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Alexandersson BT, Hugerth LW, Hedin C, Forsberg A, Talley NJ, Agreus L, Järbrink-Sehgal E, Engstrand L, Andreasson A, Schmidt PT. Diverticulosis is not associated with altered gut microbiota nor is it predictive of future diverticulitis: a population-based colonoscopy study. Scand J Gastroenterol 2023; 58:1131-1138. [PMID: 36987880 DOI: 10.1080/00365521.2023.2194010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/13/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUND The etiopathogenesis of diverticular disease is unknown. OBJECTIVE To compare the fecal and mucosa-associated microbiota between participants with and without diverticulosis and participants who later developed diverticulitis versus those that did not from a population-based study. METHODS The PopCol study, conducted in Stockholm, Sweden, invited a random sample of 3556 adults to participate, of which 745 underwent colonoscopy. Overall, 130 participants (17.5%) had diverticulosis. 16S rRNA gene sequencing was conducted on available sigmoid biopsy samples from 529 and fecal samples from 251 individuals. We identified individuals who subsequently developed acute diverticulitis up to 13 years after sample collection. In a case-control design matching for gender, age (+/-5 years), smoking and antibiotic exposure, we compared taxonomic composition, richness and diversity of the microbiota between participants with or without diverticulosis, and between participants who later developed acute diverticulitis versus those who did not. RESULTS No differences in microbiota richness or diversity were observed between participants with or without diverticulosis, nor for those who developed diverticulitis compared with those who did not. No bacterial taxa were significantly different between participants with diverticulosis compared with those without diverticulosis. Individuals who later developed acute diverticulitis (2.8%) had a higher abundance of genus Comamonas than those who did not (p = .027). CONCLUSIONS In a population-based cohort study the only significant difference was that those who later develop diverticulitis had more abundance of genus Comamonas. The significance of Comamonas is unclear, suggesting a limited role for the gut microbiota in the etiopathogenesis of diverticular disease.
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Affiliation(s)
| | - Luisa W Hugerth
- Department of Microbiology, Center for Translational Microbiome Research, CTMR, Tumour and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Charlotte Hedin
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Gastroenterology unit, Stockholm, Sweden
| | - Anna Forsberg
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas J Talley
- School of Medicine and Public Health, University of Newcastle, New South Wales, Australia
| | - Lars Agreus
- Division of Family Medicine, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Ellionore Järbrink-Sehgal
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Michael E.DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Lars Engstrand
- Department of Microbiology, Center for Translational Microbiome Research, CTMR, Tumour and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Anna Andreasson
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Stress Research Institute, Stockholm University, Stockholm, Sweden
- Department of Psychology, Macquarie University, New South Wales, Australia
| | - Peter T Schmidt
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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2
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Gudnadottir U, Du J, Hugerth LW, Engstrand L, Schuppe-Koistinen I, Wiberg Itzel E, Fransson E, Brusselaers N. Pre-pregnancy complications - associated factors and wellbeing in early pregnancy: a Swedish cohort study. BMC Pregnancy Childbirth 2023; 23:153. [PMID: 36890460 PMCID: PMC9993650 DOI: 10.1186/s12884-023-05479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND Many couples experience difficulties to become pregnant or carry a pregnancy to term due to unknown causes. Here we define pre-pregnancy complications as having prior recurrent pregnancy loss, prior late miscarriages, time to pregnancy more than one year, or the use of artificial reproductive technologies. We aim to identify factors associated with pre-pregnancy complications and poor well-being in early pregnancy. METHODS Online questionnaire data from 5330 unique pregnancies in Sweden were collected from November 2017 - February 2021. Multivariable logistic regression modelling was used to investigate potential risk factors for pre-pregnancy complications and differences in early pregnancy symptoms. RESULTS Pre-pregnancy complications were identified in 1142 participants (21%). Risk factors included diagnosed endometriosis, thyroid medication, opioids and other strong pain medication, body mass index > 25 kg/m2 and age over 35 years. Different subgroups of pre-pregnancy complications had unique risk factors. The groups also experienced different pregnancy symptoms in early pregnancy, where women that had experienced recurrent pregnancy loss were at higher risk of depression in their current pregnancy. CONCLUSION We report one of the largest pregnancy cohorts with high frequency of pre-pregnancy complications compared to the Swedish population. Prescribed drug use and body weight were the top potentially modifiable risk factors in all groups. Participants that experienced pre-pregnancy complications also had higher risk of depression and pregnancy problems in early pregnancy.
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Affiliation(s)
- Unnur Gudnadottir
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 171 65, Solna, Sweden.
| | - Juan Du
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 171 65, Solna, Sweden
| | - Luisa W Hugerth
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 171 65, Solna, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 171 65, Solna, Sweden
| | - Ina Schuppe-Koistinen
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 171 65, Solna, Sweden.,Science for Life Laboratory, 171 65, Solna, Sweden
| | - Eva Wiberg Itzel
- Department of Clinical Science and Education, Södersjukhuset, Stockholm, Sweden
| | - Emma Fransson
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 171 65, Solna, Sweden.,Department of Women's and Children's health, Uppsala University, 751 85, Uppsala, Sweden
| | - Nele Brusselaers
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 171 65, Solna, Sweden.,Global Health Institute, University of Antwerp, 2610, Antwerp, Belgium.,Department of Head and Skin, Ghent University, 9000, Ghent, Belgium
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3
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Fransson E, Gudnadottir U, Hugerth LW, Itzel EW, Hamsten M, Boulund F, Pennhag A, Du J, Schuppe-Koistinen I, Brusselaers N, Engstrand L. Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) - assessing the dynamic associations between the microbiome and maternal and neonatal adverse events. BMJ Open 2022; 12:e065825. [PMID: 36288838 PMCID: PMC9615996 DOI: 10.1136/bmjopen-2022-065825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
PURPOSE The Swedish Maternal Microbiome (SweMaMi) project was initiated to better understand the dynamics of the microbiome in pregnancy, with longitudinal microbiome sampling, shotgun metagenomics, extensive questionnaires and health registry linkage. PARTICIPANTS Pregnant women were recruited before the 20th gestational week during 2017-2021 in Sweden. In total, 5439 pregnancies (5193 unique women) were included. For 3973 pregnancies (73%), samples were provided at baseline, and for 3141 (58%) at all three timepoints (second and third trimester and postpartum). In total, 38 591 maternal microbiome samples (vaginal, faecal and saliva) and 3109 infant faecal samples were collected. Questionnaires were used to collect information on general, reproductive and mental health, diet and lifestyle, complemented by linkage to the nationwide health registries, also used to follow up the health of the offspring (up to age 10). FINDINGS TO DATE The cohort is fairly representative for the total Swedish pregnant population (data from 2019), with 41% first-time mothers. Women with university level education, born in Sweden, with normal body mass index, not using tobacco-products and aged 30-34 years were slightly over-represented. FUTURE PLANS The sample and data collection were finalised in November 2021. The next steps are the characterisation of the microbial DNA and linkage to the health and demographic information from the questionnaires and registries. The role of the microbiome on maternal and neonatal outcomes and early-childhood diseases will be explored (including preterm birth, miscarriage) and the role and interaction of other risk factors and confounders (including endometriosis, polycystic ovarian syndrome, diet, drug use). This is currently among the largest pregnancy cohorts in the world with longitudinal design and detailed and standardised microbiome sampling enabling follow-up of both mothers and children. The findings are expected to contribute greatly to the field of reproductive health focusing on pregnancy and neonatal outcomes.
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Affiliation(s)
- Emma Fransson
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Unnur Gudnadottir
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Luisa W Hugerth
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory (SciLifeLab), Stockholm, Sweden
| | - Eva Wiberg Itzel
- Department of Obstetrics and Gynecology, Södersjukhuset AB, Stockholm, Sweden
- Department of Clinical Science and Education, Karolinska Institutet, Stockholm, Sweden
| | - Marica Hamsten
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Boulund
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory (SciLifeLab), Stockholm, Sweden
| | - Alexandra Pennhag
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Juan Du
- Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Ina Schuppe-Koistinen
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory (SciLifeLab), Stockholm, Sweden
| | - Nele Brusselaers
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Global Health Institute, University of Antwerp, Antwerpen, Belgium
| | - Lars Engstrand
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Science for Life Laboratory (SciLifeLab), Stockholm, Sweden
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Rasmussen PU, Abrego N, Roslin T, Öpik M, Sepp S, Blanchet FG, Huotari T, Hugerth LW, Tack AJM. Elevation and plant species identity jointly shape a diverse arbuscular mycorrhizal fungal community in the High Arctic. New Phytol 2022; 236:671-683. [PMID: 35751540 PMCID: PMC9796444 DOI: 10.1111/nph.18342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
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.
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Affiliation(s)
- Pil U. Rasmussen
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
- The National Research Centre for the Working Environment105 Lersø ParkalléDK‐2100CopenhagenDenmark
| | - Nerea Abrego
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
| | - Tomas Roslin
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
- Department of EcologySwedish University of Agricultural SciencesBox 7044UppsalaSE‐750 07Sweden
| | - Maarja Öpik
- Department of BotanyUniversity of Tartu40 Lai StreetTartu51005Estonia
| | - Siim‐Kaarel Sepp
- Department of BotanyUniversity of Tartu40 Lai StreetTartu51005Estonia
| | - F. Guillaume Blanchet
- Département de Biologie, Faculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
- Département de Mathématiques, Faculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
- Département des Sciences de la Santé Communautaire, Faculté de Médecine et des Sciences de la SantéUniversité de Sherbrooke3001 12 Avenue NordSherbrookeQCJ1H 5N4Canada
| | - Tea Huotari
- Department of Agricultural SciencesUniversity of HelsinkiPO Box 27, (Latokartanonkaari 5)HelsinkiFI‐00014Finland
| | - Luisa W. Hugerth
- Department of Molecular, Tumor and Cell Biology, Science for Life Laboratory, Center for Translational Microbiome ResearchKarolinska InstitutetSE‐171 65SolnaSweden
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
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5
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Gudnadottir U, Debelius JW, Du J, Hugerth LW, Danielsson H, Schuppe-Koistinen I, Fransson E, Brusselaers N. The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis. Sci Rep 2022; 12:7926. [PMID: 35562576 PMCID: PMC9106729 DOI: 10.1038/s41598-022-12007-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/04/2022] [Indexed: 02/02/2023] Open
Abstract
Preterm birth is a major cause of neonatal morbidity and mortality worldwide. Increasing evidence links the vaginal microbiome to the risk of spontaneous preterm labour that leads to preterm birth. The aim of this systematic review and network meta-analysis was to investigate the association between the vaginal microbiome, defined as community state types (CSTs, i.e. dominance of specific lactobacilli spp, or not (low-lactobacilli)), and the risk of preterm birth. Systematic review using PubMed, Web of Science, Embase and Cochrane library was performed. Longitudinal studies using culture-independent methods categorizing the vaginal microbiome in at least three different CSTs to assess the risk of preterm birth were included. A (network) meta-analysis was conducted, presenting pooled odds ratios (OR) and 95% confidence intervals (CI); and weighted proportions and 95% CI. All 17 studies were published between 2014 and 2021 and included 38-539 pregnancies and 8-107 preterm births. Women presenting with "low-lactobacilli" vaginal microbiome were at increased risk (OR 1.69, 95% CI 1.15-2.49) for delivering preterm compared to Lactobacillus crispatus dominant women. Our network meta-analysis supports the microbiome being predictive of preterm birth, where low abundance of lactobacilli is associated with the highest risk, and L. crispatus dominance the lowest.
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Affiliation(s)
- Unnur Gudnadottir
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.
| | - Justine W Debelius
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden
| | - Luisa W Hugerth
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Science for Life Laboratory, 171 65, Solna, Sweden
| | - Hanna Danielsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Sach's Children's and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Ina Schuppe-Koistinen
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Science for Life Laboratory, 171 65, Solna, Sweden
| | - Emma Fransson
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Department of Women's and Children's Health, Uppsala University, 751 85, Uppsala, Sweden
| | - Nele Brusselaers
- Department of Microbiology, Tumor and Cell Biology (MTC), Centre for Translational Microbiome Research, Karolinska Institutet, Tomtebodavägen 16, 171 65, SolnaStockholm, Sweden.,Global Health Institute, University of Antwerp, 2610, Antwerp, Belgium.,Department of Head and Skin, Ghent University, 9000, Ghent, Belgium
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Krog MC, Madsen ME, Bliddal S, Bashir Z, Vexø LE, Hartwell D, Hugerth LW, Fransson E, Hamsten M, Boulund F, Wannerberger K, Engstrand L, Schuppe-Koistinen I, Nielsen HS. OUP accepted manuscript. Hum Reprod Open 2022; 2022:hoac015. [PMID: 35441092 PMCID: PMC9014536 DOI: 10.1093/hropen/hoac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/11/2022] [Indexed: 11/23/2022] Open
Abstract
STUDY QUESTION 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? WHAT IS KNOWN ALREADY The 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. STUDY DESIGN, SIZE, DURATION This 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. PARTICIPANTS/MATERIALS, SETTING, METHODS Participants 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. STUDY FUNDING/COMPETING INTEREST(S) This 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 Musikforlæggerne Agnes and Knut Mørk’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. TRIAL REGISTRATION NUMBER N/A TRIAL REGISTRATION DATE N/A DATE OF FIRST PATIENT’S ENROLMENT N/A
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Affiliation(s)
- Maria Christine Krog
- Correspondence address. The Recurrent Pregnancy Loss Unit, The Fertility Clinic 4071, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen Ø, Denmark. E-mail:
| | | | - Sofie Bliddal
- The Department of Medical Endocrinology and Metabolism, Rigshospitalet, Copenhagen University Hospital, Copenhagen Ø, Denmark
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen Ø, Denmark
| | - Zahra Bashir
- The Recurrent Pregnancy Loss Unit, The Capital Region, The Fertility Clinic, Copenhagen University Hospitals Rigshospitalet and Hvidovre, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Slagelse Hospital, Slagelse, Denmark
| | - Laura Emilie Vexø
- The Recurrent Pregnancy Loss Unit, The Capital Region, The Fertility Clinic, Copenhagen University Hospitals Rigshospitalet and Hvidovre, Copenhagen, Denmark
- Department of Gynecology, The Endometriosis Unit, Rigshospitalet, Copenhagen University Hospital, Copenhagen Ø, Denmark
| | - Dorthe Hartwell
- Department of Gynecology, The Endometriosis Unit, Rigshospitalet, Copenhagen University Hospital, Copenhagen Ø, Denmark
| | - Luisa W Hugerth
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Emma Fransson
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marica Hamsten
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Boulund
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ina Schuppe-Koistinen
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Henriette Svarre Nielsen
- The Recurrent Pregnancy Loss Unit, The Capital Region, The Fertility Clinic, Copenhagen University Hospitals Rigshospitalet and Hvidovre, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University, Copenhagen N, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
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7
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Krog MC, Hugerth LW, Fransson E, Bashir Z, Nyboe Andersen A, Edfeldt G, Engstrand L, Schuppe-Koistinen I, Nielsen HS. OUP accepted manuscript. Hum Reprod 2022; 37:1525-1543. [PMID: 35553675 PMCID: PMC9247429 DOI: 10.1093/humrep/deac094] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - Emma Fransson
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Zahra Bashir
- The Recurrent Pregnancy Loss Unit, The Capital Region, Rigshospitalet and Hvidovre Hospital, Copenhagen University Hospitals, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, University Hospital Zealand, Slagelse Hospital, Slagelse, Denmark
| | - Anders Nyboe Andersen
- The Fertility Department Section 4071, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gabriella Edfeldt
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | | | - Henriette Svarre Nielsen
- The Recurrent Pregnancy Loss Unit, The Capital Region, Rigshospitalet and Hvidovre Hospital, Copenhagen University Hospitals, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre Hospital, Copenhagen, Denmark
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8
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Bostanci N, Krog MC, Hugerth LW, Bashir Z, Fransson E, Boulund F, Belibasakis GN, Wannerberger K, Engstrand L, Nielsen HS, Schuppe-Koistinen I. Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar. Front Cell Infect Microbiol 2021; 11:625229. [PMID: 33816334 PMCID: PMC8018275 DOI: 10.3389/fcimb.2021.625229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/11/2021] [Indexed: 12/18/2022] Open
Abstract
Physiological hormonal fluctuations exert endogenous pressures on the structure and function of the human microbiome. As such, the menstrual cycle may selectively disrupt the homeostasis of the resident oral microbiome, thus compromising oral health. Hence, the aim of the present study was to structurally and functionally profile the salivary microbiome of 103 women in reproductive age with regular menstrual cycle, while evaluating the modifying influences of hormonal contraceptives, sex hormones, diet, and smoking. Whole saliva was sampled during the menstrual, follicular, and luteal phases (n = 309) of the cycle, and the participants reported questionnaire-based data concerning their life habits and oral or systemic health. No significant differences in alpha-diversity or phase-specific clustering of the overall microbiome were observed. Nevertheless, the salivary abundances of genera Campylobacter, Haemophilus, Prevotella, and Oribacterium varied throughout the cycle, and a higher species-richness was observed during the luteal phase. While the overall community structure maintained relatively intact, its functional properties were drastically affected. In particular, 11 functional modules were differentially abundant throughout the menstrual cycle, including pentose phosphate metabolism, and biosynthesis of cobalamin and neurotransmitter gamma-aminobutyric acid. The menstrual cycle phase, but not oral contraceptive usage, was accountable for greater variations in the metabolic pathways of the salivary microbiome. Further co-risk factor analysis demonstrated that Prevotella and Veillonella were increased in current smokers, whereas high dietary sugar consumption modified the richness and diversity of the microbiome during the cycle. This is the first large study to systematically address dysbiotic variations of the oral microbiome during the course of menstrual cycle, and document the additive effect of smoking and sugar consumption as environmental risk factors. It reveals the structural resilience and functional adaptability of the oral microbiome to the endogenous hormonal pressures of the menstrual cycle, while revealing its vulnerability to the exogenous exposures of diet and smoking.
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Affiliation(s)
- Nagihan Bostanci
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Christine Krog
- The Recurrent Pregnancy Loss Units, Copenhagen University Hospitals, Rigshospitalet and Hvidovre Hospital, Copenhagen, Denmark.,Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Luisa W Hugerth
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Zahra Bashir
- The Recurrent Pregnancy Loss Units, Copenhagen University Hospitals, Rigshospitalet and Hvidovre Hospital, Copenhagen, Denmark.,Department of Obstetrics and Gynaecology, Holbæk Hospital, Holbæk, Denmark
| | - Emma Fransson
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Fredrik Boulund
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Lars Engstrand
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Henriette Svarre Nielsen
- The Recurrent Pregnancy Loss Units, Copenhagen University Hospitals, Rigshospitalet and Hvidovre Hospital, Copenhagen, Denmark.,Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ina Schuppe-Koistinen
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
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9
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Talley NJ, Alexander JL, Walker MM, Jones MP, Hugerth LW, Engstrand L, Agréus L, Powell N, Andreasson A. Ileocolonic Histopathological and Microbial Alterations in the Irritable Bowel Syndrome: A Nested Community Case-Control Study. Clin Transl Gastroenterol 2020; 12:e00296. [PMID: 33464728 PMCID: PMC8345925 DOI: 10.14309/ctg.0000000000000296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/23/2020] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Histopathological alterations in the ileum and colon in irritable bowel syndrome (IBS) are controversial, and normal values are poorly established. We hypothesized that changes in mucosal immune cells characterize IBS and key changes in immune composition are associated with the mucosa-associated microbiota (MaM). METHODS A nested case-control study (48 IBS and 106 controls included) from 745 colonoscopy participants in a random population sample. Intraepithelial lymphocytes (IELs)/100 enterocytes and eosinophils/5 nonoverlapping high-power fields counted; mast cells identified by immunocytochemistry (CD117)/5 high-power fields. Paneth cells quantified per 5 crypts. 16S rRNA gene amplicon sequencing performed on available sigmoid MaM, n = 55 and fecal microbiota, n = 20. Microbiota profiles compared between samples with high and low IEL counts. RESULTS IBS had increased IELs in the terminal ileum (relative risk ratio = 1.70, 95% confidence interval 1.08-2.76, P = 0.022 adjusted for age, sex, and smoking). Cecal IELs were increased in IBS-diarrhea (relative risk ratio = 2.03, 95% confidence interval 1.13-3.63, P = 0.017). No difference was observed in alpha diversity of MaM or fecal microbiota based on IEL count. There was no difference in beta diversity of the MaM according to IEL count in the terminal ileal (TI) (P = 0.079). High TI IEL counts associated with a significant expansion of the genus Blautia (P = 0.024) and unclassified Clostridiales (P = 0.036) in colon MaM. DISCUSSION A modest but significant increase in IELs was observed in IBS vs. controls in a population-based setting. Subtle TI and cecal inflammation may play a pathogenic role in IBS but needs confirmation. Modest but discernible differences in the colonic MaM were seen according to TI IEL count but not IBS status.
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Affiliation(s)
- Nicholas J. Talley
- Faculty of Health and Medicine, University of Newcastle, Newcastle, Australia
- NHMRC Center of Research Excellence in Digestive Health Newcastle, Australia
| | | | - Marjorie M. Walker
- NHMRC Center of Research Excellence in Digestive Health Newcastle, Australia
- Department of Anatomical Pathology, University of Newcastle, Newcastle, Australia
| | - Michael P. Jones
- NHMRC Center of Research Excellence in Digestive Health Newcastle, Australia
- Department of Psychology, Macquarie University, North Ryde, Australia
| | - Luisa W. Hugerth
- Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Lars Engstrand
- Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Lars Agréus
- Division for Family Medicine and Primary Care, Karolinska Institutet, Huddinge, Sweden
| | - Nicholas Powell
- NHMRC Center of Research Excellence in Digestive Health Newcastle, Australia
- Division of Digestive Disease, Imperial College London, London, UK
| | - Anna Andreasson
- Department of Psychology, Macquarie University, North Ryde, Australia
- Stress Research Institute, Stockholm University, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Solna, Sweden
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10
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Hugerth LW, Andreasson A, Talley NJ, Forsberg AM, Kjellström L, Schmidt PT, Agreus L, Engstrand L. No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population. Gut 2020; 69:1076-1084. [PMID: 31601615 PMCID: PMC7282555 DOI: 10.1136/gutjnl-2019-318717] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVE 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. DESIGN The 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). RESULTS While 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 (R²=0.255, p<3E-11) as was diversity (R²=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. CONCLUSIONS No distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.
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Affiliation(s)
- Luisa W Hugerth
- Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Anna Andreasson
- Stress Research Institute, Stockholm University, Stockholm, Sweden,Department of Medicine, Karolinska University Hospital, Solna, Sweden,Department of Psychology, Macquarie University, Sydney, New South Wales, Australia
| | - Nicholas J Talley
- Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Anna M Forsberg
- Department of Medicine, Karolinska University Hospital, Solna, Sweden
| | | | | | - Lars Agreus
- Center for Family and Community Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Engstrand
- Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Solna, Sweden .,Bacteriology, Swedish Institute for Communicable Disease Control, Stockholm, Sweden
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11
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Sundin J, Aziz I, Nordlander S, Polster A, Hu YOO, Hugerth LW, Pennhag AAL, Engstrand L, Törnblom H, Simrén M, Öhman L. Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome. Sci Rep 2020; 10:593. [PMID: 31953505 PMCID: PMC6969101 DOI: 10.1038/s41598-020-57468-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/30/2019] [Indexed: 12/14/2022] Open
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 ≥ 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.
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Affiliation(s)
- Johanna Sundin
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Imran Aziz
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Nordlander
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Annikka Polster
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Yue O O Hu
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Luisa W Hugerth
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Alexandra A L Pennhag
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Hans Törnblom
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Centre for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lena Öhman
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden. .,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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12
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Gaiser RA, Halimi A, Alkharaan H, Lu L, Davanian H, Healy K, Hugerth LW, Ateeb Z, Valente R, Fernández Moro C, Del Chiaro M, Sällberg Chen M. Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer. Gut 2019; 68:2186-2194. [PMID: 30872392 PMCID: PMC6872446 DOI: 10.1136/gutjnl-2018-317458] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Intraductal papillary mucinous neoplasms (IPMNs) are pancreatic cysts that can progress to invasive pancreatic cancer. Associations between oncogenesis and oral microbiome alterations have been reported. This study aims to investigate a potential intracystic pancreatic microbiome in a pancreatic cystic neoplasm (PCN) surgery patient cohort. DESIGN Paired cyst fluid and plasma were collected at pancreatic surgery from patients with suspected PCN (n=105). Quantitative and qualitative assessment of bacterial DNA by qPCR, PacBio sequencing (n=35), and interleukin (IL)-1β quantification was performed. The data were correlated to diagnosis, lesion severity and clinical and laboratory profile, including proton-pump inhibitor (PPI) usage and history of invasive endoscopy procedures. RESULTS Intracystic bacterial 16S DNA copy number and IL-1β protein quantity were significantly higher in IPMN with high-grade dysplasia and IPMN with cancer compared with non-IPMN PCNs. Despite high interpersonal variation of intracystic microbiota composition, bacterial network and linear discriminant analysis effect size analyses demonstrated co-occurrence and enrichment of oral bacterial taxa including Fusobacterium nucleatum and Granulicatella adiacens in cyst fluid from IPMN with high-grade dysplasia. The elevated intracystic bacterial DNA is associated with, but not limited to, prior exposure to invasive endoscopic procedures, and is independent from use of PPI and antibiotics. CONCLUSIONS Collectively, these findings warrant further investigation into the role of oral bacteria in cystic precursors to pancreatic cancer and have added values on the aetiopathology as well as the management of pancreatic cysts.
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Affiliation(s)
| | - Asif Halimi
- Pancreatic Surgery Unit, Division of Surgery, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Universitetsjukhuset i Huddinge, Huddinge, Sweden
| | - Hassan Alkharaan
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Liyan Lu
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden,Tenth People’s Hospital, Tongji University, Shanghai, China
| | - Haleh Davanian
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Katie Healy
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Luisa W Hugerth
- Center for Translational Microbiome Research, CTMR, Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, Science for Life Laboratory, Huddinge, Sweden
| | - Zeeshan Ateeb
- Pancreatic Surgery Unit, Division of Surgery, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Universitetsjukhuset i Huddinge, Huddinge, Sweden
| | - Roberto Valente
- Pancreatic Surgery Unit, Division of Surgery, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Universitetsjukhuset i Huddinge, Huddinge, Sweden
| | - Carlos Fernández Moro
- Division of Pathology, Department of Laboratory Medicine (LABMED), Karolinska Institutet, Huddinge, Sweden,Department of Clinical Pathology/Cytology, Karolinska University Hospital, Huddinge, Sweden
| | - Marco Del Chiaro
- Pancreatic Surgery Unit, Division of Surgery, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Universitetsjukhuset i Huddinge, Huddinge, Sweden,Division of Surgical Oncology, Department of Surgery, University of Colorado at Denver—Anschutz Medical Campus, Aurora, Colorado, USA
| | - Margaret Sällberg Chen
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden,Tenth People’s Hospital, Tongji University, Shanghai, China
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13
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Davanian H, Gaiser RA, Silfverberg M, Hugerth LW, Sobkowiak MJ, Lu L, Healy K, Sandberg JK, Näsman P, Karlsson J, Jansson L, Engstrand L, Sällberg Chen M. Mucosal-associated invariant T cells and oral microbiome in persistent apical periodontitis. Int J Oral Sci 2019; 11:16. [PMID: 31068577 PMCID: PMC6506549 DOI: 10.1038/s41368-019-0049-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Opportunistic bacteria in apical periodontitis (AP) may pose a risk for systemic dissemination. Mucosal-associated invariant T (MAIT) cells are innate-like T cells with a broad and potent antimicrobial activity important for gut mucosal integrity. It was recently shown that MAIT cells are present in the oral mucosal tissue, but the involvement of MAIT cells in AP is unknown. Here, comparison of surgically resected AP and gingival tissues demonstrated that AP tissues express significantly higher levels of Vα7.2-Jα33, Vα7.2-Jα20, Vα7.2-Jα12, Cα and tumour necrosis factor (TNF), interferon (IFN)-γ and interleukin (IL)-17A transcripts, resembling a MAIT cell signature. Moreover, in AP tissues the MR1-restricted MAIT cells positive for MR1–5-OP-RU tetramer staining appeared to be of similar levels as in peripheral blood but consisted mainly of CD4+ subset. Unlike gingival tissues, the AP microbiome was quantitatively impacted by factors like fistula and high patient age and had a prominent riboflavin-expressing bacterial feature. When merged in an integrated view, the examined immune and microbiome data in the sparse partial least squares discriminant analysis could identify bacterial relative abundances that negatively correlated with Vα7.2-Jα33, Cα, and IL-17A transcript expressions in AP, implying that MAIT cells could play a role in the local defence at the oral tissue barrier. In conclusion, we describe the presence of MAIT cells at the oral site where translocation of oral microbiota could take place. These findings have implications for understanding the immune sensing of polymicrobial-related oral diseases.
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Affiliation(s)
- Haleh Davanian
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | | | | | - Luisa W Hugerth
- Department of Microbiology, Tumor and Cell Biology and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Clinical Genomics Facility, Science for Life Laboratory, Solna, Sweden
| | | | - Liyan Lu
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Katie Healy
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | | | - Peggy Näsman
- Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Jörgen Karlsson
- Clinic of Endodontics and Periodontology, Eastman Institute Stockholm, Stockholm, Sweden
| | - Leif Jansson
- Clinic of Endodontics and Periodontology, Eastman Institute Stockholm, Stockholm, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Clinical Genomics Facility, Science for Life Laboratory, Solna, Sweden
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14
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Prast-Nielsen S, Tobin AM, Adamzik K, Powles A, Hugerth LW, Sweeney C, Kirby B, Engstrand L, Fry L. Investigation of the skin microbiome: swabs vs. biopsies. Br J Dermatol 2019; 181:572-579. [PMID: 30693476 DOI: 10.1111/bjd.17691] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Human skin is populated by diverse bacteria and there is increasing evidence that resident bacteria play a key role initiating immune responses in cutaneous diseases such as atopic dermatitis, psoriasis and hidradenitis suppurativa. Bacteria are present at all layers of the skin but many studies have relied on swabs to profile the skin microbiota. OBJECTIVES As the pathogenesis of many skin conditions is dermal, we wanted to compare the microbiota obtained in swabs (surface) and biopsies (dermis). METHODS Using 16S rRNA gene sequencing we established the microbial profiles of skin swabs and skin biopsies in 16 patients. RESULTS We found differences in both diversity and taxonomic composition of the microbiome obtained from swabs and biopsies of the same individual. Several taxa were found to be more abundant in the swabs, which displayed significantly higher community richness, but Clostridiales and Bacteroidetes were significantly enriched in the biopsies. Most published research on cutaneous microbiota has been based on skin swabs, which represent the surface of the skin. CONCLUSIONS Our study demonstrated a clear difference between the microbiome observed from skin swabs and skin biopsies. These findings may be highly relevant in disorders such as psoriasis where pathogenesis arises in the dermis. What's already known about this topic? 16S RNA gene sequencing has facilitated study of the skin microbiome. Several studies have sequenced the microbiome sampled by skin swabs. What does this study add? The microbiome data obtained using swabs and biopsies were different. Diseases that are predominantly dermal should be studied using both swabs and biopsies.
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Affiliation(s)
- S Prast-Nielsen
- Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden.,Centre for Translational Microbiome Research (CTMR), Karolinska Institute, Stockholm, Sweden
| | - A-M Tobin
- Centre for Translational Microbiome Research (CTMR), Karolinska Institute, Stockholm, Sweden.,Department of Dermatology, St Vincent's University Hospital, Dublin, Ireland
| | - K Adamzik
- Department of Dermatology, St Vincent's University Hospital, Dublin, Ireland
| | | | - L W Hugerth
- Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden.,Centre for Translational Microbiome Research (CTMR), Karolinska Institute, Stockholm, Sweden
| | - C Sweeney
- Department of Dermatology, St Vincent's University Hospital, Dublin, Ireland
| | - B Kirby
- Department of Dermatology, St Vincent's University Hospital, Dublin, Ireland
| | - L Engstrand
- Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden.,Centre for Translational Microbiome Research (CTMR), Karolinska Institute, Stockholm, Sweden
| | - L Fry
- Imperial College, London, U.K
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15
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Ibrahim A, Hugerth LW, Hases L, Saxena A, Seifert M, Thomas Q, Gustafsson JÅ, Engstrand L, Williams C. Colitis-induced colorectal cancer and intestinal epithelial estrogen receptor beta impact gut microbiota diversity. Int J Cancer 2019; 144:3086-3098. [PMID: 30515752 PMCID: PMC6519213 DOI: 10.1002/ijc.32037] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 12/18/2022]
Abstract
Chronic inflammation of the colon (colitis) is a risk factor for colorectal cancer (CRC). Hormone‐replacement therapy reduces CRC incidences, and the estrogen receptor beta (ERβ/ESR2) has been implicated in this protection. Gut microbiota is altered in both colitis and CRC and may influence the severity of both. Here we test the hypothesis that intestinal ERβ impacts the gut microbiota. Mice with and without intestine‐specific deletion of ERβ (ERβKOVil) were generated using the Cre‐LoxP system. Colitis and CRC were induced with a single intraperitoneal injection of azoxymethane (AOM) followed by administration of three cycles of dextran sulfate sodium (DSS) in drinking water. The microbiota population were characterized by high‐throughput 16S rRNA gene sequencing of DNA extracted from fecal samples (N = 39). Differences in the microbiota due to AOM/DSS and absence of ERβ were identified through bioinformatic analyses of the 16S‐Seq data, and the distribution of bacterial species was corroborated using qPCR. We demonstrate that colitis‐induced CRC reduced the gut microbiota diversity and that loss of ERβ enhanced this process. Further, the Bacteroidetes genus Prevotellaceae_UCG_001 was overrepresented in AOM/DSS mice compared to untreated controls (3.5‐fold, p = 0.004), and this was enhanced in females and in ERβKOVil mice. Overall, AOM/DSS enriched for microbiota impacting immune system diseases and metabolic functions, and lack of ERβ in combination with AOM/DSS enriched for microbiota impacting carbohydrate metabolism and cell motility, while reducing those impacting the endocrine system. Our data support that intestinal ERβ contributes to a more favorable microbiome that could attenuate CRC development. What's new? Chronic inflammation of the colon is a risk factor for colorectal cancer (CRC). Hormone‐replacement therapy reduces CRC incidence, and the estrogen receptor beta (ERβ/ESR2) has been implicated in this protection. The microbiota of the gut is altered in both colitis and CRC, but whether intestinal ERβ affects gut microbiota remains to be investigated. Here, the authors demonstrate, in a mouse model, that colitis‐induced CRC reduces the gut microbiota diversity and that loss of ERβ enhances this process. The findings could enable novel therapeutic or preventive approaches toward a more favorable microbiome in inflammatory bowel disease and/or colon cancer development.
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Affiliation(s)
- Ahmed Ibrahim
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden.,Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Luisa W Hugerth
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institute, Science for Life Laboratory, Solna, Sweden
| | - Linnea Hases
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden.,Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Ashish Saxena
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, TX, USA
| | - Maike Seifert
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institute, Science for Life Laboratory, Solna, Sweden
| | - Quentin Thomas
- Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
| | - Jan-Åke Gustafsson
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, TX, USA
| | - Lars Engstrand
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institute, Science for Life Laboratory, Solna, Sweden
| | - Cecilia Williams
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden.,Department of Protein Science, KTH Royal Institute of Technology, Science for Life Laboratory, Solna, Sweden
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16
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Rasmussen PU, Hugerth LW, Blanchet FG, Andersson AF, Lindahl BD, Tack AJM. Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb. New Phytol 2018; 220:1248-1261. [PMID: 29573431 PMCID: PMC6282561 DOI: 10.1111/nph.15088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/11/2018] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.
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Affiliation(s)
- Pil U. Rasmussen
- Department of EcologyEnvironment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
| | - Luisa W. Hugerth
- School of BiotechnologyScience for Life LaboratoryKTH Royal Institute of TechnologyPO Box 1031SE‐171 21SolnaSweden
- Centre for Translational Microbiome ResearchDepartment of Molecular, Tumor and Cell BiologyScience for Life LaboratoryKarolinska Institutet171 65SolnaSweden
| | - F. Guillaume Blanchet
- Département de BiologieFaculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
| | - Anders F. Andersson
- School of BiotechnologyScience for Life LaboratoryKTH Royal Institute of TechnologyPO Box 1031SE‐171 21SolnaSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesBox 7014SE‐750 07UppsalaSweden
| | - Ayco J. M. Tack
- Department of EcologyEnvironment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
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17
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Alneberg J, Karlsson CMG, Divne AM, Bergin C, Homa F, Lindh MV, Hugerth LW, Ettema TJG, Bertilsson S, Andersson AF, Pinhassi J. Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes. Microbiome 2018; 6:173. [PMID: 30266101 PMCID: PMC6162917 DOI: 10.1186/s40168-018-0550-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/05/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. RESULTS We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. CONCLUSIONS The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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Affiliation(s)
- Johannes Alneberg
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christofer M G Karlsson
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, Sweden
| | - Anna-Maria Divne
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Claudia Bergin
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Felix Homa
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Markus V Lindh
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, Sweden
- Present address: Department of Biology, Lund University, Lund, Sweden
| | - Luisa W Hugerth
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Present address: Science for Life Laboratory, Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Solna, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders F Andersson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, Sweden.
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18
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Hugerth LW, Andersson AF. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol 2017; 8:1561. [PMID: 28928718 PMCID: PMC5591341 DOI: 10.3389/fmicb.2017.01561] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
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Affiliation(s)
- Luisa W Hugerth
- Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska InstitutetSolna, Sweden.,Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
| | - Anders F Andersson
- Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
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19
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Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C, Wilmes P. Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life. Front Microbiol 2017; 8:738. [PMID: 28512451 PMCID: PMC5411419 DOI: 10.3389/fmicb.2017.00738] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/10/2017] [Indexed: 12/26/2022] Open
Abstract
Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera Streptococcus and Staphylococcus, and a decrease in relative abundance for the genera Bifidobacterium and Bacteroides. Generally, a depletion in Bacteroidetes was detected as early as day 5 postpartum in CSD infants, causing a significantly increased Firmicutes/Bacteroidetes ratio between days 5 and 150 when compared to VD infants. Although the delivery mode appeared to have the strongest influence on differences between the infants, other factors such as a younger gestational age or maternal antibiotics intake likely contributed to the observed patterns as well. Our findings complement previous observations of a delay in colonization and succession of CSD infants, which affects not only bacteria but also archaea and microeukaryotes. This further highlights the need for resolving bacterial, archaeal, and microeukaryotic dynamics in future longitudinal studies of microbial colonization and succession within the neonatal gastrointestinal tract.
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Affiliation(s)
- Linda Wampach
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Angela Hogan
- Integrated BioBank of LuxembourgLuxembourg, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | - Luisa W Hugerth
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of TechnologyStockholm, Sweden
| | - Lutz Bindl
- Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Jean Bottu
- Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Anders F Andersson
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of TechnologyStockholm, Sweden
| | - Carine de Beaufort
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg.,Centre Hospitalier de LuxembourgLuxembourg, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
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20
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Lindh MV, Sjöstedt J, Ekstam B, Casini M, Lundin D, Hugerth LW, Hu YOO, Andersson AF, Andersson A, Legrand C, Pinhassi J. Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environ Microbiol 2017; 19:1222-1236. [PMID: 28028880 DOI: 10.1111/1462-2920.13650] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/10/2016] [Accepted: 12/18/2016] [Indexed: 12/11/2022]
Abstract
Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.
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Affiliation(s)
- Markus V Lindh
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Börje Ekstam
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, SE-45330, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Luisa W Hugerth
- Science for Life Laboratory School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-10691, Sweden
| | - Yue O O Hu
- Science for Life Laboratory School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-10691, Sweden
| | - Anders F Andersson
- Science for Life Laboratory School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-10691, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-90187, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
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21
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Hugerth LW, Larsson J, Alneberg J, Lindh MV, Legrand C, Pinhassi J, Andersson AF. Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol 2015; 16:279. [PMID: 26667648 PMCID: PMC4699468 DOI: 10.1186/s13059-015-0834-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/12/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. RESULTS We use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts. CONCLUSIONS We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.
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Affiliation(s)
- Luisa W Hugerth
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
| | - John Larsson
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Johannes Alneberg
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
| | - Markus V Lindh
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182, Kalmar, Sweden.
| | - Anders F Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden.
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22
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Lindh MV, Sjöstedt J, Andersson AF, Baltar F, Hugerth LW, Lundin D, Muthusamy S, Legrand C, Pinhassi J. Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling. Environ Microbiol 2015; 17:2459-76. [PMID: 25403576 DOI: 10.1111/1462-2920.12720] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 11/11/2014] [Accepted: 11/11/2014] [Indexed: 01/08/2023]
Abstract
Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1) . Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.
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Affiliation(s)
- Markus V Lindh
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, KTH Royal Institute of Technology, School of Biotechnology, Stockholm, SE-10691, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden.,Department of Marine Sciences, University of Otago, PO Box 56, Dunedin, NZ-9054, New Zealand
| | - Luisa W Hugerth
- Science for Life Laboratory, KTH Royal Institute of Technology, School of Biotechnology, Stockholm, SE-10691, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Saraladevi Muthusamy
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
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23
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Hugerth LW, Muller EEL, Hu YOO, Lebrun LAM, Roume H, Lundin D, Wilmes P, Andersson AF. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One 2014; 9:e95567. [PMID: 24755918 PMCID: PMC3995771 DOI: 10.1371/journal.pone.0095567] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/28/2014] [Indexed: 01/22/2023] Open
Abstract
High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems.
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Affiliation(s)
- Luisa W. Hugerth
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
| | - Emilie E. L. Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Yue O. O. Hu
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
| | - Laura A. M. Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Hugo Roume
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel Lundin
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
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