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- Engstrand Lilja, Helene, 1963-, et al.
(author)
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Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome
- 2015
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In: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 3
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Journal article (peer-reviewed)abstract
- Background: The composition of the intestinal microbiota seems to be an important factor in determining the clinical outcome in children with short bowel syndrome (SBS). Alterations in the microbiota may result in serious complications such as small bowel bacterial overgrowth (SBBO) and intestinal mucosal inflammation that lead to prolonged parenteral nutrition (PN) dependency with subsequently increased risk of liver failure and sepsis. To date, there are no reported mappings of the intestinal microbiome in children with SBS. Here, we present the first report on the intestinal microbial community profile in children with SBS. Findings: The study includes children diagnosed with SBS in the neonatal period. Healthy siblings served as controls. Fecal samples were collected, and microbial profiles were analyzed by using 16S rRNA gene sequencing on the Illumina MiSeq platform. We observed a pronounced microbial dysbiosis in children with SBS on PN treatment with an increased and totally dominating relative abundance of Enterobacteriacae in four out of five children compared to children with SBS weaned from PN and healthy siblings. Conclusions: The overall decreased bacterial diversity in children with SBS is consistent with intestinal microbiome mappings in inflammatory bowel diseases such as Crohn's disease and necrotizing enterocolitis in preterm infants. Our findings indicate that intestinal dysbiosis in children with SBS is associated with prolonged PN dependency.
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| 3. |
- Hugerth, Luisa W., et al.
(author)
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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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In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 80:16, s. 5116-5123
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Journal article (peer-reviewed)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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- Samuelsson, Annika, 1964-, et al.
(author)
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Disturbed intestinal microbiota (dysbiosis) and micro dynamics in patients treated for appendicitis and diverticulitis
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Other publication (other academic/artistic)abstract
- Introduction: The human gut microbiota is a large dynamic bacterial community, which is influenced by for instance antibiotic treatment and hospitalization. In patients with inflammatory bowel disease the diversity of gut microbiota is thought to be less diverse. The role of the gut microbiota in acute appendicitis and diverticulitis is still unclear. To investigate the microbial diversity in patients suffering from appendicitis or diverticulitis, and the microbiota dynamics after antibiotic therapy and hospitalization we performed an open observation study.Methods and population: We have performed 16S rRNA sequence analysis on 42 individuals diagnosed with appendicitis and 18 individuals with diverticulitis as well as 33 healthy controls. Cultivation of the aerobic bacterial flora was performed as a complement to sequence analysis.Results: In sequencing data at genus level, there are distinctive differences when comparing healthy controls to patients diagnosed with appendicitis. Healthy controls have a flora dominated by Bacteroides, and Faecalibacterium, Ruminococcus and Prevotella while appendicitis patients show an intestinal flora with a higher abundance of Escherichia/Shigella and unclassified Enterobacteriaceae. The same pattern, however not quite as distinct could be seen for the diverticulitis patients. The microbial diversity increases after treatment with antibiotics and hospitalization.In the cultivated aerobic flora there was a significant loss of Escherichia coli and a significant gain of Citrobacter species, in the appendicitis group. In the appendicitis group as well as in the diverticulitis group there was a significant gain of Enterococcus faecium and Yeasts.Conclusion: The main findings of this study are that patients arriving at the emergency department with acute appendicitis or diverticulitis have an already significant disturbed fecal microbiota previous to antibiotic treatment and hospitalization.
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