Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles

Abstract Background Sample collection for gut microbiota analysis from in-patients can be challenging. Collection method and storage conditions are potential sources of variability. In this study, we compared the bacterial microbiota from stool stored under different conditions, as well as stool and swab samples, to assess differences due to sample storage conditions and collection method. Methods Using bacterial 16S rRNA gene sequence analysis, we compared the microbiota profiles of stool samples stored and collected under various conditions. Stool samples (2 liquid, 1 formed) from three different patients at two hospitals were each evaluated under the following conditions: immediately frozen at -80°C, stored at 4°C for 12-48 hours before freezing at -80°C and stored at -20°C with 1-2 thaw cycles before storage at -80°C. Additionally, 8 stool and 30 rectal swab samples were collected from 8 in-patients at one hospital. Microbiota differences were assessed using the Yue and Clayton dissimilarity index (θYC distance) and analysis of molecular variance (AMOVA). Results Regardless of the storage conditions, the bacterial communities of aliquots from the same stool samples were very similar based on θYC distances (median intra-sample θYC distance: 0.035, IQR: 0.015-0.061) compared to aliquots from different stool samples (median inter-sample θYC distance: 0.93, IQR: 0.85-0.97) (Wilcoxon test p-value: <0.0001). For the stool and rectal swab comparison, samples from different patients, regardless of sample collection method, were significantly different (AMOVA p-values: <0.001-0.029) compared to no significant difference between all stool and swab samples (AMOVA p-value: 0.976). The θYC dissimilarity index between swab and stool samples was significantly lower within individuals (median 0.17, IQR: 0.10-0.27) than between individuals (median 0.93, IQR: 0.85-0.97) (Wilcoxon test p-value: <0.0001), indicating minimal differences between stool and swab samples collected from the same individual over the sampling period. Conclusion For gastrointestinal microbiota studies based on bacterial 16S rRNA gene sequence analysis, interim stool sample storage at 4 °C or -20 °C, rather than immediate storage at -80 °C, does not significantly alter results. Additionally, stool and rectal swab microbiotas from the same subject were highly similar, indicating that these sampling methods could be used interchangeably to assess the community structure of the distal GI tract.https://deepblue.lib.umich.edu/bitstream/2027.42/136214/1/12866_2017_Article_983.pd

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.

Despite the accepted health benefits of consuming dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic mouse model, in which animals were colonized with a synthetic human gut microbiota composed of fully sequenced commensal bacteria, we elucidated the functional interactions between dietary fiber, the gut microbiota, and the colonic mucus barrier, which serves as a primary defense against enteric pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium. Our work reveals intricate pathways linking diet, the gut microbiome, and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics

Identifikation nicht heilbarer Krebspatienten mit Palliativbedarf durch Screening

Hintergrund Nach der S3-Leitlinie Palliativmedizin sollen bei Patienten mit nicht heilbaren Krebserkrankungen, unabhängig von der Durchführung einer tumorspezifischen Therapie, u. a. regelmäßig Symptome und Bedürfnisse erhoben werden. Zum Screening bieten sich palliativmedizinische Selbsteinschätzungsbögen wie z. B. die Edmonton Symptom Assessment Scale (ESAS) an, die in Kanada im Rahmen einer Qualitätsoffensive in den Onkologischen Zentren eingesetzt wird. Ziel und Methode Ziel ist die Umsetzung des ESAS-Screenings bei metastasierten Patienten im Lungenkrebszentrum, im Darmkrebszentrum, im Zentrum für neuroonkologische Tumoren und im Hautkrebszentrum im Comprehensive Cancer Center (CCC) Mainfranken. Ergebnisse Von insgesamt 839 gescreenten Patienten berichteten 79,6 % mindestens eines von 10 erfragten Symptomen in mäßiger oder starker Ausprägung (ESAS-Itemwert ≥4) und benötigten damit ein genaueres klinisches Assessment und ggf. eine Intervention. Am häufigsten wurden Einschränkungen des Allgemeinbefindens, Erschöpfung und Müdigkeit, Appetitverlust oder Dyspnoe berichtet. Mindestens ein stark ausgeprägtes Symptom (ESASr-Wert ≥7) mit Interventionsbedarf zeigten 40,4 % aller Patienten. Schlussfolgerungen Ein hoher Anteil der Patienten berichtete über relevante Symptombelastung. Inwieweit klinisches Assessment und ggf. Interventionen durch die primär behandelnden Teams (allgemeine Palliativversorgung) übernommen werden können und zu welchen Zeitpunkt die Spezialisten einbezogen werden sollten, muss weiter diskutiert werden.Background The German S3 guideline on palliative care requires that symptoms and needs of patients with incurable cancerous diseases should be regularly assessed, irrespective of the tumor-specific treatment. Self-report questionnaires for palliative medicine are available for screening, such as the Edmonton Symptom Assessment Scale (ESAS), which is used in oncology centers in Canada in the context of a quality management initiative. Aims and method Implemention of the ESAS as a screening method for patients with metastases in lung cancer centers, colorectal cancer centers, in centers for neuro-oncological cancer and in the skin cancer center at the Mainfranken Comprehensive Cancer Center. Results From a total of 839 patient sceened, 79.6 % patients reported at least 1 out of 10 symptoms with moderate or severe intensity (ESAS item score ≥4), which indicates the need for a more detailed clinical assessment or intervention. The most prevalent symptoms were impairment of general well-being, fatigue and exhaustion, loss of appetite and dyspnea. Of the patients 40.4 % showed at least 1 symptom with severe intensity (ESAS score ≥7) with an ensuing need for an intervention. Conclusions A large proportion of patients reported a significant symptom burden. It should be further discussed whether clinical assessment and subsequent interventions can be provided by general palliative care teams and at what stage the inclusion of specialized teams is necessary. Access provided by DEAL DE / Springer Compact Clearingstelle Uni Freiburg