{"entity": "journal", "iuid": "e5c5551033e74764ba15c5149821310b", "timestamp": "2026-07-11T15:27:57.635Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/BMC%20Microbiol..json"}, "display": {"href": "https://publications.scilifelab.se/journal/BMC%20Microbiol."}}, "title": "BMC Microbiol.", "issn": "1471-2180", "issn-l": "1471-2180", "publications_count": 11, "publications": [{"entity": "publication", "iuid": "3d5e24e8dc3542eab9713c6df3a7e8e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d5e24e8dc3542eab9713c6df3a7e8e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d5e24e8dc3542eab9713c6df3a7e8e5"}}, "title": "Reverse microdialysis of sucrose stimulates soil fungal and bacterial growth at the microscale.", "authors": [{"family": "Schneider", "given": "Andreas N", "initials": "AN"}, {"family": "Buckley", "given": "Scott", "initials": "S"}, {"family": "Lorenzo", "given": "Zulema Carracedo", "initials": "ZC"}, {"family": "Gratz", "given": "Regina", "initials": "R"}, {"family": "Nilsson", "given": "Lina", "initials": "L"}, {"family": "Swaine", "given": "Mark", "initials": "M"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Taylor", "given": "Andy F S", "initials": "AFS"}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S"}], "type": "journal article", "published": "2025-07-14", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "436", "issn-l": "1471-2180"}, "abstract": "The rhizosphere is a critical microenvironment that plays key roles in plant nutrient availability, largely due to root interactions with rhizospheric microbes. However, we lack suitable methods that can elucidate mechanisms determining rhizospheric community structure and function within the context of a dynamic, undisturbed soil. Microdialysis has been used for low intrusive soil nutrient sampling at the scale of a fine root, with small probes that also enable release of defined compounds. We evaluated whether microdialysis could simulate exudation, by the release of sucrose, and stimulate changes in a soil microbial community, allowing us to determine the microbes that responded most to carbon release.\n\nMicrodialysis successfully stimulated growth on probe surfaces of fungi and bacteria, which were extracted and sequenced for identification. Microbial growth was also visualized with scanning electron microscopy. The majority of the species stimulated were classified as fast growing or opportunistic, e.g. yeasts, moulds, proteobacteria and actinobacteriota, which are known to respond quickly (within days) to the release of simple sugars as exudates in the rhizosphere.\n\nThe study demonstrates the potential of using microdialysis as a tool to investigate interactions between root exudation and soil microbial community composition, initially for individual compounds and in the future for more complex compositions.", "doi": "10.1186/s12866-025-04082-5", "pmid": "40660105", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12257659"}, {"db": "pii", "key": "10.1186/s12866-025-04082-5"}], "notes": [], "created": "2025-10-30T11:57:11.876Z", "modified": "2025-11-28T10:52:39.912Z"}, {"entity": "publication", "iuid": "f28f6a98aeeb4c36a667374a906d634e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f28f6a98aeeb4c36a667374a906d634e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f28f6a98aeeb4c36a667374a906d634e"}}, "title": "Impact of glucose and propionic acid on even and odd chain fatty acid profiles of oleaginous yeasts.", "authors": [{"family": "Bonzanini", "given": "Veronica", "initials": "V"}, {"family": "Haddad Momeni", "given": "Majid", "initials": "M"}, {"family": "Olofsson", "given": "Kim", "initials": "K"}, {"family": "Olsson", "given": "Lisbeth", "initials": "L"}, {"family": "Geijer", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2025-02-18", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "79", "issn-l": "1471-2180"}, "abstract": "Odd chain fatty acids (OCFAs) are gaining attention for their valuable medical and nutritional applications. Microbial fermentation offers a sustainable and environmentally friendly alternative for OCFA production compared to traditional extraction or chemical synthesis methods. To achieve an economically feasible OCFA production process, it is essential to identify and develop microbial cell factories capable of producing OCFAs with high titers and yields.\n\nWe selected 19 yeast species, including both oleaginous yeasts and representatives from the Ascomycota and Basidiomycota phyla, based on their known or potential ability to produce OCFAs. These species were screened under various growth conditions to evaluate their OCFA production potential. In glucose-based, nitrogen-limited media, the strains produced fatty acids to varying extents, with OCFAs comprising 0.5-5% of the total fatty acids. When using the OCFAs precursor propionic acid as the sole carbon source, only eight strains exhibited growth, with tolerance to propionic acid concentrations between 5 and 29 g/L. The strains also displayed varying efficiencies in converting propionic acid into fatty acids, yielding between 0.16 and 1.22 g/L of fatty acids, with OCFAs constituting 37-89% of total fatty acids. Among the top performing strains, Cutaneotrichosporon oleaginosus produced the highest OCFA titers and yields (0.94 g/L, 0.07 g/g), Yarrowia lipolytica demonstrated superior growth rates even at elevated propionic acid concentrations, and Rhodotorula toruloides achieved the highest proportion of OCFAs relative to total fatty acids (89%).\n\nOur findings highlight the diverse capacities of the selected yeast species for OCFA production, identifying several promising strains for further optimization as microbial cell factories in sustainable OCFA production processes.", "doi": "10.1186/s12866-025-03788-w", "pmid": "39966733", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11834278"}, {"db": "pii", "key": "10.1186/s12866-025-03788-w"}], "notes": [], "created": "2025-11-27T11:28:40.091Z", "modified": "2025-11-27T11:28:40.099Z"}, {"entity": "publication", "iuid": "c00a60f65c6949b7ae95fbd1ea808a22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c00a60f65c6949b7ae95fbd1ea808a22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c00a60f65c6949b7ae95fbd1ea808a22"}}, "title": "Pervasive horizontal transmission of Wolbachia in natural populations of closely related and widespread tropical skipper butterflies.", "authors": [{"family": "Ribeiro", "given": "Pedro", "initials": "P"}, {"family": "Butenko", "given": "Anzhelika", "initials": "A"}, {"family": "Linke", "given": "Daniel", "initials": "D"}, {"family": "Ghanavi", "given": "Hamid Reza", "initials": "HR"}, {"family": "Meier", "given": "Joana Isabel", "initials": "JI"}, {"family": "Wahlberg", "given": "Niklas", "initials": "N"}, {"family": "Matos-Marav\u00ed", "given": "P\u00e1vel", "initials": "P"}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "5", "issn-l": "1471-2180"}, "abstract": "The endosymbiotic relationship between Wolbachia bacteria and insects has been of interest for many years due to their diverse types of host reproductive phenotypic manipulation and potential role in the host's evolutionary history and population dynamics. Even though infection rates are high in Lepidoptera and specifically in butterflies, and reproductive manipulation is present in these taxa, less attention has been given to understanding how Wolbachia is acquired and maintained in their natural populations, across and within species having continental geographical distributions.\n\nWe used whole genome sequencing data to investigate the phylogenetics, demographic history, and infection rate dynamics of Wolbachia in four species of the Spicauda genus of skipper butterflies (Lepidoptera: Hesperiidae), a taxon that presents sympatric and often syntopic distribution, with drastic variability in species abundance in the Neotropical region. We show that infection is maintained by high turnover rates driven mainly by pervasive horizontal transmissions, while also presenting novel cases of double infection by distantly related supergroups of Wolbachia in S. simplicius.\n\nOur results suggest that Wolbachia population dynamics is host species-specific, with genetic cohesiveness across wide geographical distributions. We demonstrate that low coverage whole genome sequencing data can be used for an exhaustive assessment of Wolbachia infection in natural populations of butterflies, as well as its dynamics in closely related host species. This ultimately leads to a better understanding of the endosymbiotic population dynamics of Wolbachia and its effects on the host's biology and evolution.", "doi": "10.1186/s12866-024-03719-1", "pmid": "39773184", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11706079"}, {"db": "pii", "key": "10.1186/s12866-024-03719-1"}], "notes": [], "created": "2025-11-21T13:17:30.064Z", "modified": "2025-11-21T13:17:30.067Z"}, {"entity": "publication", "iuid": "c9468bade168413f9365ee51ab1da260", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260"}}, "title": "Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.", "authors": [{"family": "Kellgren", "given": "Therese", "initials": "T", "orcid": "0000-0002-4911-7037", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c7a5a8c5024d5186f1a4d7385778e2.json"}}, {"family": "Dwibedi", "given": "Chinmay", "initials": "C", "orcid": "0000-0001-6416-4440", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b0dbf807be449da1856c0c018f13a3.json"}}, {"family": "Widerstr\u00f6m", "given": "Micael", "initials": "M", "orcid": "0000-0002-1483-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/563f129fdb4e468395de5df2a7e80ee4.json"}}, {"family": "Sundell", "given": "David", "initials": "D", "orcid": "0000-0002-6269-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/084bd7876637499b929007562d5ac03a.json"}}, {"family": "\u00d6hrman", "given": "Caroline", "initials": "C", "orcid": "0000-0003-0516-7523", "researcher": {"href": "https://publications.scilifelab.se/researcher/a347bde191ef42a98a8aaba829adb553.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Monsen", "given": "Tor", "initials": "T", "orcid": "0000-0001-8489-757X", "researcher": {"href": "https://publications.scilifelab.se/researcher/804b654aa0be4d7a9ecdf113487fe443.json"}}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}}, {"family": "Johansson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0548-5943", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4cd5b852fab4d5da3231939f060e3f5.json"}}], "type": "journal article", "published": "2024-06-19", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "24", "issue": "1", "pages": "215", "issn-l": "1471-2180"}, "abstract": "A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings.\n\nWe completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2.\n\nThis study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.", "doi": "10.1186/s12866-024-03367-5", "pmid": "38890594", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11186124"}, {"db": "pii", "key": "10.1186/s12866-024-03367-5"}], "notes": [], "created": "2024-06-28T06:39:22.789Z", "modified": "2024-11-25T10:30:17.631Z"}, {"entity": "publication", "iuid": "641969a706f64f77a960eb7a359de6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/641969a706f64f77a960eb7a359de6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/641969a706f64f77a960eb7a359de6c4"}}, "title": "Difference in virulence between Neisseria meningitidis serogroups W and Y in transgenic mice.", "authors": [{"family": "Eriksson", "given": "Lorraine", "initials": "L"}, {"family": "Stenmark", "given": "Bianca", "initials": "B", "orcid": "0000-0003-4637-8626", "researcher": {"href": "https://publications.scilifelab.se/researcher/726c71c7aca148c981b48bde574a2e1c.json"}}, {"family": "Deghmane", "given": "Ala-Eddine", "initials": "A"}, {"family": "Thulin Hedberg", "given": "Sara", "initials": "S"}, {"family": "S\u00e4ll", "given": "Olof", "initials": "O"}, {"family": "Fredlund", "given": "Hans", "initials": "H"}, {"family": "M\u00f6lling", "given": "Paula", "initials": "P"}, {"family": "Taha", "given": "Muhamed-Kheir", "initials": "M"}], "type": "comparative study", "published": "2020-04-15", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "issn-l": "1471-2180", "volume": "20", "issue": "1", "pages": "92"}, "abstract": "Neisseria meningitidis serogroups W and Y are the most common serogroups causing invasive meningococcal disease in Sweden. The majority of cases are caused by the serogroup W UK 2013 strain of clonal complex (cc) 11, and subtype 1 of the serogroup Y, YI strain of cc23. In this study, virulence factors of several lineages within cc11 and cc23 were investigated in transgenic BALB/c mice expressing human transferrin. Transgenic mice were infected intraperitoneally with serogroup W and Y isolates. Levels of bacteria and the proinflammatory cytokine CXCL1 were determined in blood collected 3 h and 24 h post-infection. Apoptosis was investigated in immune cells from peritoneal washes of infected mice. Adhesion and induction of apoptosis in human epithelial cells were also scored.\r\n\r\nThe levels of bacteraemia, CXCL1, and apoptosis were higher in serogroup W infected mice than in serogroup Y infected mice. Serogroup W isolates also induced higher levels of apoptosis and adhesion in human epithelial cells. No significant differences were observed between different lineages within cc11 and cc23.\r\n\r\nN. meningitidis Serogroup W displayed a higher virulence in vivo in transgenic mice, compared to serogroup Y. This was reflected by higher bacteremia, proinflammatory activity, and ability to induce apoptosis in mouse immune cells and human epithelial cells.", "doi": "10.1186/s12866-020-01760-4", "pmid": "32295520", "labels": {"Clinical Genomics \u00d6rebro": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-020-01760-4"}, {"db": "pmc", "key": "PMC7160935"}], "notes": [], "created": "2020-11-27T13:57:27.487Z", "modified": "2021-12-08T12:31:42.333Z"}, {"entity": "publication", "iuid": "28e9976dd34d4b74925aac29d26d0dcb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28e9976dd34d4b74925aac29d26d0dcb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28e9976dd34d4b74925aac29d26d0dcb"}}, "title": "Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection.", "authors": [{"family": "Zhao", "given": "Hongxing", "initials": "H", "orcid": "0000-0002-6915-2729", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce92393b5ec7435eae512f37cce8f895.json"}}, {"family": "Chen", "given": "Maoshan", "initials": "M"}, {"family": "Vald\u00e9s", "given": "Alberto", "initials": "A"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB"}, {"family": "Pettersson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2019-01-14", "journal": {"volume": "19", "issn": "1471-2180", "issue": "1", "pages": "15", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "Human adenovirus (Ad) infection leads to the changes of host cell gene expression and biosynthetic processes. Transcriptomics in adenovirus type 2 (Ad2)-infected lung fibroblasts (IMR-90) cells has previously been studied using RNA sequencing. However, this study included only two time points (12 and 24 hpi) using constrained 76 bp long sequencing reads. Therefore, a more detailed study of transcription at different phases of infection using an up-graded sequencing technique is recalled. Furthermore, the correlation between transcription and protein expression needs to be addressed.\n\nIn total, 3556 unique cellular genes were identified as differentially expressed at the transcriptional level with more than 2-fold changes in Ad2-infected cells as compared to non-infected cells by using paired-end sequencing. Based on the kinetics of the gene expression changes at different times after infection, these RNAs fell into 20 clusters. Among them, cellular genes involved in immune response were highly up-regulated in the early phase before becoming down-regulated in the late phase. Comparison of differentially expressed genes at transcriptional and posttranscriptional levels revealed low correlation. Particularly genes involved in cellular immune pathways showed a negative correlation. Here, we highlight the genes which expose inconsistent expression profiles with an emphasis on key factors in cellular immune pathways including NF\u03baB, JAK/STAT, caspases and MAVS. Different from their transcriptional profiles with up- and down-regulation in the early and late phase, respectively, these proteins were up-regulated in the early phase and were sustained in the late phase. A surprising finding was that the target genes of the sustained activators failed to show response.\n\nThere were features common to genes which play important roles in cellular immune pathways. Their expression was stimulated at both RNA and protein levels during the early phase. In the late phase however, their transcription was suppressed while protein levels remained stable. These results indicate that Ad2 and the host cell use different strategies to regulate cellular immune pathways. A control mechanism at the post-translational level must thus exist which is under the control of Ad2.", "doi": "10.1186/s12866-018-1375-5", "pmid": "30642258", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-018-1375-5"}, {"db": "pmc", "key": "PMC6332865"}], "notes": [], "created": "2019-04-23T09:56:25.854Z", "modified": "2021-06-16T14:57:18.495Z"}, {"entity": "publication", "iuid": "0eaade49c88145f3916df8e923cc24b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0eaade49c88145f3916df8e923cc24b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0eaade49c88145f3916df8e923cc24b4"}}, "title": "Proteomic analysis of enterotoxigenic Escherichia coli (ETEC) in neutral and alkaline conditions.", "authors": [{"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Kenny", "given": "Diarmuid", "initials": "D"}, {"family": "Karlsson", "given": "Anders", "initials": "A"}, {"family": "Sj\u00f6ling", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-01-07", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "17", "issue": "1", "pages": "11", "issn-l": "1471-2180"}, "abstract": "Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and travelers to endemic areas. Secretion of the heat labile AB 5 toxin (LT) is induced by alkaline conditions. In this study, we determined the surface proteome of ETEC exposed to alkaline conditions (pH 9) as compared to neutral conditions (pH 7) using a LPI Hexalane FlowCell combined with quantitative proteomics. Relative quantitation with isobaric labeling (TMT) was used to compare peptide abundance and their corresponding proteins in multiple samples at MS/MS level. For protein identification and quantification samples were analyzed using either a 1D-LCMS or a 2D-LCMS approach.\n\nStrong up-regulation of the ATP synthase operon encoding F1Fo ATP synthase and down-regulation of proton pumping proteins NuoF, NuoG, Ndh and WrbA were detected among proteins involved in regulating the proton and electron transport under alkaline conditions. Reduced expression of proteins involved in osmotic stress was found at alkaline conditions while the Sec-dependent transport over the inner membrane and outer membrane protein proteins such as OmpA and the \u03b2-Barrel Assembly Machinery (BAM) complex were up-regulated.\n\nETEC exposed to alkaline environments express a specific proteome profile characterized by up-regulation of membrane proteins and secretion of LT toxin. Alkaline microenvironments have been reported close to the intestinal epithelium and the alkaline proteome may hence represent a better view of ETEC during infection.", "doi": "10.1186/s12866-016-0914-1", "pmid": "28061865", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-016-0914-1"}, {"db": "pmc", "key": "PMC5219706"}], "notes": [], "created": "2020-01-30T16:00:21.978Z", "modified": "2024-01-16T13:46:32.900Z"}, {"entity": "publication", "iuid": "1b2aca9d2d7c4d25a074fd670c0e2291", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b2aca9d2d7c4d25a074fd670c0e2291.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b2aca9d2d7c4d25a074fd670c0e2291"}}, "title": "Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.", "authors": [{"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Angelin", "given": "Martin", "initials": "M"}, {"family": "Marathe", "given": "Nachiket", "initials": "N"}, {"family": "Shouche", "given": "Yogesh S", "initials": "YS"}, {"family": "Johansson", "given": "Anders", "initials": "A"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2015-10-24", "journal": {"volume": "15", "issn": "1471-2180", "issue": null, "pages": "235", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "International travel contributes to the spread of antibiotic resistant bacteria over the world. Most studies addressing travel-related changes in the faecal flora have focused on specific mobile resistance genes, or depended on culturing of individual bacterial isolates. Antibiotic resistance can, however, also spread via travellers colonized by bacteria carrying chromosomal antibiotic resistance mutations, but this has received little attention so far. Here we aimed at exploring the abundance of chromosomal quinolone resistance mutations in Escherichia communities residing in the gut of Swedish travellers, and to determine potential changes after visiting India. Sweden is a country with a comparably low degree of quinolone use and quinolone resistance, whereas the opposite is true for India.\n\nMassively parallel amplicon sequencing targeting the quinolone-resistance determining region of gyrA and parC was applied to total DNA extracted from faecal samples. Paired samples were collected from 12 Swedish medical students before and after a 4-15 week visit to India. Twelve Indian residents were included for additional comparisons. Methods known resistance mutations were common in Swedes before travel as well as in Indians, with a trend for all mutations to be more common in the Indian sub group. There was a significant increase in the abundance of the most common amino acid substitution in GyrA (S83L, from 44 to 72%, p=0.036) in the samples collected after return to Sweden. No other substitution, including others commonly associated with quinolone resistance (D87N in GyrA, S80I in ParC) changed significantly. The number of distinct genotypes encoded in each traveller was significantly reduced after their visit to India for both GyrA (p=0.0020) and ParC (p=0.0051), indicating a reduced genetic diversity, similar to that found in the Indians.\n\nInternational travel can alter the composition of the Escherichia communities in the faecal flora, favouring bacteria carrying certain resistance mutations, and, thereby, contributes to the global spread of antibiotic resistance. A high abundance of specific mutations in Swedish travellers before visiting India is consistent with the hypothesis that these mutation have no fitness cost even in the absence of an antibiotic selection pressure.", "doi": "10.1186/s12866-015-0574-6", "pmid": "26498929", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-015-0574-6"}, {"db": "pmc", "key": "PMC4619388"}, {"db": "BioProject", "key": "PRJNA241337"}], "notes": [], "created": "2017-05-02T12:57:29.368Z", "modified": "2020-01-21T13:56:00.939Z"}, {"entity": "publication", "iuid": "1fb2ba1b0a454809ae68eb474ba9963b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fb2ba1b0a454809ae68eb474ba9963b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fb2ba1b0a454809ae68eb474ba9963b"}}, "title": "Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics.", "authors": [{"family": "Mushtaq", "given": "Mamoona", "initials": "M"}, {"family": "Zubair", "given": "Saima", "initials": "S"}, {"family": "R\u00e5sb\u00e4ck", "given": "Therese", "initials": "T"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Jansson", "given": "D\u00e9sir\u00e9e S", "initials": "DS"}], "type": "journal article", "published": "2015-10-12", "journal": {"volume": "15", "issn": "1471-2180", "issue": null, "pages": "208", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "The genus Brachyspira currently encompasses seven valid species that colonize the intestines of mammals and birds. In a previous study a group of strongly haemolytic isolates from pigs and mallards was provisionally described as a new species within genus Brachyspira, \"B. suanatina\", and enteropathogenic properties were demonstrated in a porcine challenge model.\n\nIn the current study characterization of B. suanatina was performed on the basis of cell morphology, growth characteristics, enzyme profiles, DNA-DNA hybridization (DDH) and whole genome comparisons. The draft genome sequence of B. suanatina strain AN4859/03 was determined and compared with the available genomes of all valid species of Brachyspira.\n\nAccording to morphological traits, growth characteristics and enzymatic profiles, B. suanatina was similar to the type strain of B. hyodysenteriae, but using the recommended threshold value of 70% similarity by DDH it did not belong to any of the recognized Brachyspira species (range 16-64% similarity). This was further supported by average nucleotide identity values. Phylogenetic analysis performed using housekeeping genes and core genomes of all valid Brachyspira sp. and \"B. hampsonii\" revealed that B. suanatina and B. intermedia formed a clade distinct from B. hyodysenteriae. By comparing the genomes of the three closely related species B. intermedia, B. hyodysenteriae and B. suanatina similar profiles of general genomic features and distribution of genes in different functional categories were obtained. However, the genome size of B. hyodysenteriae was smallest among the species, suggesting the possibility of reductive evolution in the divergence of this species. A bacteriophage region and a putative plasmid sequence were also found in the genome of B. suanatina strain AN4859/03.\n\nThe results of our study suggest that despite being similar to B. hyodysenteriae phenotypically, B. suanatina should be regarded as a separate species based on its genetic characteristics. Based on characteristics presented in this report we propose that strains AN4859/03, AN1681:1/04, AN2384/04 and Dk12570-2 from pigs in Sweden and Denmark, and strains AN3949:2/02 and AN1418:2/01 isolated from mallards in Sweden, represent a unique species within genus Brachyspira. For this new species we propose the name B. suanatina for which the type strain is AN4859/03T (=ATCC\u00ae BAA-2592\u2122=DSM 100974T).", "doi": "10.1186/s12866-015-0537-y", "pmid": "26458507", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-015-0537-y"}, {"db": "pmc", "key": "PMC4603578"}], "notes": [], "created": "2017-05-02T12:57:55.544Z", "modified": "2020-01-21T13:56:01.027Z"}, {"entity": "publication", "iuid": "3e542af66758413d8305a824c4580c52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e542af66758413d8305a824c4580c52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e542af66758413d8305a824c4580c52"}}, "title": "Disturbance induced decoupling between host genetics and composition of the associated microbiome.", "authors": [{"family": "Wegner", "given": "Karl Mathias", "initials": "KM"}, {"family": "Volkenborn", "given": "Nils", "initials": "N"}, {"family": "Peter", "given": "Hannes", "initials": "H"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2013-11-09", "journal": {"volume": "13", "issn": "1471-2180", "issue": null, "pages": "252", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "Studies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host.\n\nWhile the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains.\n\nThe decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.", "doi": "10.1186/1471-2180-13-252", "pmid": "24206899", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2180-13-252"}, {"db": "pmc", "key": "PMC3840651"}], "notes": [], "created": "2017-05-04T14:57:50.614Z", "modified": "2020-01-21T13:56:01.793Z"}, {"entity": "publication", "iuid": "85f6c19f555c4c98970dbe95b129cc87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85f6c19f555c4c98970dbe95b129cc87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85f6c19f555c4c98970dbe95b129cc87"}}, "title": "Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.", "authors": [{"family": "Butler", "given": "\u00c8ile", "initials": "\u00c8"}, {"family": "Alsterfjord", "given": "Magnus", "initials": "M"}, {"family": "Olofsson", "given": "Tobias C", "initials": "TC"}, {"family": "Karlsson", "given": "Christofer", "initials": "C"}, {"family": "Malmstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "V\u00e1squez", "given": "Alejandra", "initials": "A"}], "type": "journal article", "published": "2013-10-22", "journal": {"volume": "13", "issn": "1471-2180", "issue": null, "pages": "235", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "Lactic acid bacteria (LAB) has been considered a beneficial bacterial group, found as part of the microbiota of diverse hosts, including humans and various animals. However, the mechanisms of how hosts and LAB interact are still poorly understood. Previous work demonstrates that 13 species of Lactobacillus and Bifidobacterium from the honey crop in bees function symbiotically with the honeybee. They protect each other, their hosts, and the surrounding environment against severe bee pathogens, bacteria, and yeasts. Therefore, we hypothesized that these LAB under stress, i.e. in their natural niche in the honey crop, are likely to produce bioactive substances with antimicrobial activity.\n\nThe genomic analysis of the LAB demonstrated varying genome sizes ranging from 1.5 to 2.2 mega-base pairs (Mbps) which points out a clear difference within the protein gene content, as well as specialized functions in the honeybee microbiota and their adaptation to their host. We demonstrate a clear variation between the secreted proteins of the symbiotic LAB when subjected to microbial stressors. We have identified that 10 of the 13 LAB produced extra-cellular proteins of known or unknown function in which some are arranged in interesting putative operons that may be involved in antimicrobial action, host interaction, or biofilm formation. The most common known extra-cellular proteins secreted were enzymes, DNA chaperones, S-layer proteins, bacteriocins, and lysozymes. A new bacteriocin may have been identified in one of the LAB symbionts while many proteins with unknown functions were produced which must be investigated further.\n\nThe 13 LAB symbionts likely play different roles in their natural environment defending their niche and their host and participating in the honeybee's food production. These roles are partly played through producing extracellular proteins on exposure to microbial stressors widely found in natural occurring flowers. Many of these secreted proteins may have a putative antimicrobial function. In the future, understanding these processes in this complicated environment may lead to novel applications of honey crop LAB proteins.", "doi": "10.1186/1471-2180-13-235", "pmid": "24148670", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2180-13-235"}, {"db": "pmc", "key": "PMC4015849"}, {"db": "GENBANK", "key": "KC776061"}, {"db": "GENBANK", "key": "KC776062"}, {"db": "GENBANK", "key": "KC776063"}, {"db": "GENBANK", "key": "KC776064"}, {"db": "GENBANK", "key": "KC776065"}, {"db": "GENBANK", "key": "KC776066"}, {"db": "GENBANK", "key": "KC776067"}, {"db": "GENBANK", "key": "KC776068"}, {"db": "GENBANK", "key": "KC776069"}, {"db": "GENBANK", "key": "KC776070"}, {"db": "GENBANK", "key": "KC776071"}, {"db": "GENBANK", "key": "KC776073"}, {"db": "GENBANK", "key": "KC776074"}, {"db": "GENBANK", "key": "KC776075"}, {"db": "GENBANK", "key": "KC776076"}, {"db": "GENBANK", "key": "KC776077"}, {"db": "GENBANK", "key": "KC776078"}, {"db": "GENBANK", "key": "KC776079"}, {"db": "GENBANK", "key": "KC776080"}, {"db": "GENBANK", "key": "KC776081"}, {"db": "GENBANK", "key": "KC776082"}, {"db": "GENBANK", "key": "KC776083"}, {"db": "GENBANK", "key": "KC776084"}, {"db": "GENBANK", "key": "KC776085"}, {"db": "GENBANK", "key": "KC776086"}, {"db": "GENBANK", "key": "KC776087"}, {"db": "GENBANK", "key": "KC776088"}, {"db": "GENBANK", "key": "KC776089"}, {"db": "GENBANK", "key": "KC776090"}, {"db": "GENBANK", "key": "KC776091"}, {"db": "GENBANK", "key": "KC776092"}, {"db": "GENBANK", "key": "KC776093"}, {"db": "GENBANK", "key": "KC776094"}, {"db": "GENBANK", "key": "KC776095"}, {"db": "GENBANK", "key": "KC776096"}, {"db": "GENBANK", "key": "KC776097"}, {"db": "GENBANK", "key": "KC776098"}, {"db": "GENBANK", "key": "KC776099"}, {"db": "GENBANK", "key": "KC776100"}, {"db": "GENBANK", "key": "KC776101"}, {"db": "GENBANK", "key": "KC776102"}, {"db": "GENBANK", "key": "KC776103"}, {"db": "GENBANK", "key": "KC776104"}, {"db": "GENBANK", "key": "KC776105"}, {"db": "GENBANK", "key": "KC776106"}, {"db": "GENBANK", "key": "KC776107"}, {"db": "GENBANK", "key": "KC776108"}, {"db": "GENBANK", "key": "KC776109"}, {"db": "GENBANK", "key": "KC776110"}, {"db": "GENBANK", "key": "KC776111"}, {"db": "GENBANK", "key": "KC789963"}, {"db": "GENBANK", "key": "KC789964"}, {"db": "GENBANK", "key": "KC789965"}, {"db": "GENBANK", "key": "KC789966"}, {"db": "GENBANK", "key": "KC789967"}, {"db": "GENBANK", "key": "KC789968"}, {"db": "GENBANK", "key": "KC789969"}, {"db": "GENBANK", "key": "KC789970"}, {"db": "GENBANK", "key": "KC789971"}, {"db": "GENBANK", "key": "KC789972"}, {"db": "GENBANK", "key": "KC789973"}, {"db": "GENBANK", "key": "KC789974"}, {"db": "GENBANK", "key": "KC789975"}, {"db": "GENBANK", "key": "KC789976"}, {"db": "GENBANK", "key": "KC789977"}, {"db": "GENBANK", "key": "KC789978"}, {"db": "GENBANK", "key": "KC789979"}, {"db": "GENBANK", "key": "KC789980"}, {"db": "GENBANK", "key": "KC789981"}, {"db": "GENBANK", "key": "KC789982"}, {"db": "GENBANK", "key": "KC789983"}, {"db": "GENBANK", "key": "KC789984"}, {"db": "GENBANK", "key": "KC789985"}, {"db": "GENBANK", "key": "KC789986"}, {"db": "GENBANK", "key": "KC789987"}, {"db": "GENBANK", "key": "KC789988"}, {"db": "GENBANK", "key": "KC789989"}, {"db": "GENBANK", "key": "KC789990"}, {"db": "GENBANK", "key": "KC789991"}, {"db": "GENBANK", "key": "KC789992"}, {"db": "GENBANK", "key": "KC789993"}, {"db": "GENBANK", "key": "KC789994"}, {"db": "GENBANK", "key": "KC789995"}, {"db": "GENBANK", "key": "KC789996"}, {"db": "GENBANK", "key": "KC789997"}, {"db": "GENBANK", "key": "KC789998"}, {"db": "GENBANK", "key": "KC789999"}, {"db": "GENBANK", "key": "KC790000"}, {"db": "GENBANK", "key": "KC790001"}, {"db": "GENBANK", "key": "KC790002"}, {"db": "GENBANK", "key": "KC790003"}, {"db": "GENBANK", "key": "KC790004"}, {"db": "GENBANK", "key": "KC790005"}, {"db": "GENBANK", "key": "KC790006"}, {"db": "GENBANK", "key": "KC790007"}, {"db": "GENBANK", "key": "KC790008"}, {"db": "GENBANK", "key": "KC790009"}, {"db": "GENBANK", "key": "KC790010"}, {"db": "GENBANK", "key": "KC790011"}, {"db": "GENBANK", "key": "KC790012"}, {"db": "GENBANK", "key": "KC790013"}, {"db": "GENBANK", "key": "KC790014"}, {"db": "GENBANK", "key": "KC790015"}, {"db": "GENBANK", "key": "KC790016"}, {"db": "GENBANK", "key": "KC790017"}, {"db": "GENBANK", "key": "KC790018"}, {"db": "GENBANK", "key": "KC801035"}], "notes": [], "created": "2017-05-04T14:56:21.844Z", "modified": "2020-01-21T13:53:20.622Z"}], "created": "2017-05-09T09:12:05.373Z", "modified": "2020-11-27T13:14:03.647Z"}