| 1. |
- 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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| 2. |
- Johansson, Malin E V, 1971, et al.
(författare)
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Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization
- 2015
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Ingår i: Cell Host & Microbe. - : Elsevier BV. - 1931-3128 .- 1934-6069. ; 18:5, s. 582-592
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Tidskriftsartikel (refereegranskat)abstract
- The intestinal mucus layer provides a barrier limiting bacterial contact with the underlying epithelium. Mucus structure is shaped by intestinal location and the microbiota. To understand how commensals modulate gut mucus, we examined mucus properties under germ-free (GF) conditions and during microbial colonization. Although the colon mucus organization of GF mice was similar to that of conventionally raised (Convr) mice, the GF inner mucus layer was penetrable to bacteria-sized beads. During colonization, in which GF mice were gavaged with Convr microbiota, the small intestine mucus required 5 weeks to be normally detached and colonic inner mucus 6 weeks to become impenetrable. The composition of the small intestinal microbiota during colonization was similar to Convr donors until 3 weeks, when Bacteroides increased, Firmicutes decreased, and segmented filamentous bacteria became undetectable. These findings highlight the dynamics of mucus layer development and indicate that studies of mature microbe-mucus interactions should be conducted weeks after colonization.
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| 3. |
- Salvà-Serra, Francisco, 1989, et al.
(författare)
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Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198(T) and CCUG 4207(T), the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198(T) and CCUG 4207(T) are derived from deposit of the same strain at two different culture collections. NCTC 8198(T) was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207(T) was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.
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| 4. |
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| 5. |
- 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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| 6. |
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| 7. |
- 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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| 8. |
- 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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| 9. |
- 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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| 10. |
- 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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