Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

Salonen, Anne; Nikkilä, Janne; Jalanka, Jonna; Immonen, Outi; Rajilić‐Stojanović, Mirjana; Kekkonen, Riina A.; Palva, Airi; Vos, Willem M. de

doi:10.1016/j.mimet.2010.02.007

Cited by 478 publications

(478 citation statements)

References 45 publications

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“…Bead beating was required to extract DNA from this sample set, yet bead beating may be destructive to the DNA quality and too extensive bead beating should be avoided, since impaired DNA integrity may interfere with downstream applications [42]. A repeated set of bead beatings were shown to reduce DNA shear compared to one long bead-beating step (data not shown).…”

Section: Discussionmentioning

confidence: 99%

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

Eriksson

Mourkas

González‐Acuña

et al. 2017

Infection Ecology & Epidemiology

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Introduction: Advances in the development of nucleic acid-based methods have dramatically facilitated studies of host–microbial interactions. Fecal DNA analysis can provide information about the host’s microbiota and gastrointestinal pathogen burden. Numerous studies have been conducted in mammals, yet birds are less well studied. Avian fecal DNA extraction has proved challenging, partly due to the mixture of fecal and urinary excretions and the deficiency of optimized protocols. This study presents an evaluation of the performance in avian fecal DNA extraction of six commercial kits from different bird species, focusing on penguins. Material and methods: Six DNA extraction kits were first tested according to the manufacturers’ instructions using mallard feces. The kit giving the highest DNA yield was selected for further optimization and evaluation using Antarctic bird feces. Results: Penguin feces constitute a challenging sample type: most of the DNA extraction kits failed to yield acceptable amounts of DNA. The QIAamp cador Pathogen kit (Qiagen) performed the best in the initial investigation. Further optimization of the protocol resulted in good yields of high-quality DNA from seven bird species of different avian orders. Conclusion: This study presents an optimized approach to DNA extraction from challenging avian fecal samples.

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Section: Discussionmentioning

confidence: 99%

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

Eriksson

Mourkas

González‐Acuña

et al. 2017

Infection Ecology & Epidemiology

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“…Total bacterial DNA from fecal samples was extracted using the DNeasy Blood and Tissue Mini Kit (Qiagen, Duesseldorf, Germany) as reported by Salonen et al 32 The V4 region of the 16S rRNA gene was amplified using the primers 520F and 802R, as in the study by Centanni et al 33 Pyrosequencing of pooled amplicons was performed according to the GS-FLX Titanium sequencing protocol, as described by Schnorr et al 34 Sequencing reads were analyzed using the QIIME pipeline. 34 For bacterial taxonomy assignment, RDP-classifier (version 2.2) was used.…”

Section: S Rrna Gene Pyrosequencing and Bioinformatic Analysismentioning

confidence: 99%

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT

Biagi

Zama

Nastasi

et al. 2015

Bone Marrow Transplant

115

143

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Acute GvHD (aGvHD) is the main complication of hematopoietic SCT (HSCT) during the treatment of hematological disorders. We carried out the first longitudinal study to follow the gut microbiota trajectory, from both the phylogenetic and functional points of view, in pediatric patients undergoing HSCT. Gut microbiota trajectories and short-chain fatty acid production profiles were followed starting from before HSCT and through the 3-4 months after transplant in children developing and not developing aGvHD. According to our findings, HSCT procedures temporarily cause a structural and functional disruption of the gut microbial ecosystem, describing a trajectory of recovery during the following 100 days. The onset of aGvHD is associated with specific gut microbiota signatures both along the course of gut microbiota reconstruction immediately after transplant and, most interestingly, prior to HSCT. Indeed, in pre-HSCT samples, non-aGvHD patients showed higher abundances of propionate-producing Bacteroidetes, highly adaptable microbiome mutualists that showed to persist during the HSCT-induced ecosystem disruption. Our data indicate that structure and temporal dynamics of the gut microbial ecosystem can be a relevant factor for the success of HSCT and opens the perspective to the manipulation of the pre-HSCT gut microbiota configuration to favor mutualistic persisters with immunomodulatory properties in the gut.Bone Marrow Transplantation (2015) 50, 992-998;

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“…Microbiota composition: networks and dynamics DNA was isolated from faecal samples as previously described (Salonen et al, 2010) and used for the characterization of the intestinal microbiota composition using the Human Intestinal Tract Chip (HITChip), a phylogenetic microarray containing a duplicated set of over 5000 probes based on 16S rRNA gene sequences of 1140 intestinal bacterial phylotypes (Rajilic-Stojanovic et al, 2009). This microarray provides information regarding both composition and relative quantity of bacteria that make up the human intestinal tract communities.…”

Section: Study Design and Populationmentioning

confidence: 99%

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

et al. 2014

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Recurrent Clostridium difficile infection (CDI) can be effectively treated by infusion of a healthy donor faeces suspension. However, it is unclear what factors determine treatment efficacy. By using a phylogenetic microarray platform, we assessed composition, diversity and dynamics of faecal microbiota before, after and during follow-up of the transplantation from a healthy donor to different patients, to elucidate the mechanism of action of faecal infusion. Global composition and network analysis of the microbiota was performed in faecal samples from nine patients with recurrent CDI. Analyses were performed before and after duodenal donor faeces infusion, and during a follow-up of 10 weeks. The microbiota data were compared with that of the healthy donors. All patients successfully recovered. Their intestinal microbiota changed from a low-diversity diseased state, dominated by Proteobacteria and Bacilli, to a more diverse ecosystem resembling that of healthy donors, dominated by Bacteroidetes and Clostridium groups, including butyrate-producing bacteria. We identified specific multi-species networks and signature microbial groups that were either depleted or restored as a result of the treatment. The changes persisted over time.Comprehensive and deep analyses of the microbiota of patients before and after treatment exposed a therapeutic reset from a diseased state towards a healthy profile. The identification of microbial groups that constitute a niche for C. difficile overgrowth, as well as those driving the reinstallation of a healthy intestinal microbiota, could contribute to the development of biomarkers predicting recurrence and treatment outcome, identifying an optimal microbiota composition that could lead to targeted treatment strategies.

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Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

Cited by 478 publications

References 45 publications

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

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