{"entity": "researcher", "timestamp": "2026-06-15T13:54:12.680Z", "family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "affiliations": ["Centre for Translational Microbiome Research, Department of Microbiology, Tumour and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade"}}, "publications": [{"entity": "publication", "iuid": "c432e16534c042828949dad3d3c7d52e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c432e16534c042828949dad3d3c7d52e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c432e16534c042828949dad3d3c7d52e"}}, "title": "Predicting allergy and postpartum depression from an incomplete compositional microbiome", "authors": [{"family": "Shternshis", "given": "Andrey", "initials": "A", "orcid": "0000-0002-9299-369X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c813415242504d84878495f76514059a.json"}}, {"family": "Tong", "given": "Bangzhuo", "initials": "B", "orcid": "0000-0002-5463-5699", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95b7213f0ed449718c2bd47c2ab0bd0e.json"}}, {"family": "Skalkidou", "given": "Alkistis", "initials": "A", "orcid": "0000-0002-4935-7532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/882f68bd159a46e5999dedb151bd7ea4.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}, {"family": "Zachariah", "given": "Dave", "initials": "D", "orcid": "0000-0002-6698-0166", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76aa850a94d44237b89940bf4d007a6e.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Singh", "given": "Prashant", "initials": "P", "orcid": "0000-0002-3123-3478", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f19f17dbc48047f98bf209175b935bc3.json"}}], "type": "posted-content", "published": "2025-03-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.28.640766", "pmid": null, "labels": {"Prashant Singh": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2025-11-28T05:42:26.583Z", "modified": "2025-12-05T10:16:41.017Z"}, {"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": "b6884adebcd44c5f85555627116b94ea", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b6884adebcd44c5f85555627116b94ea.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b6884adebcd44c5f85555627116b94ea"}}, "title": "Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women.", "authors": [{"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"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": "Prast-Nielsen", "given": "Stefanie", "initials": "S", "orcid": "0000-0001-5877-7988", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe13dffa03b24588a919b6b028788a6e.json"}}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc30318aa3ca4720ac5aa3a982c9f730.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5c6814a31e644b9bc544d4da759a438.json"}}, {"family": "Schacht", "given": "Simon R\u00f8nnow", "initials": "SR"}, {"family": "Tetens", "given": "Inge", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}], "type": "journal article", "published": "2024-07-02", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "volume": "14", "pages": "1324794", "issn-l": "2235-2988"}, "abstract": "Despite mounting evidence of gut-brain involvement in psychiatric conditions, functional data remain limited, and analyses of other microbial niches, such as the vaginal microbiota, are lacking in relation to mental health. This aim of this study was to investigate if the connections between the gut microbiome and mental health observed in populations with a clinical diagnosis of mental illness extend to healthy women experiencing stress and depressive symptoms. Additionally, this study examined the functional pathways of the gut microbiota according to the levels of psychological symptoms. Furthermore, the study aimed to explore potential correlations between the vaginal microbiome and mental health parameters in young women without psychiatric diagnoses.\n\nIn this cross-sectional study, 160 healthy Danish women (aged 18-40 years) filled out questionnaires with validated scales measuring symptoms of stress and depression and frequency of dietary intake. Fecal and vaginal microbiota samples were collected at the beginning of the menstrual cycle and vaginal samples were also collected at cycle day 8-12 and 18-22. Shotgun metagenomic profiling of the gut and vaginal microbiome was performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for functional profiling and 56 Gut Brain Modules were analyzed in the fecal samples.\n\nThe relative abundance in the gut of the genera Escherichia, Parabacteroides, and Shigella was higher in women with elevated depressive symptoms. Women with high perceived stress showed a tendency of increased abundance of Escherichia, Shigella, and Blautia. Amongst others, the potentially pathogenic genera, Escherichia and Shigella correlate with alterations in the neuroactive pathways such as the glutamatergic, GABAeric, dopaminergic, and Kynurenine pathways. Vaginosis symptoms were more prevalent in women reporting high levels of stress and depressive symptoms.\n\nThe findings of this study support the concept of a microbiota-associated effect on the neuroactive pathways even in healthy young women. This suggest, that targeting the gut microbiome could be a promising approach for future psychiatric interventions.", "doi": "10.3389/fcimb.2024.1324794", "pmid": "39015337", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11249552"}], "notes": [], "created": "2025-03-19T07:35:43.556Z", "modified": "2025-04-08T06:08:56.327Z"}, {"entity": "publication", "iuid": "c02cf8e5eac24ecfa226cc6368b1aecc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c02cf8e5eac24ecfa226cc6368b1aecc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c02cf8e5eac24ecfa226cc6368b1aecc"}}, "title": "Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia.", "authors": [{"family": "Norenhag", "given": "Johanna", "initials": "J"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc30318aa3ca4720ac5aa3a982c9f730.json"}}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ca801fe1aba4d04a06eaf9f6e3407dd.json"}}, {"family": "Garcia", "given": "Fabricio", "initials": "F"}, {"family": "Hugerth", "given": "Luisa Warchavchik", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Du", "given": "Juan", "initials": "J", "orcid": "0000-0001-7649-9571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f67834a614ca4cd4aff026e5e9a1a1e4.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Olovsson", "given": "Matts", "initials": "M"}], "type": "journal article", "published": "2024-05-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "11183", "issn-l": "2045-2322"}, "abstract": "Alterations in the vaginal microbiota, including both species composition and functional pathways, have been associated with HPV infection and progression of dysplasia to cervical cancer. To further explore this, shotgun metagenomic sequencing was used to taxonomically and functionally characterize the vaginal microbiota of women with and without cervical dysplasia. Women with histologically verified dysplasia (n = 177; low grade dysplasia (LSIL) n = 81, high-grade dysplasia (HSIL) n = 94, cancer n = 2) were compared with healthy controls recruited from the cervical screening programme (n = 177). Women with dysplasia had a higher vaginal microbial diversity, and higher abundances of Gardnerella vaginalis, Aerococcus christensenii, Peptoniphilus lacrimalis and Fannyhessea vaginae, while healthy controls had higher relative abundance of Lactobacillus crispatus. Genes involved in e.g. nucleotide biosynthesis and peptidoglycan biosynthesis were more abundant in women with dysplasia. Healthy controls showed higher abundance of genes important for e.g. amino acid biosynthesis, (especially L-lysine) and sugar degradation. These findings suggest that the microbiota may have a role in creating a pro-oncogenic environment in women with dysplasia. Its role and potential interactions with other components in the microenvironment deserve further exploration.", "doi": "10.1038/s41598-024-61942-2", "pmid": "38755259", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11099171"}, {"db": "pii", "key": "10.1038/s41598-024-61942-2"}], "notes": [], "created": "2025-03-19T07:35:42.306Z", "modified": "2025-04-08T06:11:08.307Z"}, {"entity": "publication", "iuid": "3278c59c61e340e486c23565f6981adb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3278c59c61e340e486c23565f6981adb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3278c59c61e340e486c23565f6981adb"}}, "title": "Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic.", "authors": [{"family": "Rasmussen", "given": "Pil U", "initials": "PU", "orcid": "0000-0003-0607-4230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80035ea7380843aa9d2c58a3ebfa3d4b.json"}}, {"family": "Abrego", "given": "Nerea", "initials": "N", "orcid": "0000-0001-6347-6127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/224552896bb04ea6a2cf695729ea94f7.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4b6e491ae382479b8e92eda9a11cabae.json"}}, {"family": "\u00d6pik", "given": "Maarja", "initials": "M", "orcid": "0000-0001-8025-7460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d4aa2839065c4a0f86a008d9c6a8bb57.json"}}, {"family": "Sepp", "given": "Siim-Kaarel", "initials": "SK", "orcid": "0000-0003-2906-4609", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76351ce330da4f2eaf2c12948882dfbb.json"}}, {"family": "Blanchet", "given": "F Guillaume", "initials": "FG", "orcid": "0000-0001-5149-2488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5332dbed91464890b63acd68c6770254.json"}}, {"family": "Huotari", "given": "Tea", "initials": "T"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20531f32048b4cd498311138500cc6bc.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "236", "issue": "2", "pages": "671-683", "issn-l": "0028-646X"}, "abstract": "Knowledge about the distribution and local diversity patterns of arbuscular mycorrhizal (AM) fungi are limited for extreme environments such as the Arctic, where most studies have focused on spore morphology or root colonization. We here studied the joint effects of plant species identity and elevation on AM fungal distribution and diversity. We sampled roots of 19 plant species in 18 locations in Northeast Greenland, using next generation sequencing to identify AM fungi. We studied the joint effect of plant species, elevation and selected abiotic conditions on AM fungal presence, richness and composition. We identified 29 AM fungal virtual taxa (VT), of which six represent putatively new VT. Arbuscular mycorrhizal fungal presence increased with elevation, and as vegetation cover and the active soil layer decreased. Arbuscular mycorrhizal fungal composition was shaped jointly by elevation and plant species identity. We demonstrate that the Arctic harbours a relatively species-rich and nonrandomly distributed diversity of AM fungi. Given the high diversity and general lack of knowledge exposed herein, we encourage further research into the diversity, drivers and functional role of AM fungi in the Arctic. Such insight is urgently needed for an area with some of the globally highest rates of climate change.", "doi": "10.1111/nph.18342", "pmid": "35751540", "labels": {"DDLS Fellow": null, "Luisa Hugerth": null}, "xrefs": [{"db": "pmc", "key": "PMC9796444"}, {"db": "RefSeq", "key": "PRJEB40490"}], "notes": [], "created": "2023-05-12T13:20:04.309Z", "modified": "2023-05-12T13:20:04.514Z"}, {"entity": "publication", "iuid": "5abd3e284dc941a7adec38a1ed7d3bad", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5abd3e284dc941a7adec38a1ed7d3bad.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5abd3e284dc941a7adec38a1ed7d3bad"}}, "title": "The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle.", "authors": [{"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Nyboe Andersen", "given": "Anders", "initials": "A"}, {"family": "Edfeldt", "given": "Gabriella", "initials": "G", "orcid": "0000-0003-0366-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc30318aa3ca4720ac5aa3a982c9f730.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}], "type": "journal article", "published": "2022-06-30", "journal": {"title": "Hum. Reprod.", "issn": "1460-2350", "volume": "37", "issue": "7", "pages": "1525-1543", "issn-l": "0268-1161"}, "abstract": "How does hormonal contraceptive use and menstrual cycle phase affect the female microbiome across different body sites?\n\nThe menstrual cycle phase, but not hormonal contraceptive use, is associated with the vaginal and oral but not the gut microbiome composition in healthy young women.\n\nWomen with low vaginal levels of Lactobacillus crispatus are at increased risk of pre-term birth, fertility treatment failure, sexually transmitted infections and gynaecological cancers. Little is known about the effect of hormonal fluctuations on other body site's microbiomes as well as the interplay between them.\n\nThis study includes a cohort of 160 healthy young Danish women using three different contraceptive regimens: non-hormonal methods (n = 54), combined oral contraceptive (COC, n = 52) or levonorgestrel intrauterine system (LNG-IUS, n = 54). Samples were collected from four body sites during the menstrual cycle (menses, follicular and luteal phases) at Copenhagen University Hospital, Rigshospitalet, Denmark.\n\nThe oral, vaginal, rectal and faecal microbiomes were characterized by shotgun sequencing. Microbial diversity and community distance measures were compared between study groups, menstrual phase timepoints and body sites. All participants answered an extensive questionnaire on current health, lifestyle and sex life. Confounding factors such as smoking, BMI and diet were analysed by PERMANOVA. Plasma oestradiol and progesterone levels are correlated with microbiome composition.\n\nThe use of COC and LNG-IUS was not associated with the microbiome composition or diversity. However, increased diversity in the vaginal microbiome was observed during menses, followed by a subsequent expansion of Lactobacillus spp. during the follicular and luteal phases which correlated with measured serum oestradiol levels (r = 0.11, P < 0.001). During menses, 89 women (58%) had a dysbiotic vaginal microbiome with <60% Lactobacillus spp. This declined to 49 (32%) in the follicular phase (P < 0.001) and 44 (29%) in the luteal phase (P < 0.001). During menses, bacterial richness and diversity in saliva reached its lowest point while no differences were observed in the faecal microbiome. The microbiome in different body sites was on average more similar within the same individual than between individuals, despite phase or hormonal treatment. Only the vagina presented a clear cluster structure with dominance of either L. crispatus, Lactobacillus iners, Gardnerella vaginalis or Prevotella spp.\n\nThe microbiome samples analysed in this study were submitted to the European Nucleotide Archive under project number PRJEB37731, samples ERS4421369-ERS4422941.\n\nThe cohort is homogenous which limits extrapolation of the effects of ethnicity and socio-economic status on the microbiome. We only present three defined timepoints across the menstrual phase and miss potential important day to day fluctuations.\n\nThe use of hormonal contraception did not significantly associate with the microbiome composition in the vagina, faeces, rectum or saliva in healthy young women. This is a welcome finding considering the widespread and prolonged use of these highly efficient contraceptive methods. The menstrual cycle is, however, a major confounding factor for the vaginal microbiome. As such, the time point in the menstrual cycle should be considered when analysing the microbiome of women of reproductive age, since stratifying by vaginal dysbiosis status during menstruation could be misleading. This is the first study to confirm by direct measurements of oestradiol, a correlation with the presence of L. crispatus, adding evidence of a possible hormonal mechanism for the maintenance of this desirable microbe.\n\nThis work was partly funded by the Ferring Pharmaceuticals through a research collaboration with The Centre for Translational Microbiome Research (CTMR) at the Karolinska Institutet (L.W.H., E.F., G.E. and I.S.-K.). Ferring Pharmaceuticals also funded the infrastructure to obtain the clinical samples at Copenhagen University Hospital ([#MiHSN01], M.C.K., Z.B., and H.S.N.). This work was also supported by funding from Rigshospitalet's Research Funds ([#E-22614-01 and #E-22614-02] to M.C.K.) and Oda and Hans Svenningsen's Foundation ([#F-22614-08] to H.S.N.). M.C.K., L.W.H., E.F., Z.B., G.E., L.E., I.S.-K. and H.S.N., are partially funded by Ferring Pharmaceuticals, which also provided funds for the collection and processing of the samples analysed in this study. H.S.N.'s research is further supported by Freya Biosciences and the BioInnovation Institute. H.S.N. has received honoraria from Ferring Pharmaceuticals, Merck A/S, Astra-Zeneca, Cook Medical and Ibsa Nordic. A.N.A. reports no competing interests.", "doi": "10.1093/humrep/deac094", "pmid": "35553675", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9247429"}, {"db": "pii", "key": "6584540"}], "notes": [], "created": "2022-11-08T07:02:56.315Z", "modified": "2023-10-27T09:27:54.965Z"}, {"entity": "publication", "iuid": "5da495110d404371b5693f5854cbfca2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5da495110d404371b5693f5854cbfca2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5da495110d404371b5693f5854cbfca2"}}, "title": "The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design.", "authors": [{"family": "Krog", "given": "Maria Christine", "initials": "MC", "orcid": "0000-0002-2110-0479", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdd65c5105f4480692383dae8d4ac986.json"}}, {"family": "Madsen", "given": "Mette Elkj\u00e6r", "initials": "ME", "orcid": "0000-0001-7767-9849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8d263e2f4d4507bc2510f04869a5a5.json"}}, {"family": "Bliddal", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2456-1019", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58a6059b93a14a6e80514e744893acdd.json"}}, {"family": "Bashir", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-2497-282X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d15fce497fe4cdabd82e994e7cd83ad.json"}}, {"family": "Vex\u00f8", "given": "Laura Emilie", "initials": "LE"}, {"family": "Hartwell", "given": "Dorthe", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Fransson", "given": "Emma", "initials": "E", "orcid": "0000-0001-9010-8522", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c05290187ec426b8804eefc3d954971.json"}}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Boulund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3806-323X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a5c6814a31e644b9bc544d4da759a438.json"}}, {"family": "Wannerberger", "given": "Kristin", "initials": "K"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I", "orcid": "0000-0002-1423-3089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/659fb04e6a1a430cbd707b8a50d500a3.json"}}, {"family": "Nielsen", "given": "Henriette Svarre", "initials": "HS", "orcid": "0000-0003-2106-8103", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a99fa7ebb204c618ed70f29be0085b3.json"}}], "type": "journal article", "published": "2022-03-23", "journal": {"title": "Hum Reprod Open", "issn": "2399-3529", "volume": "2022", "issue": "2", "pages": "hoac015", "issn-l": null}, "abstract": "What is the microbiome profile across different body sites in relation to the normal menstrual cycle (with and without hormonal contraception), recurrent pregnancy loss (RPL) (before and during pregnancy, pregnancy loss or birth) and endometriosis (before, during and after surgery)? How do these profiles interact with genetics, environmental exposures, immunological and endocrine biomarkers?\n\nThe microbiome is a key factor influencing human health and disease in areas as diverse as immune functioning, gastrointestinal disease and mental and metabolic disorders. There is mounting evidence to suggest that the reproductive microbiome may be influential in general and reproductive health, fertility and pregnancy outcomes.\n\nThis is a prospective, longitudinal, observational study using a systems biology approach in three cohorts totalling 920 participants. Since microbiome profiles by shot-gun sequencing have never been investigated in healthy controls during varying phases of the menstrual cycle, patients with RPL and patients with endometriosis, no formal sample size calculation can be performed. The study period is from 2017 to 2024 and allows for longitudinal profiling of study participants to enable deeper understanding of the role of the microbiome and of host-microbe interactions in reproductive health.\n\nParticipants in each cohort are as follows: Part 1 MiMens-150 healthy women with or without hormonal contraception; Part 2 MiRPL-200 couples with RPL, 50 healthy couples with prior uncomplicated pregnancy and 150 newborns; Part 3 MiEndo-120 patients with endometriosis requiring surgery with or without hormonal treatment. Microbiome profiles from saliva, faeces, rectal mucosa, vaginal fluid and endometrium will be studied, as well as the Omics profile, endocrine disrupting chemicals and endocrine and immune factors in blood, hair, saliva and urine. Pregnancy loss products, seminal microbiome, HLA types, endometriotic tissue and genetic risk and comprehensive questionnaire data will also be studied, where appropriate. Correlations with mental and physical health will be evaluated.\n\nThis work is supported by funding from Ferring Pharmaceuticals ([#MiHSN01] to H.S.N., M.C.K., M.E.M., L.E.V., L.E., I.S.-K., F.B., L.W.H., E.F. and M.H.), Rigshospitalet's Research Funds ([#E-22614-01 and #E-22614-02] to M.C.K. and [#E-22222-06] to S.B.), Niels and Desiree Yde's Foundation (S.B., endocrine analyses [#2015-2784]), the Musikforl\u00e6ggerne Agnes and Knut M\u00f8rk's Foundation (S.B., endocrine and immune analyses [#35108-001]) and Oda and Hans Svenningsen's Foundation ([#F-22614-08] to H.S.N.). Medical writing assistance with this manuscript was provided by Caroline Loat, PhD, and funded by Ferring Pharmaceuticals. H.S.N. reports personal fees from Ferring Pharmaceuticals, Merck Denmark A/S, Ibsa Nordic, Astra Zeneca and Cook Medical outside the submitted work. K.W. is a full-time employee of Ferring Pharmaceuticals. No other conflicts are reported.\n\nN/A.\n\nN/A.\n\nN/A.", "doi": "10.1093/hropen/hoac015", "pmid": "35441092", "labels": {"DDLS Fellow": null, "Luisa Hugerth": null}, "xrefs": [{"db": "pmc", "key": "PMC9014536"}, {"db": "pii", "key": "hoac015"}], "notes": [], "created": "2023-05-12T13:20:12.988Z", "modified": "2023-10-27T09:28:00.116Z"}, {"entity": "publication", "iuid": "397f64b1e292432395bfc779c01f202d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/397f64b1e292432395bfc779c01f202d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/397f64b1e292432395bfc779c01f202d"}}, "title": "Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Pereira", "given": "Marcela", "initials": "M"}, {"family": "Zha", "given": "Yinghua", "initials": "Y"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Krog", "given": "Maria C", "initials": "MC"}, {"family": "Bashir", "given": "Zahra", "initials": "Z"}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "Fransson", "given": "Emma", "initials": "E"}, {"family": "Svarre-Nielsen", "given": "Henriette", "initials": "H"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02d8684df81e42169e613de803446fbf.json"}}], "type": "journal article", "published": "2020-11-18", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "5", "issue": "6", "issn-l": "2379-5042"}, "abstract": "The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing.IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.", "doi": "10.1128/mSphere.00448-20", "pmid": "33208514", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7677004"}, {"db": "pii", "key": "5/6/e00448-20"}], "notes": [], "created": "2022-11-08T06:59:04.474Z", "modified": "2023-10-27T09:32:00.743Z"}, {"entity": "publication", "iuid": "32cbf2082eef4e7ca0da7c4676b7d67f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/32cbf2082eef4e7ca0da7c4676b7d67f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/32cbf2082eef4e7ca0da7c4676b7d67f"}}, "title": "Genome sequence of segmented filamentous bacteria present in the human intestine.", "authors": [{"family": "Jonsson", "given": "Hans", "initials": "H"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Lundin", "given": "Eva", "initials": "E"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}], "type": "journal article", "published": "2020-09-04", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "485", "issn-l": "2399-3642"}, "abstract": "Segmented filamentous bacteria (SFB) are unique immune modulatory bacteria colonizing the small intestine of a variety of animals in a host-specific manner. SFB exhibit filamentous growth and attach to the host's intestinal epithelium, offering a physical route of interaction. SFB affect functions of the host immune system, among them IgA production and T-cell maturation. Until now, no human-specific SFB genome has been reported. Here, we report the metagenomic reconstruction of an SFB genome from a human ileostomy sample. Phylogenomic analysis clusters the genome with SFB genomes from mouse, rat and turkey, but the genome is genetically distinct, displaying 65-71% average amino acid identity to the others. By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB genome. We thus conclude that a unique SFB variant exists in humans and foresee a renewed interest in the elucidation of SFB functionality in this environment.", "doi": "10.1038/s42003-020-01214-7", "pmid": "32887924", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7474095"}, {"db": "pii", "key": "10.1038/s42003-020-01214-7"}], "notes": [], "created": "2022-11-08T06:59:09.556Z", "modified": "2023-10-27T09:32:03.497Z"}, {"entity": "publication", "iuid": "c88c0bad902a4361ae98e9187f3092d5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c88c0bad902a4361ae98e9187f3092d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c88c0bad902a4361ae98e9187f3092d5"}}, "title": "No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-2537-3092", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9dd6bee0a1b4cf4831de933a8d28ecf.json"}}, {"family": "Forsberg", "given": "Anna M", "initials": "AM"}, {"family": "Kjellstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Schmidt", "given": "Peter Thelin", "initials": "PT"}, {"family": "Agreus", "given": "Lars", "initials": "L"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "69", "issue": "6", "pages": "1076-1084", "issn-l": "0017-5749"}, "abstract": "The ethiopathogenesis of irritable bowel syndrome (IBS) is unknown. While a link to the gut microbiome is postulated, the heterogeneity of the healthy gut makes it difficult to draw definitive conclusions. We aimed to describe the faecal and mucosa-associated microbiome (MAM) and health correlates on a community cohort of healthy and IBS individuals with no colonoscopic findings.\n\nThe PopCol study recruited a random sample of 3556 adults; 745 underwent colonoscopy. IBS was defined by Rome IV criteria and organic disease excluded. 16S rRNA gene sequencing was conducted on sigmoid biopsy samples from 376 representative individuals (63 IBS cases) and faecal samples from 185 individuals (32 IBS cases).\n\nWhile sigmoid MAM was dominated by Lachnospiraceae, faeces presented a higher relative abundance of Ruminococcaceae. Microbial richness in MAM was linearly correlated to that in faeces from the same individual (R\u00b2=0.255, p<3E-11) as was diversity (R\u00b2=0.06, p=0.0022). MAM diversity decreased with increasing body mass index (BMI; Pearson's r=-0.1, p=0.08) and poorer self-rated health (r=-0.15, p=0.007), but no other health correlates. Faecal microbiome diversity was correlated to stool consistency (r=-0.16, p=0.043). Several taxonomic groups were correlated to age, BMI, depression and self-reported health, including Coprococcus catus associated with lower levels of depression (r=-0.003, p=0.00017). The degree of heterogeneity observed between IBS patients is higher than that observed between healthy individuals.\n\nNo distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.", "doi": "10.1136/gutjnl-2019-318717", "pmid": "31601615", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7282555"}, {"db": "pii", "key": "gutjnl-2019-318717"}], "notes": [], "created": "2022-11-08T06:59:14.279Z", "modified": "2023-10-27T09:32:13.928Z"}, {"entity": "publication", "iuid": "c8385f8f71824af899b09096683dd49e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c8385f8f71824af899b09096683dd49e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c8385f8f71824af899b09096683dd49e"}}, "title": "Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome.", "authors": [{"family": "Sundin", "given": "Johanna", "initials": "J"}, {"family": "Aziz", "given": "Imran", "initials": "I"}, {"family": "Nordlander", "given": "Sofia", "initials": "S"}, {"family": "Polster", "given": "Annikka", "initials": "A"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO", "orcid": "0000-0002-2025-2198", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54d7339204704cb2b511f8ac6c8f0395.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Pennhag", "given": "Alexandra A L", "initials": "AAL"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "T\u00f6rnblom", "given": "Hans", "initials": "H"}, {"family": "Simr\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "\u00d6hman", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2020-01-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "593", "issn-l": "2045-2322"}, "abstract": "Altered bacterial composition and small intestinal bacterial overgrowth (SIBO) may be associated with irritable bowel syndrome (IBS). This study aimed to determine the fecal and mucosa-associated bacterial composition along the gastrointestinal (GI) tract and to assess SIBO in IBS. Bacterial composition of feces, and mucosa of the duodenum and sigmoid colon was determined by 16S rRNA-amplicon-sequencing. SIBO was evaluated by bacterial culture of duodenal aspirate, glucose and lactulose breath tests. Mucosal antibacterial gene expression was assessed by PCR Array. The bacterial profiles of feces and the mucosa of sigmoid colon, but not duodenum, differed between IBS patients (n = 17) and HS (n = 20). The IBS specific bacterial profiles were linked to the colonic antibacterial gene expression. Fecal bacterial profile differed between IBS subtypes, while the mucosa-associated bacterial profile was associated with IBS symptom severity and breath tests results at baseline (H2 and/or CH4 \u2265 15 ppm). The prevalence of SIBO was similar between IBS patients and HS. This study demonstrates that alterations in the bacterial composition of the sigmoid colon of IBS patients were linked to symptoms and immune activation. While breath tests reflected the mucosa-associated bacterial composition, there was no evidence for high prevalence of SIBO or small intestinal bacterial alterations in IBS.", "doi": "10.1038/s41598-020-57468-y", "pmid": "31953505", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6969101"}, {"db": "pii", "key": "10.1038/s41598-020-57468-y"}], "notes": [], "created": "2022-11-08T06:59:06.940Z", "modified": "2023-10-27T09:32:08.890Z"}, {"entity": "publication", "iuid": "6bec8b54783c46e08477226aee284887", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6bec8b54783c46e08477226aee284887.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6bec8b54783c46e08477226aee284887"}}, "title": "Effects of sampling strategy and DNA extraction on human skin microbiome investigations.", "authors": [{"family": "Bjerre", "given": "Rie Dybboe", "initials": "RD", "orcid": "0000-0002-0110-6320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f928bb58156d40f8b51a5b03714a8bf9.json"}}, {"family": "Hugerth", "given": "Luisa Warchavchik", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Seifert", "given": "Maike", "initials": "M"}, {"family": "Johansen", "given": "Jeanne Duus", "initials": "JD"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2019-11-21", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "17287", "issn-l": "2045-2322"}, "abstract": "The human skin is colonized by a wide array of microorganisms playing a role in skin disorders. Studying the skin microbiome provides unique obstacles such as low microbial biomass. The objective of this study was to establish methodology for skin microbiome analyses, focusing on sampling technique and DNA extraction. Skin swabs and scrapes were collected from 9 healthy adult subjects, and DNA extracted using 12 commercial kits. All 165 samples were sequenced using the 16S rRNA gene. Comparing the populations captured by eSwabs and scrapes, 99.3% of sequences overlapped. Using eSwabs yielded higher consistency. The success rate of library preparation applying different DNA extraction kits ranged from 39% to 100%. Some kits had higher Shannon alpha-diversity. Metagenomic shotgun analyses were performed on a subset of samples (N = 12). These data indicate that a reduction of human DNA from 90% to 57% is feasible without lowering the success of 16S rRNA library preparation and without introducing taxonomic bias. Using swabs is a reliable technique to investigate the skin microbiome. DNA extraction methodology is crucial for success of sequencing and adds a substantial amount of variation in microbiome analyses. Reduction of host DNA is recommended for interventional studies applying metagenomics.", "doi": "10.1038/s41598-019-53599-z", "pmid": "31754146", "labels": {"Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6872721"}, {"db": "pii", "key": "10.1038/s41598-019-53599-z"}, {"db": "figshare", "key": "10.6084/m9.figshare.8319842.v1"}], "notes": [], "created": "2022-11-08T06:59:19.169Z", "modified": "2023-10-27T09:32:11.437Z"}, {"entity": "publication", "iuid": "ad0fda02bf0b4d2b9d39efae19bc03e9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ad0fda02bf0b4d2b9d39efae19bc03e9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ad0fda02bf0b4d2b9d39efae19bc03e9"}}, "title": "Mineral Type Structures Soil Microbial Communities", "authors": [{"family": "Ahmed", "given": "Engy", "initials": "E", "orcid": "0000-0002-1386-134X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d72646279dd40e1a5549232e3dbce5a.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW", "orcid": "0000-0001-5432-1764", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/246ed7b405dd4c3f9ec5e7ff9f1d3ade.json"}}, {"family": "Logue", "given": "J\u00fcrg B", "initials": "JB"}, {"family": "Br\u00fcchert", "given": "Volker", "initials": "V"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}, {"family": "Holmstr\u00f6m", "given": "Sara J M", "initials": "SJM"}], "type": "journal-article", "published": "2017-07-03", "journal": {"title": "Geomicrobiology Journal", "issn": "0149-0451", "volume": "34", "issue": "6", "pages": "538-545", "issn-l": null}, "abstract": null, "doi": "10.1080/01490451.2016.1225868", "pmid": null, "labels": {"Affiliated researcher": null, "Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-05T13:16:09.801Z", "modified": "2025-12-04T17:03:25.207Z"}]}