{"entity": "journal", "iuid": "eb531909d6f94e53822ac78742a4dae5", "timestamp": "2026-08-15T12:43:37.730Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Nat.%20Microbiol.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Nat.%20Microbiol"}}, "title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276", "publications_count": 6, "publications": [{"entity": "publication", "iuid": "c0cf16af36db4481865c4c6ccffb5d75", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c0cf16af36db4481865c4c6ccffb5d75.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c0cf16af36db4481865c4c6ccffb5d75"}}, "title": "Atlas of mRNA translation and decay for bacteria.", "authors": [{"family": "Huch", "given": "Susanne", "initials": "S", "orcid": "0000-0003-3956-7197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d0b94cf87e4243efa8e6229f49403d0f.json"}}, {"family": "Nersisyan", "given": "Lilit", "initials": "L", "orcid": "0000-0001-8525-420X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c77363d1fa7f4ea6b50c22590c23a163.json"}}, {"family": "Ropat", "given": "Maria", "initials": "M"}, {"family": "Barrett", "given": "Donal", "initials": "D", "orcid": "0000-0001-5381-5391", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fb0f798fb9e4095af7146e8bc79feee.json"}}, {"family": "Wu", "given": "Mengjun", "initials": "M"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Valeriano", "given": "Valerie D", "initials": "VD", "orcid": "0000-0002-4396-346X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c444998f561a43e8a8a8295b5ead218b.json"}}, {"family": "Vardazaryan", "given": "Nelli", "initials": "N", "orcid": "0000-0002-7972-8912", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dabc3fd207b54423bf21dcbee3ca03ee.json"}}, {"family": "Huerta-Cepas", "given": "Jaime", "initials": "J", "orcid": "0000-0003-4195-5025", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c8c00b0396840c480fa3f57a376ce00.json"}}, {"family": "Wei", "given": "Wu", "initials": "W", "orcid": "0000-0001-5643-8739", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bff283faf0147eebbb8ac9d00fae099.json"}}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Steinmetz", "given": "Lars M", "initials": "LM"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Pelechano", "given": "Vicent", "initials": "V", "orcid": "0000-0002-9415-788X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e893b93b7654d10b4072e1b5de0bd71.json"}}], "type": "journal article", "published": "2023-05-22", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276"}, "abstract": "Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA decay intermediates (5'P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5'-3' exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5'-3' exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5'P degradome) sequencing approach, we characterize 5'P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5'P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.", "doi": "10.1038/s41564-023-01393-z", "pmid": "37217719", "labels": {"SciLifeLab Fellow": null, "Vicent Pelechano": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-023-01393-z"}], "notes": [], "created": "2023-05-29T07:36:18.693Z", "modified": "2023-05-29T07:36:18.872Z"}, {"entity": "publication", "iuid": "083054c2bb8c462d80cd031cf5550bf8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/083054c2bb8c462d80cd031cf5550bf8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/083054c2bb8c462d80cd031cf5550bf8"}}, "title": "Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.", "authors": [{"family": "Barandun", "given": "Jonas", "initials": "J", "orcid": "0000-0003-2971-8190", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604d83e342b8407d81e97a301db0f067.json"}}, {"family": "Hunziker", "given": "Mirjam", "initials": "M"}, {"family": "Vossbrinck", "given": "Charles R", "initials": "CR"}, {"family": "Klinge", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9373-4737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d66bc3613efa43108246251d7b6f381c.json"}}], "type": "journal article", "published": "2019-11-00", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276", "volume": "4", "issue": "11", "pages": "1798-1804"}, "abstract": "Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance1-3, and are significant opportunistic parasites of humans4. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle5, rudimentary mitochondria and the smallest known eukaryotic genomes5-7. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome8-10. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.", "doi": "10.1038/s41564-019-0514-6", "pmid": "31332387", "labels": {"Jonas Barandun": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-019-0514-6"}, {"db": "pmc", "key": "PMC6814508"}, {"db": "mid", "key": "NIHMS1052135"}], "notes": [], "created": "2020-09-29T14:02:18.804Z", "modified": "2022-11-04T11:32:15.828Z"}, {"entity": "publication", "iuid": "8218cfa66e574583b9d300b455ba81ce", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8218cfa66e574583b9d300b455ba81ce.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8218cfa66e574583b9d300b455ba81ce"}}, "title": "Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.", "authors": [{"family": "Tramontano", "given": "Melanie", "initials": "M", "orcid": "0000-0001-6407-527X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7eb22c8f8f17483ca714daa532e877c9.json"}}, {"family": "Andrejev", "given": "Sergej", "initials": "S", "orcid": "0000-0002-7875-0261", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fbe1b5aed7d4931896ef1c99dafcfc4.json"}}, {"family": "Pruteanu", "given": "Mihaela", "initials": "M", "orcid": "0000-0003-0484-8503", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b7d7b54ba2149289249a07339f63993.json"}}, {"family": "Kl\u00fcnemann", "given": "Martina", "initials": "M"}, {"family": "Kuhn", "given": "Michael", "initials": "M", "orcid": "0000-0002-2841-872X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e248cde011f94e6b9dd2de922062d0d6.json"}}, {"family": "Galardini", "given": "Marco", "initials": "M", "orcid": "0000-0003-2018-8242", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bade63af21bc49e59c5687ea303157de.json"}}, {"family": "Jouhten", "given": "Paula", "initials": "P"}, {"family": "Zelezniak", "given": "Aleksej", "initials": "A"}, {"family": "Zeller", "given": "Georg", "initials": "G", "orcid": "0000-0003-1429-7485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/414382373eb5447186a7e6c925aa067f.json"}}, {"family": "Bork", "given": "Peer", "initials": "P", "orcid": "0000-0002-2627-833X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b2c7fb225454cb592da4b2af6d6b645.json"}}, {"family": "Typas", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-0797-9018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d38ea7a531ad47cfa26df998f0e54dbe.json"}}, {"family": "Patil", "given": "Kiran Raosaheb", "initials": "KR", "orcid": "0000-0002-6166-8640", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/093a0e7ad5e0464a993d8e00861eea15.json"}}], "type": "journal article", "published": "2018-04-00", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276", "volume": "3", "issue": "4", "pages": "514-522"}, "abstract": "Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences. We identify mucin utilizers and species inhibited by amino acids and short-chain fatty acids. Our analysis also uncovers media for in vitro studies wherein growth capacity correlates well with in vivo abundance. Further value of the underlying resource is demonstrated by correcting pathway gaps in available genome-scale metabolic models of gut microorganisms. Together, the media resource and the extracted knowledge on growth abilities widen experimental and computational access to the gut microbiota.", "doi": "10.1038/s41564-018-0123-9", "pmid": "29556107", "labels": {"Aleksej Zelezniak": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-018-0123-9"}], "notes": [], "created": "2018-12-03T14:45:45.267Z", "modified": "2022-11-04T11:51:57.019Z"}, {"entity": "publication", "iuid": "6f00885801904675a8c53a12144092fa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6f00885801904675a8c53a12144092fa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6f00885801904675a8c53a12144092fa"}}, "title": "Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.", "authors": [{"family": "Nielsen", "given": "Jens Christian", "initials": "JC"}, {"family": "Grijseels", "given": "Sietske", "initials": "S"}, {"family": "Prigent", "given": "Sylvain", "initials": "S"}, {"family": "Ji", "given": "Boyang", "initials": "B"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Nielsen", "given": "Kristian Fog", "initials": "KF"}, {"family": "Frisvad", "given": "Jens Christian", "initials": "JC"}, {"family": "Workman", "given": "Mhairi", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2017-04-03", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "volume": "2", "issue": null, "pages": "17044", "issn-l": "2058-5276"}, "abstract": "Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were identified, and polyketide synthase and non-ribosomal peptide synthetase based BGCs were grouped into gene cluster families and mapped to known pathways. The grouping of BGCs allowed us to study the evolutionary trajectory of pathways based on 6-methylsalicylic acid (6-MSA) synthases. Finally, we cross-referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic diversity of Penicillia and highlights the potential of these species as a source of new antibiotics and other pharmaceuticals.", "doi": "10.1038/nmicrobiol.2017.44", "pmid": "28368369", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "nmicrobiol201744"}], "notes": [], "created": "2018-12-05T09:57:07.148Z", "modified": "2018-12-05T09:57:07.168Z"}, {"entity": "publication", "iuid": "f55ddd940d5b477d83ed6d9077463ba3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f55ddd940d5b477d83ed6d9077463ba3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f55ddd940d5b477d83ed6d9077463ba3"}}, "title": "Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.", "authors": [{"family": "Baker", "given": "Brett J", "initials": "BJ"}, {"family": "Saw", "given": "Jimmy H", "initials": "JH"}, {"family": "Lind", "given": "Anders E", "initials": "AE"}, {"family": "Lazar", "given": "Cassandre Sara", "initials": "CS"}, {"family": "Hinrichs", "given": "Kai-Uwe", "initials": "KU"}, {"family": "Teske", "given": "Andreas P", "initials": "AP"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJ"}], "type": "journal article", "published": "2016-02-15", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "volume": "1", "issue": null, "pages": "16002", "issn-l": "2058-5276"}, "abstract": "The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5\u2005Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere. ", "doi": "10.1038/nmicrobiol.2016.2", "pmid": "27572167", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "nmicrobiol20162"}], "notes": [], "created": "2018-12-05T09:11:26.290Z", "modified": "2018-12-05T09:11:26.310Z"}, {"entity": "publication", "iuid": "471721f939454a778abebdc25391fe66", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/471721f939454a778abebdc25391fe66.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/471721f939454a778abebdc25391fe66"}}, "title": "The metabolic background is a global player in Saccharomyces gene expression epistasis", "authors": [{"family": "Alam", "given": "Mohammad Tauqeer", "initials": "MT"}, {"family": "Zelezniak", "given": "Aleksej", "initials": "A"}, {"family": "M\u00fclleder", "given": "Michael", "initials": "M"}, {"family": "Shliaha", "given": "Pavel", "initials": "P"}, {"family": "Schwarz", "given": "Roland", "initials": "R"}, {"family": "Capuano", "given": "Floriana", "initials": "F"}, {"family": "Vowinckel", "given": "Jakob", "initials": "J"}, {"family": "Radmaneshfar", "given": "Elahe", "initials": "E"}, {"family": "Kr\u00fcger", "given": "Antje", "initials": "A"}, {"family": "Calvani", "given": "Enrica", "initials": "E"}, {"family": "Michel", "given": "Steve", "initials": "S"}, {"family": "B\u00f6rno", "given": "Stefan", "initials": "S"}, {"family": "Christen", "given": "Stefan", "initials": "S"}, {"family": "Patil", "given": "Kiran Raosaheb", "initials": "KR"}, {"family": "Timmermann", "given": "Bernd", "initials": "B"}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS"}, {"family": "Ralser", "given": "Markus", "initials": "M"}], "type": "journal-article", "published": "2016-02-01", "journal": {"title": "Nat. Microbiol", "issn": "2058-5276", "issn-l": "2058-5276", "volume": "1", "issue": "3", "pages": "15030"}, "abstract": null, "doi": "10.1038/nmicrobiol.2015.30", "pmid": "27572163", "labels": {"Aleksej Zelezniak": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:41:06.061Z", "modified": "2022-11-04T11:52:53.960Z"}], "created": "2018-12-03T14:41:06.076Z", "modified": "2020-11-27T13:12:58.953Z"}