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- Angell, IL, et al.
(författare)
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De novo species identification using 16S rRNA gene nanopore sequencing
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8, s. e10029-
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Tidskriftsartikel (refereegranskat)abstract
- Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
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| 4. |
- Kreyberg, I, et al.
(författare)
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Erratum: "Stopping when knowing: use of snus and nicotine during pregnancy in Scandinavia". Ina Kreyberg, Karen E.S. Bains, Kai-H. Carlsen, Berit Granum, Hrefna K. Gudmundsdóttir, Guttorm Haugen, Gunilla Hedlin, Katarina Hilde, Christine M. Jonassen, Live S. Nordhagen, Björn Nordlund, Katrine D. Sjøborg, Håvard O. Skjerven, Anne C. Staff, Cilla Söderhäll, Riyas M. Vettukattil and Karin C. Lødrup Carlsen on behalf of the PreventADALL study group. ERJ Open Res 2019; 5: 00197-2018
- 2020
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Ingår i: ERJ open research. - : European Respiratory Society (ERS). - 2312-0541. ; 6:1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Magi, CAO, et al.
(författare)
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Allergic disease and risk of stress in pregnant women: a PreventADALL study
- 2020
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Ingår i: ERJ open research. - : European Respiratory Society (ERS). - 2312-0541. ; 6:4
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Tidskriftsartikel (refereegranskat)abstract
- Maternal stress during pregnancy may negatively affect the health of mother and child. We therefore aimed to identify the proportion of women reporting high maternal stress in mid and late pregnancy and explore whether symptoms of maternal allergic disease are associated with perceived maternal stress in late pregnancy.MethodThe population-based Preventing Atopic Dermatitis and Allergy in Children (PreventADALL) study enrolled 2697 pregnant women at their 18-week routine ultrasound examination in Norway and Sweden. Information about sociodemographic factors, symptoms and doctor-diagnosed asthma, allergic rhinitis, atopic dermatitis, food allergy, and anaphylaxis and stress using the 14-item perceived stress scale (PSS) was collected at 18 weeks (mid) and 34 weeks (late) pregnancy. High stress was defined as a PSS score ≥29. Scores were analysed using multivariate logistic and linear regression.ResultsAmong the 2164 women with complete PSS data, 17% reported asthma, 20% atopic dermatitis, 23% allergic rhinitis, 12% food allergy and 2% anaphylaxis. The proportion of women reporting high stress decreased from 15% at mid to 13% at late pregnancy (p<0.01). The adjusted odds ratio for high stress in late pregnancy was 2.25 (95% CI 1.41–3.58) for self-reported symptoms of asthma, 1.46 (95% CI 1.02–2.10) for allergic rhinitis and 2.25 (95% CI 1.32–3.82) for food allergy. A multivariate linear regression model confirmed that symptoms of asthma (β coefficient 2.11; 0.71–3.51), atopic dermatitis (β coefficient 1.76; 0.62–2.89) and food allergy (β coefficient 2.24; 0.63–3.84) were independently associated with increased PSS score.ConclusionAllergic disease symptoms in pregnancy were associated with increased stress, highlighting the importance of optimal disease control in pregnancy.
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| 6. |
- Nilsen, M, et al.
(författare)
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Butyrate Levels in the Transition from an Infant- to an Adult-Like Gut Microbiota Correlate with Bacterial Networks Associated with Eubacterium Rectale and Ruminococcus Gnavus
- 2020
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Relatively little is known about the ecological forces shaping the gut microbiota composition during infancy. Therefore, the objective of the present study was to identify the nutrient utilization- and short-chain fatty acid (SCFA) production potential of gut microbes in infants during the first year of life. Stool samples were obtained from mothers at 18 weeks of pregnancy and from infants at birth (first stool) at 3, 6, and 12-months of age from the general population-based PreventADALL cohort. We identified the taxonomic and SCFA composition in 100 mother-child pairs. The SCFA production and substrate utilization potential of gut microbes were observed by multiomics (shotgun sequencing and proteomics) on six infants. We found a four-fold increase in relative butyrate levels from 6 to 12 months of infant age. The increase was correlated to Eubacterium rectale and its bacterial network, and Faecalibacterium prausnitzii relative abundance, while low butyrate at 12 months was correlated to Ruminococcus gnavus and its associated network of bacteria. Both E. rectale and F. prausnitzii expressed enzymes needed for butyrate production and enzymes related to dietary fiber degradation, while R. gnavus expressed mucus-, fucose, and human milk oligosaccharides (HMO)-related degradation enzymes. Therefore, we believe that the presence of E. rectale, its network, and F. prausnitzii are key bacteria in the transition from an infant- to an adult-like gut microbiota with respect to butyrate production. Our results indicate that the transition from an infant- to an adult-like gut microbiota with respect to butyrate producing bacteria, occurs between 6 and 12 months of infant age. The bacteria associated with the increased butyrate ratio/levels were E. rectale and F. prausnitzii, which potentially utilize a variety of dietary fibers based on the glycoside hydrolases (GHs) expressed. R. gnavus with a negative association to butyrate potentially utilizes mucin, fucose, and HMO components. This knowledge could have future importance in understanding how microbial metabolites can impact infant health and development.
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