1984):20221070 (DOI:10.1098/rspb.2022.1070).

Werner KA, Poehlein A, Schneider D, El-Said K, Wöhrmann M, Linkert I, Hübner T, Brüggemann N, Prost K, Daniel R, Grohmann E (2022) Thermophilic composting of human feces: development of bacterial community composition and antimicrobial resistance gene pool. Front Microbiol 13:824834 (DOI:10.3389/fmicb.2022.824834).

Werner KA, Schneider D, Poehlein A, Diederich N, Feyen L, Axtmann K, Hübner T, Brüggemann N, Prost K, Daniel R, Grohmann E (2022) Metagenomic insights into the changes of antibiotic resistance and pathogenicity factor pools upon thermophilic composting of human excreta. Front Microbiol 13:826071 (DOI:10.3389/fmicb.2022.826071).

Ponraj DS, Lange J, Falstie-Jensen T, Jørgensen P, Ravn C, Poehlein A, Brüggemann H (2022) Amplicon-based next-generation sequencing as a diagnostic tool for the detection of phylotypes of Cutibacterium acnes in orthopedic implant-associated infections. Front Microbiol 13:866893 (DOI:10.3389/fmicb.2022.866893).

Zucker F, Bischoff V,Ndela EO, Heyerhoff B, Poehlein A, Freese HM, Roux S, Simon M, Enault F, Moraru Ch (2022) New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria. Virus Evol 8(2):1-18 (DOI:10.1093/ve/veac070).


2021

Afshar M, Poehlein A, Söderquist B, Brüggemann H (2021) Complete genome sequences of two Staphylococcus saccharolyticus strains isolated from prosthetic joint infections. Microbiol Resour Announc 10(10):e00157-21 (DOI:10.1128/MRA.00157-21).

Ahle CM, Stødkilde-Jørgensen K, Poehlein A, Streit WR, Hüpeden J, Brüggemann H (2021) Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin. BMC Microbiol 21(1):221 (DOI:10.1186/s12866-021-02284-1).

Alio I, Gudzuhn M, Pérez García P, Danso D, Schoelmerich M, Mamat U, Schaible UE, Steinmann J, Yero D, Gibert I, Kohl TA, Niemann S, Gröschel MI, Haerdter J, Hackl T, Vollstedt CH, Bömeke M, Egelkamp R, Daniel R, Poehlein A, Streit WR (2021) Erratum for "Phenotypic and transcriptomic analysis of seven clinical Stenotrophomonas maltophilia isolates identify a small set of shared and commonly regulated genes involved in biofilm lifestyle". Appl Environ Microbiol 87(18):e0130421 (DOI:10.1128/AEM.01304-21).

Aloo BN, Mbega ER, Makumba BA, Hertel R, Daniel R (2021) Molecular identification and in vitro plant growth-promoting activities of culturable potato (Solanum tuberosum L.) rhizobacteria in Tanzania. Potato Res 64:67–95 (DOI:10.1007/s11540-020-09465-x).

Arif S, Nacke H, Hoppert M (2021) Metagenome-assembled genome sequences of a biofilm derived from Marsberg copper mine. Microbiol Resour Announc 10(2):e01253-20 (DOI:10.1128/MRA.01253-20).

Arif S, Willenberg C, Dreyer A, Nacke H, Hoppert M (2021) Sasso Pisano geothermal field environment harbours diverse Ktedonobacteria representatives and illustrates habitat-specific adaptations. Microorganisms 9(7):1402 (DOI:10.3390/microorganisms9071402).

Ballauff J, Schneider D, Edy N, Irawan B, Daniel R, Polle A (2021) Shifts in root and soil chemistry drive the assembly of belowground fungal communities in tropical land-use systems. Soil Biol Biochem 154:108140 (DOI:10.1016/j.soilbio.2021.108140).

Benda M, Woelfel S, Faßhauer P, Gunka K, Klumpp S, Poehlein A, Kálalová D, Šanderová H, Daniel R, Krásný L, Stülke J (2021) Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis. Nucleic Acids Res 49(12):7088-7102 (DOI:10.1093/nar/gkab528).

Borges LMS, Pfeiffer B, Pandur S, Toubarro D, Tanase A-M, Chiciudean I, Menzel MN, Hoppert M, Daniel R, Simões N, Altermark B (2021) A picture is worth a thousand words: novel photographic evidence on the anatomy of the digestive system of three shipworm species (Bivalvia, Teredinidae). Zoomorphol 140:469-485 (DOI:10.1007/s00435-021-00540-6).

Chea L, Pfeiffer B, Schneider D, Daniel R, Pawelzik E, Naumann M (2021) Morphological and metabolite responses of potatoes under various phosphorus levels and their amelioration by plant growth-promoting rhizobacteria. Int J Mol Sci 22:5162 (DOI:10.3390/ijms22105162).

Clausing S, Likulunga LE, Janz D, Feng HY, Schneider D, Daniel R, Krüger J, Lang F, Polle A (2021) Impact of nitrogen and phosphorus addition on resident soil and root mycobiomes in beech forests. Biol Fertil Soils 57:1031–1052 (DOI:10.1007/s00374-021-01593-x).

Diaz Valerio S, Lev Hacohen A, Schöppe R, Liesegang H (2021) IDOPS, a profile HMM-based tool to detect pesticidal sequences and compare their genetic context. Front Microbiol 12:664476 (DOI:10.3389/fmicb.2021.664476).

Eze MO, Hose GC, George SC, Daniel R (2021) Diversity and metagenome analysis of a hydrocarbon‑degrading bacterial consortium from asphalt lakes located in Wietze, Germany. AMB Express 11:89 (DOI:10.1186/s13568-021-01250-4).

Faßhauer P, Busche T, Kalinowski J, Mäder U, Poehlein A, Daniel R, Stülke J (2021) Functional redundancy and specialization of the conserved cold shock proteins in Bacillus subtilis. Microorganisms 9(7):1434 (DOI:10.3390/microorganisms9071434).

Friedrich I, Hollensteiner J, Scherf J, Weyergraf J, Klassen A, Poehlein A, Hertel R, Daniel R (2021) Complete genome sequence of Stenotrophomonas indicatrix DAIF1. Microbiol Resour Announc 10(6):e01484-20 (DOI:10.1128/MRA.01484-20).

Friedrich I, Klassen A, Neubauer H, Schneider D, Hertel R, Daniel R (2021) Living in a puddle of mud: isolation and characterization of two novel Caulobacteraceae strains Brevundimonas pondensis sp. nov. and Brevundimonas goettingensis sp. nov.. Appl Microbiol 1:38-59 (DOI:10.3390/applmicrobiol1010005).

Friedrich I, Bodenberger B, Neubauer H, Hertel R, Daniel R (2021) Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog’s lettuce (Groenlandia densa). PLoS One 16(11):e0259673 (DOI:10.1371/journal.pone.0259673).

Gerke J, Schneider D, Poehlein A, Cornish VW, Braus GH (2021) Draft genome sequence of Saccharomyces cerevisiae LW2591Y, a laboratory strain for in vivo multigene assemblies. Microbiol Resour Announc 10(9):e01418-20 (DOI:10.1128/MRA.01418-20).

Göbbels L, Poehlein A, Dumnitch A, Egelkamp R, Kröger C, Haerdter J, Hackl T, Feld A, Weller H, Daniel R, Streit WR, Schoelmerich MC (2021) Cysteine: an overlooked energy and carbon source. Sci Rep 11:2139 (DOI:10.1038/s41598-021-81103-z).

Guzman J, Sombolestani AS, Poehlein A, Daniel R, Cleenwerck I, Vandamme P, Vilcinskas A (2021) Entomobacter blattae gen. nov., sp. nov., a new member of the Acetobacteraceae isolated from the gut of the cockroach Gromphadorhina portentosa. Int J Syst Evol Microbiol 71(3): (DOI:10.1099/ijsem.0.004666).

Harting R, Starke J, Kusch H, Pöggeler S, Maurus I, Schlüter R, Landesfeind M, Bulla I, Nowrousian M, de Jonge R, Stahlhut G, Hoff KJ, Aßhauer KP, Thürmer A, Stanke M, Daniel R, Morgenstern B, Thomma BPHJ, Kronstad JW, Braus-Stromeyer SA, Braus GH (2021) A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum. Mol Plant Pathol 22(8):939-953 (DOI:10.1111/mpp.13071).

Hertel R (2021) SPβ, ein Bacillus-Phage mit vielen Geheimnissen. BIOspektrum 27:781 (DOI:10.1007/s12268-021-1666-5).

Hollensteiner J, Friedrich I, Hollstein L, Lamping J-P,Wolf K, Liesegang H, Poehlein A, Hertel R, Daniel R (2021) Complete genome sequence of Kinneretia sp. strain DAIF2, isolated from a freshwater pond. Microbiol Resour Announc 10(8):e00003-21 (DOI:10.1128/MRA.00003-21).

Khokon AM, Schneider D, Daniel R, Polle A (2021) Soil layers matter: Vertical stratification of root-associated fungal assemblages in temperate forests reveals differences in habitat colonization. Microorganisms 9(10):2131 (DOI:10.3390/microorganisms9102131).

Kohm K, Hertel R (2021) The life cycle of SPβ and related phages. Arch Virol 166:2119-2130 (DOI:10.1007/s00705-021-05116-9).

Kohm K, Basu S, Nawaz MM, Hertel R (2021) Chances and limitations when uncovering essential and non‐essential genes of Bacillus subtilis phages with CRISPR‐Cas9. Environ Microbiol Rep 13(6):934-944 (DOI:10.1111/1758-2229.13005).

Krüger L, Herzberg Ch, Rath H, Pedreira T, Ischebeck T, Poehlein A, Gundlach J, Daniel R, Völker U, Mäder U, Stülke J (2021) Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis. PLoS Genetics 17:e1009092 (DOI:10.1371/journal.pgen.1009092).

Lu M, Daniel R (2021) A novel carboxylesterase derived from a compost metagenome exhibiting high stability and activity towards high salinity. Genes 12:122 (DOI:10.3390/ genes12010122).

Michalik S, Reder A, Richts B, Faßhauer P, Mäder U, Pedreira T, Poehlein A, van Heel AJ, van Tilburg AY, Altenbuchner J, Klewing A, Reuß DR, Daniel R, Commichau FM, Kuipers OP, Hamoen LW, Völker U, Stülke J (2021) The Bacillus subtilis minimal genome compendium. ACS Synth Biol 10(10):2767–2771 (DOI:10.1021/acssynbio.1c00339).

Migliorini LB, de Sales RO, Koga PCM, Doi AM, Poehlein A, Toniolo AR, Menezes FG, Martino MDV, Gales AC, Brüggemann H, Severino P (2021) Prevalence of blaKPC-2, blaKPC-3 and blaKPC-30—carrying plasmids in Klebsiella pneumoniae isolated in a Brazilian hospital. Pathogens 10(3):332 (DOI:10.3390/pathogens10030332).

Moon J, Dönig J, Kramer S, Poehlein A, Daniel R, Müller V (2021) Formate metabolism in the acetogenic bacterium Acetobacterium woodii. Environ Microbiol 23(8):4214-4227 (DOI:10.1111/1462-2920.15598).

Nguyen M, Wemheuer B, Laffy PW, Webster NS, Thomas T (2021) Taxonomic, functional and expression analysis of viral communities associated with marine sponges. Peer J 9:e10715 (DOI:10.7717/peerj.10715).

Obermeier MM, Wicaksono WA, Taffner J, Bergna A, Poehlein A, Cernava T, Lindstaedt S, Lovric M, Müller Bogotá CA, Berg G (2021) Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance. ISME J 15:921–937 (DOI:10.1038/s41396-020-00822-9).

Pereyra MM, Díaz MA, Soliz-Santander FF, Poehlein A, Meinhardt F, Daniel R, Dib JR (2021) Screening methods for isolation of biocontrol epiphytic yeasts against Penicillium digitatum in lemons. J Fungi 7(3):166 (DOI:10.3390/jof7030166).

Perez MF, Saona LA, Farías ME, Poehlein A, Meinhardt F, Daniel R, Dib JR (2021) Assessment of the plasmidome of an extremophilic microbial community from the Diamante Lake, Argentina. Sci Rep 11:21459 (DOI:10.1038/s41598-021-00753-1).

Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M (2021) Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. Microbiome 9:55 (DOI:10.1186/s40168-020-00981-z).

Richts B, Lentes S, Poehlein A, Daniel R, Commichau FM (2021) A Bacillus subtilis ΔpdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation. Environ Microbiol Rep 13(2):218-233 (DOI:10.1111/1758-2229.12936).

Rosenbaum FP, Poehlein A, Egelkamp R, Daniel R, Harder S, Schlüter H, Schoelmerich MC (2021) Lactate metabolism in strictly anaerobic microorganisms with a soluble NAD+-dependent l-lactate dehydrogenase. Environ Microbiol 23(8):4661-4672 (DOI:10.1111/1462-2920.15657).

Sagerfors S, Poehlein A, Afshar M, Lindblad BE, Brüggemann H, Söderquist B (2021) Clinical and genomic features of Corynebacterium macginleyi-associated infectious keratitis. Sci Rep 11:6015 (DOI:10.1038/s41598-021-85336-w).

Sagerfors S, Poehlein A, Söderquist B, Brüggemann H (2021) Complete genome sequences of two Corynebacterium macginleyi strains isolated from infectious keratitis. Microbiol Resour Announc 10(17):e00207-21 (DOI:10.1128/MRA.00207-21).

Salar-Vidal L, Achermann I, Aguilera-Correa J-J, Poehlein A, Esteban J, Brüggemann H (2021) Genomic analysis of Cutibacterium acnes strains isolated from prosthetic joint infections. Microorganisms 9(7):1500 (DOI:10.3390/microorganisms9071500).

Schneider D, Zühlke D, Poehlein A, Riedel K, Daniel R (2021) Metagenome-assembled genome sequences from different wastewater treatment stages in Germany. Microbiol Resour Announc 10(27):e00504-21 (DOI:10.1128/MRA.00504-21).

Söderquist B, Afshar M, Poehlein A, Brüggemann H (2021) Staphylococcus saccharolyticus associated with prosthetic joint infections: clinical features and genomic characteristics. Pathogens 10(4):397 (DOI:10.3390/pathogens10040397).

Song W, Wemheuer B, Steinberg PD, Marzinelli EM, Thomas T (2021) Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. ISME J 15:807–817 (DOI:10.1038/s41396-020-00815-8).

Taylor JA, Palladino G, Wemheuer B, Steinert G, Sipkema D, Williams TJ, Thomas T (2021) Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME J 15:503–519 (DOI:10.1038/s41396-020-00791-z).

TrifunoviĆ D, Moon J, Poehlein A, Daniel R, Müller V (2021) Growth of the acetogenic bacterium Acetobacterium woodii on glycerol and dihydroxyacetone. Environ Microbiol 23(5):2648-2658 (DOI:10.1111/1462-2920.15503).

von Hoyningen-Huene AJE, Schlotthauer TJ, Schneider D, Poehlein A, Daniel R (2021) Pontibacillus sp. ALD_SL1 and Psychroflexus sp. ALD_RP9, two novel moderately halophilic bacteria isolated from sediment and water from the Aldabra Atoll, Seychelles. PLoS One 16(8):e0256639 (DOI:10.1371/journal.pone.0256639).

Wang H, Beule L, Zang H, Pfeiffer B, Ma S, Karlovsky P, Dittert K (2021) The potential of ryegrass as cover crop to reduce soil N2O emissions and increase the population size of denitrifying bacteria. Soil Sci 72(3):1447-1461 (DOI:10.1111/ejss.13047).

Willms IM, Grote M, Kocatürk M, Singhoff L, Kraft AA, Bolz SH, Nacke H (2021) Novel soil-derived beta-lactam, chloramphenicol, fosfomycin and trimethoprim resistance genes revealed by functional metagenomics. Antibiotics 10(4):378 (DOI:10.3390/antibiotics10040378).

Willms IM, Bolz SH, Yuan J, Krafft L, Schneider D, Schöning I, Schrumpf M, Nacke H (2021) The ubiquitous soil verrucomicrobial clade ‘Candidatus Udaeobacter’ shows preferences for acidic pH. Environ Microbiol Rep 13(6):878-883 (DOI:10.1111/1758-2229.13006).

Wolter LA, Wietz M, Ziesche L, Breider S, Leinberger J, Poehlein A, Daniel R, Schulz S, Brinkhoff T (2021) Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle. Syst Appl Microbiol 44(1):126166 (DOI:10.1016/j.syapm.2020.126166).

Wolter LA, Mitulla M, Kalem J, Daniel R, Simon M, Wietz M (2021) CAZymes in Maribacter dokdonensis 62-1 from the Patagonian shelf: Genomics and physiology compared to related flavobacteria and a co-occurring Alteromonas strain. Front Microbiol 12:628055 (DOI:10.3389/fmicb.2021.628055).


2020

Ahle CM, Stødkilde K, Afshar M, Poehlein A, Ogilvie LA, Söderquist B, Hüpeden J, Brüggemann H (2020) Staphylococcus saccharolyticus: An overlooked human skin colonizer. Microorganisms 8(8):1105 (DOI:10.3390/microorganisms8081105).

Alio I, Gudzuhn M, Pérez García P, Danso D, Schoelmerich M, Mamat U, Schaible UE, Steinmann J, Yero D, Gibert I, Kohl TA, Niemann S, Gröschel MI, Haerdter J, Hackl T, Vollstedt CH, Bömeke M, Egelkamp R, Daniel R, Poehlein A, Streit WR (2020) Phenotypic and transcriptomic analysis of seven clinical Stenotrophomonas maltophilia isolates identify a small set of shared and commonly regulated genes involved in biofilm lifestyle. Appl Environ Microbiol 86:e02038-20 (DOI:10.1128/AEM.02038-20).

Aloo BN, Mbega ER, Makumba BA, Friedrich I, Hertel R, Daniel R (2020) Whole-genome sequences of three plant growth-promoting rhizobacteria isolated from Solanum tuberosum L. rhizosphere in Tanzania. Microbiol Resour Announc 9(20):e00371-20 (DOI:10.1128/MRA.00371-20).

Baena Lozada LP, Hoppert M, Hertel R (2020) Phage vB_BmeM-Goe8 infecting Bacillus megaterium DSM319. Arch Virol 165:515–517 (DOI:10.1007/s00705-019-04513-5).

Ballau ff J, Zemp DC, Schneider D, Irawan B, Daniel R, Polle A (2020) Legacy effects overshadow tree diversity effects on soil fungal communities in oil palm-enrichment plantations. Microorganisms 8(10):E1577 (DOI:10.3390/microorganisms8101577).

Berkelmann D, Schneider D, Meryandini A, Daniel R (2020) Unravelling the effects of tropical land use conversion on the soil microbiome. Environ Microbiome 15:5 (DOI:10.1186/s40793-020-0353-3).

Berkelmann D, Schneider D, Hennings N, Meryandini A, Daniel R (2020) Soil bacterial community structures in relation to different oil palm management practices. Sci Data 7:421 (DOI:10.1038/s41597-020-00752-3).

Chibani CM, Roth O, Liesegang H, Wendling CC (2020) Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements. BMC Genomics 21(1):354 (DOI:10.1186/s12864-020-6735-5).

Chibani CM, Hertel R, Hoppert M, Liesegang H, Wendling CC (2020) Closely related Vibrio alginolyticus strains encode an identical repertoire of Caudovirales-like regions and filamentous phages. Viruses 12(12):1359 (DOI:10.3390/v12121359).

Coffey MJ, Low I, Stelzer-Braid S, Wemheuer B, Garg M, Thomas T, Jaffe A, Rawlinson WD, Ooi CY (2020) The intestinal virome in children with cystic fibrosis differs from healthy controls. PLoS ONE 15(5):e0233557 (DOI:10.1371/journal.pone.0233557).

Czieborowski M, Hübenthal A, Poehlein A, Vogt I, Philipp B (2020) Genetic and physiological analysis of biofilm formation on different plastic surfaces by Sphingomonas sp. strain S2M10 reveals an essential function of sphingan biosynthesis. Microbiol 166(10):918-935 (DOI:10.1099/mic.0.000961).

Egelkamp R, Friedrich I, Hertel R, Daniel R (2020) From sequence to function: a new workflow for nitrilase identification. Appl Microbiol Biotechnol 104:4957–4970 (DOI:10.1007/s00253-020-10544-9).

Eze MO, Lütgert SA, Neubauer H, Balouri A, Kraft AA, Sieven A, Daniel R, Wemheuer B (2020) Metagenome assembly and metagenome-assembled genome sequences from a historical oil field located in Wietze, Germany. Microbiol Resour Announc 9(21):e00333-20 (DOI:10.1128/MRA.00333-20).

Flaiz M, Baur T, Brahner S, Poehlein A, Daniel R, Bengelsdorf FR (2020) Caproicibacter fermentans gen. nov., sp. nov., a new caproate- producing bacterium and emended description of the genus Caproiciproducens. Int J Syst Evol Microbiol 70(7):4269–4279 (DOI:10.1099/ijsem.0.004283).

Friedrich I, Hollensteiner J, Schneider D, Poehlein A, Hertel R, Daniel R (2020) First complete genome sequences of Janthinobacterium lividum EIF1 and EIF2 and their comparative genome analysis. Genome Biol Evol 12(10):1782-1788 (DOI:10.1093/gbe/evaa148).

Furrer AD, Bömeke M, Hoppert M, Hertel R (2020) Phage vB_BveM-Goe7 represents a new genus in the subfamily Bastillevirinae. Arch Virol 165(4):959-962 (DOI:10.1007/s00705-020-04546-1).

Fussmann D, von Hoyningen-Huene A, Reimer A, Schneider D, Babková H, Peticzka R, Maier A, Arp G, Daniel R, Meister P (2020) Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria. Biogeosciences 17:2085–2106 (DOI:10.5194/bg-17-2085-2020).

Gerke J, Frauendorf H, Schneider D, Wintergoller M, Hofmeister T, Poehlein A, Zebec Z, Takano E, Scrutton NS, Braus GH (2020) Production of the fragrance geraniol in peroxisomes of a product-tolerant baker's yeast. Front Bioeng Biotechnol 8:582052 (DOI:10.3389/fbioe.2020.582052).

Grass I, Kubitza C, Krishna VV, Corre MD, Mußhoff O, Pütz P, Drescher J, Rembold K, Ariyanti ES, Barnes AD, Brinkmann N, Brose U, Brümmer B, Buchori D, Daniel R, Darras KFA, Faust H, Fehrmann L, Hein J, Hennings N, Hidayat P, Hölscher D, Jochum M, Knohl A, Kotowska MM, Krashevska V, Kreft H, Leuschner C, Lobite NJS, Panjaitan R, Polle A, Potapov AM, Purnama E, Qaim M, Röll Al, Scheu S, Schneider D, Tjoa A, Tscharntke T, Veldkamp E, Wollni M (2020) Trade-offs between multifunctionality and profit in tropical smallholder landscapes. Nat Commun 11:1186 (DOI:10.1038/s41467-020-15013-5).

Heinrichs ME, Tebbe DA, Wemheuer B, Niggemann J, Engelen B (2020) Impact of viral lysis on the composition of bacterial communities and dissolved organic matter in deep-sea sediments. Viruses 12(9):922 (DOI:10.3390/v12090922).

Hetz SA, Poehlein A, Horn MA (2020) Whole-genome sequences of two new Caballeronia strains isolated from cryoturbated peat circles of the permafrost-affected eastern european tundra. Microbiol Resour Announc 9(31):e00731-20 (DOI:10.1128/MRA.00731-20).

Ho A, Mendes LW, Lee HJ, Kaupper T, Mo Y, Poehlein A, Bodelier PLE, Jia Z, Horn M (2020) Response of a methane-driven interaction network to stressor intensification. FEMS Microbiol Ecol 96(10):fiaa180 (DOI:10.1093/femsec/fiaa180).

Hollensteiner J, Poehlein A, Kloskowski P, Tammam Ali T, Daniel R (2020) Genome sequence of Komagataeibacter saccharivorans strain JH1, isolated from fruit flies. Microbiol Resour Announc 9(13):e00098-20 (DOI:10.1128/MRA.00098-20).

Hollensteiner J, Schneider D, Poehlein A, Daniel R (2020) Complete genome of Roseobacter ponti DSM 106830T. Genome Biol Evol 12(7):1013-1018 (DOI:10.1093/gbe/evaa114).

Kaupper T, Mendes LW, Lee HJ, Mo Y, Poehlein A, Jia Z, Horn MA, Ho A (2020) When the going gets tough: Emergence of a complex methane-driven interaction network during recovery from desiccation-rewetting. Soil Biol Biochem 153:108109 (DOI:10.1016/j.soilbio.2020.108109).

Klewing A, Koo BM , Krüger L, Poehlein A, Reuß D, Daniel R, Gross CA, Stülke J (2020) Resistance to serine in Bacillus subtilis: identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism. Environ Microbiol 22(8):3937-3949 (DOI:10.1111/1462-2920.15179).

Krüger L, Herzberg C, Warneke R, Poehlein A, Stautz J, Weiß M, Daniel R, Hänelt I, Stülke J (2020) Two ways to convert a low- to a high-affinity potassium channel: Control of Bacillus subtilis KtrCD by glutamate. J Bacteriol 202(12):e00138-20 (DOI:10.1128/JB.00138-20).

Müller K, Kubsch N, Marhan S, Mayer-Gruner P, Nassal P, Schneider D, Daniel R, Piepho H-P, Polle A and Kandeler E (2020) Saprotrophic and ectomycorrhizal fungi contribute differentially to organic P mobilization in beech-dominated forest ecosystems. Front For Glob Change 3:47 (DOI:10.3389/ffgc.2020.00047).

Nacke H, Kirck LL,Schwarz S, Schneider D, Poehlein A, Daniel R (2020) Metagenome sequences of a wastewater treatment plant digester sludge-derived enrichment culture. Microbiol Resour Announc 9(32):e00712-20 (DOI:10.1128/MRA.00712-20).

Nguyen DQ, Schneider D, Brinkmann N, Song B, Janz D, Schöning I, Daniel R, Pena R, Polle A (2020) Soil and root nutrient chemistry structure root-associated fungal assemblages in temperate forests. Environ Microbiol 22(8):3081-3095 (DOI:10.1111/1462-2920.15037).

Otte K, Kühne NM, Furrer AD, Baena Lozada LP, Lutz VT, Schilling T, Hertel R (2020) A CRISPR‐Cas9 tool to explore the genetics of Bacillus subtilis phages. Lett Appl Microbiol 71(6):588-595 (DOI:10.1111/lam.13349).

Perez MF, Kurth D, Farías ME, Soria MN, Castillo Villamizar GA, Poehlein A, Daniel R, Dib JR (2020) First report on the plasmidome from a high-altitude lake of the Andean Puna. Front Microbiol 11:1343 (DOI:10.3389/fmicb.2020.01343).

Poehlein A, Hollensteiner J, Dreyer A, Gavrilova I, Daniel R (2020) Complete genome sequence of Sporomusa termitida DSM 4440T. Microbiol Resour Announc 9(11):e00046-20 (DOI:10.1128/MRA.00046-20).

Protasov E, Reeh H, Liu P, Poehlein A, Platt K, Heimerl T, Hervé V, Daniel R, Brune A (2020) Genome reduction in novel, obligately methyl-reducing Methanosarcinales isolated from arthropod guts (Methanolapillus gen. nov. and Methanimicrococcus). FEMS Microbiol Ecol 100(9):fiae111 (DOI:10.1093/femsec/fiae111).

Rao SC, Esvaran M, Patole SK, Simmer KN, Gollow I, Keil A, Wemheuer B, Chen L, Conway PL (2020) Gut microbiota in neonates with congenital gastrointestinal surgical conditions: a prospective study. Pediatr Res 88:878-886 (DOI:10.1038/s41390-020-0824-7).

Redl S, Poehlein A, Esser C, Bengelsdorf FR, Jensen TØ, Jendresen CB, Tindall BJ, Daniel R, Dürre P, Nielsen AT (2020) Genome-based comparison of all species of the genus Moorella, and status of the species Moorella thermoacetica and Moorella thermoautotrophica. Front Microbiol 10:3070 (DOI:10.3389/fmicb.2019.03070).

Richts B, Hertel R, Potot S, Poehlein A, Daniel R, Schyns G, Pragai Z, Commichau FM (2020) Complete genome sequence of the prototrophic Bacillus subtilis subsp. subtilis strain SP1. Microbiol Resour Announc 9(32):e00825-20 (DOI:10.1128/MRA.00825-20).

Rummel PS, Pfeiffer B, Pausch J, Well R, Schneider D, Dittert K (2020) Maize root and shoot litter quality controls short-term CO2 and N2O emissions and bacterial community structure of arable soil. Biogeosciences 17:1181–1198 (DOI:10.5194/bg-2019-320).

Salgar-Chaparro SJ, Castillo-Villamizar G, Poehlein A, Daniel R, Machuca LL (2020) Complete genome sequence of Pseudomonas balearica strain EC28, an iron-oxidizing bacterium isolated from corroded steel. Microbiol Resour Announc 9(19):e00275-20 (DOI:10.1128/MRA.00275-20).

Salgar-Chaparro SJ, Castillo-Villamizar G, Poehlein A, Daniel R, Machuca LL (2020) Draft genome sequence of Enterobacter roggenkampii strain OS53, isolated from corroded pipework at an offshore oil production facility. Microbiol Resour Announc 9(34):e00583-20 (DOI:10.1128/MRA.00583-20).

Salgar-Chaparro SJ, Castillo-Villamizar G, Poehlein A, Daniel R, Machuca LL (2020) Complete genome sequence of Shewanella chilikensis strain DC57, isolated from corroded seal rings at a floating oil production system in Australia. Microbiol Resour Announc 9(38):e00584-20 (DOI:10.1128/MRA.00584-20).

Schneider D, Aßmann N, Wicke D, Poehlein A, Daniel R (2020) Metagenomes of wastewater at different treatment stages in Central Germany. Microbiol Resour Announc 9(15):e00201-20 (DOI:10.1128/MRA.00201-20).

Schneider D, Zühlke D, Petscheleit T, Poehlein A, Riedel K, Daniel R (2020) Complete genome sequence of Escherichia coli GW-AmxH19, isolated from hospital wastewater in Greifswald, Germany. Microbiol Resour Announc 9(21):e00279-20 (DOI:10.1128/MRA.00279-20).

Schroeder J, Jannoura R, Beuschel R, Pfeiffer B, Dyckmans J, Murugan R, Chavannavar S, Wachendorf CH, Joergensen RG (2020) Carbon use efficiency and microbial functional diversity in a temperate Luvisol and a tropical Nitisol after millet litter and N addition. Biol Fertil Soils 56:1139-1150 (DOI:10.1007/s00374-020-01487-4).

Schüler MA, Stegmann BA, Poehlein A, Daniel R, Dürre P (2020) Genome sequence analysis of the temperate bacteriophage TBP2 of the solvent producer Clostridium saccharoperbutylacetonicum N1-4 (HMT, ATCC 27021). FEMS Microbiol Lett 367(14):fnaa103 (DOI:10.1093/femsle/fnaa103).

Stødkilde K, Poehlein A, Brüggemann H (2020) Draft genome sequence of a new Staphylococcal species isolated from human skin. Microbiol Resour Announc 9(6):e01499-19 (DOI:10.1128/MRA.01499-19).

Tiede J, Diepenbruck M, Gadaub J, Wemheuer B, Daniel R, Scherber C (2020) Seasonal variation in the diet of the serotine bat (Eptesicus serotinus): A high-resolution analysis using DNA metabarcoding. Basic Appl Ecol 49:1-12 (DOI:10.1016/j.baae.2020.09.004).

Vendl C, Slavich E, Wemheuer B, Nelson T, Ferrari B, Thomas T, Rogers T (2020) Respiratory microbiota of humpback whales may be reduced in diversity and richness the longer they fast. Sci Rep 10:12645 (DOI:10.1038/s41598-020-69602-x).

Wemheuer F, Berkelmann D, Wemheuer B, Daniel R, Vidal S, Bisseleua Daghela HB, (2020) Agroforestry management systems drive the composition, diversity, and function of fungal and bacterial endophyte communities in Theobroma cacao leaves. Microorganisms 8(3):405 (DOI:10.3390/microorganisms8030405).

Wemheuer, F., Taylor, J.A., Daniel, R, Johnston E, Meinicke P, Thomas T, Wemheuer B (2020) Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environ Microbiome 15:11 (DOI:10.1186/s40793-020-00358-7).

Willms IM, Yuan J, Penone C, Goldmann K, Vogt J, Wubet T, Schöning I, Schrumpf M, Buscot F, Nacke H (2020) Distribution of medically relevant antibiotic resistance genes and mobile genetic elements in soils of temperate forests and grasslands varying in land use. Genes 11(2):150 (DOI:10.3390/genes11020150).

Willms IM, Rudolph AY, Göschel I, Bolz SH, Schneider D, Penone C, Poehlein A, Schöning I, Nacke H (2020) Globally abundant “Candidatus Udaeobacter” benefits from release of antibiotics in soil and potentially performs trace gas scavenging. mSphere 5(4):e00186-20 (DOI:10.1128/mSphere.00186-20).

Winkler L, Münker MF, Brunotte S, Rohlmann L, Alfageme AD, Poehlein A, Hoppert M, Reitner J, Nacke H (2020) Metagenome-assembled genome sequences from an anoxygenic photosynthetic consortium involved in sulfur cycling. Microbiol Resour Announc 9(38):e00819-20 (DOI:10.1128/MRA.00819-20).

Wischer D, Schneider D, Poehlein A, Herrmann F, Oruc H, Meinhardt J, Wagner O, Kharin S, Novikova N, Haag R, Daniel R, Grohmann E (2020) Novel antimicrobial cellulose fleece inhibits growth of human-derived biofilm-forming Staphylococci during the SIRIUS19 simulated space mission. Front Microbiol 11:1626 (DOI:10.3389/fmicb.2020.01626).

Wübbeler JH, Oppermann-Sanio FB, Ockenfels A, Röttig A, Osthaar-Ebker A, Verbarg S, Poehlein A, Madkour MH, Al-Ansari AM, Almakishah NH, Daniel R, Steinbüchel A (2020) Corrigendum: Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil. Int J Syst Evol Microbiol 70(4):2955 (DOI:10.1099/ijsem.0.004039).