| 1. |
- Abrahamsson, Thomas, et al.
(författare)
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Low diversity of the gut microbiota in infants with atopic eczema
- 2012
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Ingår i: Journal of Allergy and Clinical Immunology. - New York, USA : Elsevier BV. - 0091-6749 .- 1097-6825. ; 129:2, s. 434-U244
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: It is debated whether a low total diversity of the gut microbiota in early childhood is more important than an altered prevalence of particular bacterial species for the increasing incidence of allergic disease. The advent of powerful, cultivation-free molecular methods makes it possible to characterize the total microbiome down to the genus level in large cohorts. OBJECTIVE: We sought to assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to atopic eczema development. METHODS: Microbial diversity and composition were analyzed with barcoded 16S rDNA 454-pyrosequencing in stool samples at 1 week, 1 month, and 12 months of age in 20 infants with IgE-associated eczema and 20 infants without any allergic manifestation until 2 years of age (ClinicalTrials.gov ID NCT01285830). RESULTS: Infants with IgE-associated eczema had a lower diversity of the total microbiota at 1 month (P= .004) and a lower diversity of the bacterial phylum Bacteroidetes and the genus Bacteroides at 1 month (P= .02 and P= .01) and the phylum Proteobacteria at 12 months of age (P= .02). The microbiota was less uniform at 1 month than at 12 months of age, with a high interindividual variability. At 12 months, when the microbiota had stabilized, Proteobacteria, comprising gram-negative organisms, were more abundant in infants without allergic manifestation (Empirical Analysis of Digital Gene Expression in R edgeR test: P= .008, q= 0.02). CONCLUSION: Low intestinal microbial diversity during the first month of life was associated with subsequent atopic eczema.
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| 2. |
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| 3. |
- Engström Jakobsson, Hedvig
(författare)
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Molecular characterization of the dynamics and development of the human microbiota
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The human body contains an enormous amount of bacteria, which are important in processes such as colonization resistance, digestion of food particles, and in the development of the immune system. Most host-microbe interactions are not harmful. Each individual harbors a unique and site-specific microbiota which is considered to be relatively stable within an individual over time. For many years, the indigenous microbiota was characterized using culture-based methods. The use of culture-based methods is quite time consuming and not completely comprehensive: a large fraction of the bacteria are not detected because of unknown growth conditions. Through the use of high-throughput sequencing technologies, based on analysis of the 16S rRNA gene, knowledge about the microbiota residing within human has increased. In this thesis the 454 pyrosequencing technology was used in order to characterize the human indigenous microbiota in infants and adults. By developing primers specific for a certain region of the 16S rRNA gene and by the addition of a 4-5 nucleotide long barcode to each primer the 454 pyrosequencing was developed to fit multiple samples in a single run. When the microbiota was analyzed in infants during the first two years of life, it was observed that mode of delivery had an impact on the early microbiota composition as well as chemokine levels. The diversity within the Bacteroidetes phylum was higher in vaginal delivered infants through the first six months of life and the major genus Bacteroides was detected significantly more frequently in the vaginally delivered infants. Moreover, a significant association between the presence of the genus Bacteroides in the infants’ stool at one and three months and high levels of the Th1- associated chemokines CXCL10 and CXCL11 was found. This thesis provide evidence that the Bacteroidetes are transferred from mother to child during vaginal delivery and that impaired colonization of this phylum may lead to an altered Th1/Th2 balance. The findings could help to explain the association between mode of delivery and allergy development in children. The etiology of allergy is, however, multifactorial, with many variables contributing to the final expression of atopic disease. The prevalence of allergic disease has increased markedly, especially in the Western world, and a combination of genetics and environmental factors has been proposed as a cause of this rise. Specific genera have been suggested to be part of this etiology, but with differing results. In this thesis, a specific genus was not correlated to allergic disease, but instead a low diversity of the total microbiota early in life was associated with development of allergic disease at two years of age. In this thesis, the stability of the gastrointestinal microbiota in healthy adults and following perturbation with antibiotics was also analyzed. A relatively, but not completely stable microbiota was found in adults. Following antibiotic treatment, dramatic short-term effects were observed in throat and fecal samples. Long-term perturbations were also observed in the microbiota and also a dramatic increase and persistence in antibiotic resistance genes causing macrolide resistance was seen.
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| 4. |
- Gonzales-Siles, Lucia, et al.
(författare)
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Mass Spectrometry Proteotyping of Streptococcus pneumoniae and commensal Streptococcus: identification of biomarkers for infectious strain characterization
- 2016
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Ingår i: 26th ECCMID 2016 Amsterdam, The Netherlands. 9 - 12 April 2016.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Background: Streptococcus pneumoniae (pneumococcus) is the leading cause of community-acquired pneumonia, with morbidity and mortality worldwide. S. pneumoniae belongs to the S. mitis-Group (viridans streptococci), phenotypically and genotypically similar to commensal species of the upper respiratory tract, S. mitis, S. oralis, and S. pseudopneumoniae, causing problems for identifications in clinical laboratories. In this project, we apply state-of-the-art proteomics for Streptococcus spp. 'proteotyping'; identifying and characterizing protein biomarkers for species-level identification, antibiotic resistance, virulence and strain typing for epidemiological analyses (1). Material/methods: Bacterial proteins, from intact bacteria or cell fractions, are bound to a membrane surface, using patented (WO2006068619) FlowCell (LPITM) technology. Peptides are generated from the bound proteins, by enzymatic digestion, separated and analyzed, using LC-MS/MS. The mass spectra profiles are compared to reference peptide sequences and whole genome sequence (wgs) data of the NCBI RefSeq Database. The S. mitis-Group specie, S. pneumoniae, S. mitis, S. oralis, S. psedopneumoniae, as well as the more distantly-related, Group A Streptococcus (GAS) species, S. pyogenes , were analyzed individually and in mixtures, to demonstrate the resolution of proteotyping for differentiating bacteria. Results: Using proteotyping protocols, S. pneumoniae were detected and differentiated from other streptococci, S. mitis, S. oralis, S. psedopneumoniae and the more distant relative, S. pyogenes, by identification of unique discriminatory peptides. Metabolic protein biomarkers were identified, including for antibiotic resistance and virulence. It was possible to find discriminatory biomarkers for a target species when analyzing 1:1 mixes of S. pneumoniae and other species from the S. mitis-Group. The different strains of S. pneumoniae, analyzed in different ratio combinations, were successfully differentiated and identified. For successful proteotyping, a comprehensive and accurate genomic database was observed to be key for obtaining reliable peptide matching and proteotyping data. Importantly, because of observed high rates of misclassified wgs data in the public databases, the taxonomic classifications of genomes in GenBank were analyzed against reference type strain genomes of target species by calculating wgs similarities, using Average Nucleotide Identity with BLAST (ANIb). While wgs data for S. pneumoniae were confirmed to be classified correctly, approximately one-third of wgs data for other species of the S. mitis-Group were determined to be misclassified. Streptococci strains that could not be identified, using standard genotypic and phenotypic approaches, were characterized by proteotyping and genome sequencing to establish their taxonomy and biomarker features to enhance species database matching. Conclusions: Proteotyping enables differentiation, identification and characterization of pneumococcus from the most closely related species attaining, as well, strain-level discrimination from single LC-MS/MS analyses. The protocol enhances identification and characterization of pathogenic bacterial isolates through identifications of expressed biomarkers, ultimately for cultivation-independent analyses of clinical samples. 1) Karlsson et al., 2015. Syst Appl Microbiol. 38:246-257.
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| 5. |
- Hugerth, Luisa W., et al.
(författare)
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DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies
- 2014
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 80:16, s. 5116-5123
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e. g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571-1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.
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| 6. |
- Jakobsson, Hedvig E., et al.
(författare)
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Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section
- 2014
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Ingår i: Gut. - London : BMJ. - 0017-5749 .- 1468-3288. ; 63:4, s. 559-566
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Tidskriftsartikel (refereegranskat)abstract
- important stimuli for immune development, and a reduced microbial exposure as well as caesarean section (CS) has been associated with the development of allergic disease. Here we address how microbiota development in infants is affected by mode of delivery, and relate differences in colonisation patterns to the maturation of a balanced Th1/Th2 immune response. Design The postnatal intestinal colonisation pattern was investigated in 24 infants, born vaginally (15) or by CS (nine). The intestinal microbiota were characterised using pyrosequencing of 16S rRNA genes at 1 week and 1, 3, 6, 12 and 24 months after birth. Venous blood levels of Th1- and Th2-associated chemokines were measured at 6, 12 and 24 months. Results Infants born through CS had lower total microbiota diversity during the first 2 years of life. CS delivered infants also had a lower abundance and diversity of the Bacteroidetes phylum and were less often colonised with the Bacteroidetes phylum. Infants born through CS had significantly lower levels of the Th1-associated chemokines CXCL10 and CXCL11 in blood. Conclusions CS was associated with a lower total microbial diversity, delayed colonisation of the Bacteroidetes phylum and reduced Th1 responses during the first 2 years of life.
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| 7. |
- Jakobsson, Hedvig E, et al.
(författare)
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Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.
- 2016
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Ingår i: Genome Announcements. - 2169-8287. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human respiratory tract. It is associated with otitis media and respiratory tract infections. Here, we report the draft genome sequence of M. catarrhalis type strain CCUG 353(T), composed of 18 contigs and a total size of 1.89 Mb.
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| 8. |
- Jakobsson, Hedvig E, et al.
(författare)
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Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F
- 2017
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Ingår i: Genome Announcements. - 2169-8287. ; 5:14
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Tidskriftsartikel (refereegranskat)abstract
- Streptococcus pneumoniae is a pathogenic bacterium found most commonly in the respiratory tract of humans and is a common cause of pneumonia and bacterial meningitis. Here, we report the draft genome sequences of six S. pneumoniae strains: CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG 35272.
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| 9. |
- Jakobsson, Hedvig E, et al.
(författare)
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Proteotyping of Streptococcus pneumoniae, using tandem mass spectrometry for identification of biomarkers for species and strain differentiation
- 2016
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Ingår i: 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI) 9 - 12 March 2016, Estoril, Portugal. - : European Society for Clinical Microbiology and Infectious Diseases.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Background. Streptococcus pneumoniae (pneumococcus) is the leading cause of community-acquired pneumonia and a major cause of morbidity and mortality worldwide. S. pneumoniae is phenotypically and genotypically similar to commensal species of the upper respiratory tract of the Streptococcus mitis-Group (viridans streptococci), S. mitis, S. oralis, and S. pseudopneumoniae, causing problems of identification in clinical microbiology laboratories. We have applied state-of-the-art proteomics techniques for Streptococcus spp. proteotyping; to detecting and characterizing expressed protein biomarkers for species-level identification, determination of antibiotic resistance and virulence biomarkers and strain typing for epidemiological analyses. Material and methods. The proteins of intact bacteria or cell fractions are bound to a membrane surface, using patented (WO2006068619) Lipid-based Protein Immobilization (LPITM) technology. Peptides are generated from the bound proteins, using enzymatic digestion, separated and analyzed, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The mass spectra profiles are compared to a database of reference peptide sequences. Subsequently, the identified peptides are compared to a database of reference genome sequences, all complete genomes of the NCBI Reference Sequence (RefSeq) Database. In this study, the type strains of the close-related mitis complex species S. pneumoniae (CCUG 28588T), S. mitis (CCUG 31611T), S. oralis (CCUG 13229T), S. psedopneumoniae (CCUG 49455T) and the more distantly-related S. pyogenes (CCUG 4207T) were analysed individually and in mixtures, to demonstrate proteotyping capability and differentiate closely related species,. Additionally, mixes containing different S. pneumoniae strains were analyzed. Results. Using proteotyping protocols, it was possible to detect and correctly identify S. pneumoniae from the closely related bacterial species, S. mitis, S. oralis S. psedopneumoniae and S. pyogenes, as well as different strains of S. pneumoniae by identification of unique discriminatory peptides. For successful proteotyping,a comprehensive and accurate genomic database is the key to obtaining reliable proteotyping data. Importantly, because of questionable classifications of sequenced genomes in the public databases, before incorporation of reference genomic sequence data for proteotyping, the genome sequences should be verified and confirmed for accurate classifications. Furthermore, it is also essential to include all relevant species with as many as 25 genomes in order to obtain a comprehensive coverage of coding sequences for accurate peptide matching and to be able to discriminate between the most closely related species. In this study, all genomes of the S. mitis-Group in the database were analyzed, using Average Nucleotide Identity Blast (ANIb) and S. mitis-Group strains that cannot be identified to the species level, using standard genotypic and phenotypic approaches, where characterized by proteotyping and whole genome sequencing to describe their taxonomy and to improve the database matching. Conclusions: Proteotyping, using LC-MS/MS, enabled the differentiation and identification of pneumococcus from its closely related species and sub-species-level strain discrimination, all from single MS analyses. The whole method will enhance the identification and characterization of microorganisms, allowing high-resolution discrimination of closely related species through the confident identification of new biomarkers, ultimately for cultivation-independent application to the analyses of clinical samples.
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| 10. |
- Jakobsson, Hedvig E, et al.
(författare)
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The composition of the gut microbiota shapes the colon mucus barrier.
- 2015
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Ingår i: EMBO reports. - : EMBO. - 1469-3178 .- 1469-221X. ; 16, s. 164-177
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Tidskriftsartikel (refereegranskat)abstract
- Two C57BL/6 mice colonies maintained in two rooms of the same specific pathogen-free (SPF) facility were found to have different gut microbiota and a mucus phenotype that was specific for each colony. The thickness and growth of the colon mucus were similar in the two colonies. However, one colony had mucus that was impenetrable to bacteria or beads the size of bacteria-which is comparable to what we observed in free-living wild mice-whereas the other colony had an inner mucus layer penetrable to bacteria and beads. The different properties of the mucus depended on the microbiota, as they were transmissible by transfer of caecal microbiota to germ-free mice. Mice with an impenetrable mucus layer had increased amounts of Erysipelotrichi, whereas mice with a penetrable mucus layer had higher levels of Proteobacteria and TM7 bacteria in the distal colon mucus. Thus, our study shows that bacteria and their community structure affect mucus barrier properties in ways that can have implications for health and disease. It also highlights that genetically identical animals housed in the same facility can have rather distinct microbiotas and barrier structures.
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