{"entity": "journal", "iuid": "c63e2f1ae8314a2fa8ef4a9ddbb86f17", "timestamp": "2026-07-20T22:55:27.133Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Microbiome.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Microbiome"}}, "title": "Microbiome", "issn": "2049-2618", "issn-l": "2049-2618", "publications_count": 10, "publications": [{"entity": "publication", "iuid": "f90df874d6ad48c58ed647c139f3997e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f90df874d6ad48c58ed647c139f3997e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f90df874d6ad48c58ed647c139f3997e"}}, "title": "Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Vomstein", "given": "Kilian", "initials": "K"}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}], "type": "journal article", "published": "2024-08-19", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "12", "issue": "1", "pages": "153", "issn-l": "2049-2618"}, "abstract": "The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.\n\nBased on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.\n\nThe VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.", "doi": "10.1186/s40168-024-01870-5", "pmid": "39160615", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11331738"}, {"db": "pii", "key": "10.1186/s40168-024-01870-5"}], "notes": [], "created": "2025-03-19T07:35:44.797Z", "modified": "2025-04-08T06:08:00.287Z"}, {"entity": "publication", "iuid": "8495f35a8b6243688a5302fecccdf9b7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8495f35a8b6243688a5302fecccdf9b7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8495f35a8b6243688a5302fecccdf9b7"}}, "title": "Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.", "authors": [{"family": "Inda-D\u00edaz", "given": "Juan Salvador", "initials": "JS"}, {"family": "Lund", "given": "David", "initials": "D"}, {"family": "Parras-Molt\u00f3", "given": "Marcos", "initials": "M"}, {"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}], "type": "video-audio media", "published": "2023-03-08", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "11", "issue": "1", "pages": "44", "issn-l": "2049-2618"}, "abstract": "Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants.\n\nA reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs.\n\nOur results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.", "doi": "10.1186/s40168-023-01479-0", "pmid": "36882798", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pmc", "key": "PMC9993715"}, {"db": "pii", "key": "10.1186/s40168-023-01479-0"}], "notes": [], "created": "2024-11-18T11:42:49.594Z", "modified": "2024-11-18T11:42:49.599Z"}, {"entity": "publication", "iuid": "a94bd281182c4ab884ba8ec5f6ce9a1a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a94bd281182c4ab884ba8ec5f6ce9a1a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a94bd281182c4ab884ba8ec5f6ce9a1a"}}, "title": "Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Izabel-Shen", "given": "Dandan", "initials": "D"}, {"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2022-08-15", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "10", "issue": "1", "pages": "126", "issn-l": "2049-2618"}, "abstract": "Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea.\n\nThe composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments.\n\nThis study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.", "doi": "10.1186/s40168-022-01321-z", "pmid": "35965333", "labels": {"SciLifeLab Fellow": null, "Sarahi Garcia": null}, "xrefs": [{"db": "pmc", "key": "PMC9377124"}, {"db": "pii", "key": "10.1186/s40168-022-01321-z"}], "notes": [], "created": "2022-12-04T13:44:59.305Z", "modified": "2023-05-15T12:36:14.732Z"}, {"entity": "publication", "iuid": "1c619a21890b4a04a96ac708f21c8847", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1c619a21890b4a04a96ac708f21c8847.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1c619a21890b4a04a96ac708f21c8847"}}, "title": "Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Karlsson", "given": "Christofer M G", "initials": "CMG"}, {"family": "Divne", "given": "Anna-Maria", "initials": "AM"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Homa", "given": "Felix", "initials": "F"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28b77762086343048e74046a6486caff.json"}}], "type": "journal article", "published": "2018-09-28", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "6", "issue": "1", "pages": "173", "issn-l": "2049-2618"}, "abstract": "Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.\n\nWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.\n\nThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.", "doi": "10.1186/s40168-018-0550-0", "pmid": "30266101", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6162917"}, {"db": "pii", "key": "10.1186/s40168-018-0550-0"}], "notes": [], "created": "2022-11-08T07:01:16.695Z", "modified": "2023-10-27T09:33:54.810Z"}, {"entity": "publication", "iuid": "60ac528c470a45b7bbd3760ebd37cd06", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/60ac528c470a45b7bbd3760ebd37cd06.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/60ac528c470a45b7bbd3760ebd37cd06"}}, "title": "The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c666068e9d34939b0252a627007cec7.json"}}], "type": "journal article", "published": "2018-07-07", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "6", "issue": "1", "pages": "125", "issn-l": "2049-2618"}, "abstract": "Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a given environment, but this assumption has not been verified. In this study, this hypothesis is tested, using the resistance gene profiles of 1109 metagenomes from various environments.\n\nThis study shows that the diversity and abundance of known antibiotic resistance genes can generally predict the diversity and abundance of undescribed resistance genes. However, the extent of this predictability is dependent on the type of environment investigated. Furthermore, it is shown that carefully selected small sets of resistance genes can describe total resistance gene diversity remarkably well.\n\nThe results of this study suggest that knowledge gained from large-scale quantifications of known resistance genes can be utilized as a proxy for unknown resistance factors. This is important for current and proposed monitoring efforts for environmental antibiotic resistance and has implications for the design of risk ranking strategies and the choices of measures and methods for describing resistance gene abundance and diversity in the environment.", "doi": "10.1186/s40168-018-0508-2", "pmid": "29981578", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-018-0508-2"}, {"db": "pmc", "key": "PMC6035801"}], "notes": [], "created": "2022-11-08T09:28:30.629Z", "modified": "2022-11-08T09:28:30.678Z"}, {"entity": "publication", "iuid": "62ce46f9bd544109b71d54435029b753", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62ce46f9bd544109b71d54435029b753.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62ce46f9bd544109b71d54435029b753"}}, "title": "Identification of 76 novel B1 metallo-\u03b2-lactamases through large-scale screening of genomic and metagenomic data.", "authors": [{"family": "Berglund", "given": "Fanny", "initials": "F"}, {"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kotsakis", "given": "Stathis", "initials": "S"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}, {"family": "Kristiansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8609-2414", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18d5538c8c0749199a6f1b51d15eec69.json"}}], "type": "journal article", "published": "2017-10-12", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "5", "issue": "1", "pages": "134", "issn-l": "2049-2618"}, "abstract": "Metallo-\u03b2-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-\u03b2-lactamases, some of which may spread to pathogens, thereby threatening public health. The aim of this study was to identify novel metallo-\u03b2-lactamases of class B1, the most clinically important subclass of these enzymes.\n\nBased on a new computational method using an optimized hidden Markov model, we analyzed over 10,000 bacterial genomes and plasmids together with more than 5 terabases of metagenomic data to identify novel metallo-\u03b2-lactamase genes. In total, 76 novel genes were predicted, forming 59 previously undescribed metallo-\u03b2-lactamase gene families. The ability to hydrolyze imipenem in an Escherichia coli host was experimentally confirmed for 18 of the 21 tested genes. Two of the novel B1 metallo-\u03b2-lactamase genes contained atypical zinc-binding motifs in their active sites, which were previously undescribed for metallo-\u03b2-lactamases. Phylogenetic analysis showed that B1 metallo-\u03b2-lactamases could be divided into five major groups based on their evolutionary origin. Our results also show that, except for one, all of the previously characterized mobile B1 \u03b2-lactamases are likely to have originated from chromosomal genes present in Shewanella spp. and other Proteobacterial species.\n\nThis study more than doubles the number of known B1 metallo-\u03b2-lactamases. The findings have further elucidated the diversity and evolutionary history of this important class of antibiotic resistance genes and prepare us for some of the challenges that may be faced in clinics in the future.", "doi": "10.1186/s40168-017-0353-8", "pmid": "29020980", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0353-8"}, {"db": "pmc", "key": "PMC5637372"}], "notes": [], "created": "2022-11-08T09:29:03.058Z", "modified": "2022-11-08T09:29:03.139Z"}, {"entity": "publication", "iuid": "08088d084c4541e2b182432886bd39ac", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/08088d084c4541e2b182432886bd39ac.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/08088d084c4541e2b182432886bd39ac"}}, "title": "Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.", "authors": [{"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Pedersen", "given": "Karsten", "initials": "K"}, {"family": "Edlund", "given": "Johanna", "initials": "J"}, {"family": "Eriksson", "given": "Lena", "initials": "L"}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-03-23", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "5", "issue": "1", "pages": "37", "issn-l": "2049-2618"}, "abstract": "Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere.\n\nIn this study, flow cells were attached to boreholes containing either \"modern marine\" or \"old saline\" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria.\n\nPopulations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.", "doi": "10.1186/s40168-017-0253-y", "pmid": "28335808", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0253-y"}, {"db": "pmc", "key": "PMC5364579"}], "notes": [], "created": "2018-12-05T12:31:55.154Z", "modified": "2018-12-05T12:31:55.173Z"}, {"entity": "publication", "iuid": "19cadf1ebb5f494fbd2820f03f143563", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/19cadf1ebb5f494fbd2820f03f143563.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/19cadf1ebb5f494fbd2820f03f143563"}}, "title": "The structure and diversity of human, animal and environmental resistomes.", "authors": [{"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2016-10-07", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "4", "issue": "1", "pages": "54", "issn-l": "2049-2618"}, "abstract": "Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments.\n\nWe provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n = 350), animals (n = 145) and external environments (n = 369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event.\n\nOur study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.", "doi": "10.1186/s40168-016-0199-5", "pmid": "27717408", "labels": {"DDLS Fellow": null, "Johan Bengtsson-Palme": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-016-0199-5"}, {"db": "pmc", "key": "PMC5055678"}], "notes": [], "created": "2022-11-08T09:29:30.040Z", "modified": "2022-11-08T09:29:30.065Z"}, {"entity": "publication", "iuid": "47103c6f9ef644e3807af1c35338e5a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47103c6f9ef644e3807af1c35338e5a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47103c6f9ef644e3807af1c35338e5a1"}}, "title": "Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.", "authors": [{"family": "Hammond", "given": "Maria", "initials": "M"}, {"family": "Homa", "given": "Felix", "initials": "F"}, {"family": "Andersson-Svahn", "given": "Helene", "initials": "H"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJ"}, {"family": "Joensson", "given": "Haakan N", "initials": "HN"}], "type": "journal article", "published": "2016-10-06", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "4", "issue": "1", "pages": "52", "issn-l": "2049-2618"}, "abstract": "Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet.\n\nAs a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion.\n\nPartitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.", "doi": "10.1186/s40168-016-0197-7", "pmid": "27716450", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-016-0197-7"}, {"db": "pmc", "key": "PMC5054601"}], "notes": [], "created": "2018-12-05T12:15:58.894Z", "modified": "2018-12-05T12:15:58.918Z"}, {"entity": "publication", "iuid": "cd55ee001e6b439788bc570413ff89e3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cd55ee001e6b439788bc570413ff89e3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cd55ee001e6b439788bc570413ff89e3"}}, "title": "Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome.", "authors": [{"family": "Engstrand Lilja", "given": "Helene", "initials": "H"}, {"family": "Wefer", "given": "Hugo", "initials": "H"}, {"family": "Nystr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Finkel", "given": "Yigael", "initials": "Y"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2015-05-04", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "3", "issue": null, "pages": "18", "issn-l": "2049-2618"}, "abstract": "The composition of the intestinal microbiota seems to be an important factor in determining the clinical outcome in children with short bowel syndrome (SBS). Alterations in the microbiota may result in serious complications such as small bowel bacterial overgrowth (SBBO) and intestinal mucosal inflammation that lead to prolonged parenteral nutrition (PN) dependency with subsequently increased risk of liver failure and sepsis. To date, there are no reported mappings of the intestinal microbiome in children with SBS. Here, we present the first report on the intestinal microbial community profile in children with SBS.\n\nThe study includes children diagnosed with SBS in the neonatal period. Healthy siblings served as controls. Fecal samples were collected, and microbial profiles were analyzed by using 16S rRNA gene sequencing on the Illumina MiSeq platform. We observed a pronounced microbial dysbiosis in children with SBS on PN treatment with an increased and totally dominating relative abundance of Enterobacteriacae in four out of five children compared to children with SBS weaned from PN and healthy siblings.\n\nThe overall decreased bacterial diversity in children with SBS is consistent with intestinal microbiome mappings in inflammatory bowel diseases such as Crohn's disease and necrotizing enterocolitis in preterm infants. Our findings indicate that intestinal dysbiosis in children with SBS is associated with prolonged PN dependency.", "doi": "10.1186/s40168-015-0084-7", "pmid": "25941569", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "84"}, {"db": "pmc", "key": "PMC4418071"}], "notes": [], "created": "2018-12-05T09:19:20.961Z", "modified": "2018-12-05T09:19:20.996Z"}], "created": "2018-12-05T09:19:20.974Z", "modified": "2020-11-27T13:12:58.874Z"}