Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome.

Amplicon-based next-generation sequencing (NGS) of the 16S ribosomal RNA (16S) regions is a culture-free method used to identify and analyze Procaryota occurring within a given sample. The prokaryotic 16S rRNA gene contains conserved regions and nine variable regions (V1-V9) frequently used for phylogenetic classification of genus or species in diverse microbial populations. This work compares the accuracy and efficacy of two platforms, iSeq and MiSeq from Illumina, used in sequencing 16S rRNA. The most important similarities and differences of 16S microbiome sequencing in 20 fecal rat samples were described. Genetic libraries were prepared according to 16S Metagenomic Sequencing Library Preparation (Illumina) for the V3 and V4 regions of the 16S. The species richness obtained using iSeq technology was lower compared to MiSeq. At the second taxonomy level (L2), the abundance of taxa was comparable for both platforms. At the L7, the taxa abundance was significantly different, and the number of taxa was higher for the MiSeq. The alpha diversity was lower for iSeq than for MiSeq, starting from the order to the species level. The beta diversity estimation revealed statistically significant differences in microbiota diversity starting from the class level to the species level in samples sequenced on two investigated platforms. This work disclosed that the iSeq platform could be used to evaluate the bacterial profile of the samples to characterize the overall profile. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition. KEY POINTS: • iSeq platform allows to shorten the sequencing time three times compared to the MiSeq. • iSeq can only be used for an initial and quick microbiome assessment. • MiSeq is better for a detailed analysis of the differences in the microbiota composition.

Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study.

Gut microbiome and colonic inflammation can be associated with the predisposition and progression of Parkinson's disease (PD). The presented study aimed to compare gastrointestinal microbiota composition between patients diagnosed with PD and treated only with Levodopa to healthy controls. In this prospective study, patients were recruited in 1 academic hospital from July 2019 to July 2020. The detailed demographic data and medical history were collected using a set of questionnaires. Fecal samples were obtained from all participants. Next-Generation Sequencing was used to assess the microbiota composition. The endpoint was the difference in composition of the gut microbiota. In this study, we enrolled 27 hospitalized PD patients with well-controlled symptoms. The control group included 44 healthy subjects matched for age. Among PD patients, our results presented a higher abundance of Bacteroides phylum, class Corynebacteria among phylum Actinobacteria, class Deltaproteobacteria among phylum Proteobacteria, and genera such as Butyricimonas, Robinsoniella, and Flavonifractor. The species Akkermansia muciniphila, Eubacterium biforme, and Parabacteroides merdae were identified as more common in the gut microbiota of PD patients. In conclusion, the patients diagnosed with PD have significantly different gut microbiota profiles in comparison with healthy controls.

Does Postoperative Oral and Intestinal Microbiota Correlate with the Weight-Loss Following Bariatric Surgery?-A Cohort Study.

The composition of the gastrointestinal microbiota is associated with obesity. The aim of this study was to verify if, six months after bariatric surgery, patients who achieve satisfying weight-loss after sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB) have a different composition of oral and intestinal microbiota in comparison with those who do not. This prospective cohort study was conducted between November 2018 and November 2020. Participants underwent either SG or RYGB and were allocated into: Group 1-participants who achieved a percentage of excess weight loss (%EWL) of ≥ 50%, and Group 2-patients with %EWL of < 50%. The %EWL was measured 6 months following surgery. At this time, oral swabs were obtained and stool samples were provided. The endpoint was the composition of the gut microbiota. Group 1 comprised 20 participants and Group 2 comprised 11 participants. Group 1 had oral microbiota more abundant in phylum Fusobacteria and intestinal microbiota more abundant in phylum Firmicutes. Group 2 had oral microbiota was more enriched in phylum Actinobacteria and intestinal microbiota was more enriched in phylum Bacteroidetes. The compositions of the microbiota of the oral cavity and large intestine 6 months after bariatric surgery are related to the weight-loss.

Primary cutaneous CD30+ lymphoproliferative disorder--a 10-year follow-up. A case report and differential diagnosis.

Primary cutaneous CD30+ lymphoproliferative disorders (LPDs) are the second most common group of primary cutaneous T-cell lymphomas (CTCLs). The spectrum of LPDs includes lymphomatoid papulosis (LyP), primary cutaneous anaplastic large cell lymphoma (C-ALCL) and borderline cases. The term "borderline lesions" refers to cases where histological features are similar to LyP, but clinically behave as C-ALCL, or to cases where histological features are typical for C-ALCL, but clinically behave as LyP. We present a clinical and morphological picture of LPD in a 57-year old patient treated in the Department of Oncology and of a relapse after ten years of follow-up and discuss clinical and morphological differential diagnosis and the significance of such diagnosis.

The gain-of-function JAK2 V617F mutation shifts the phenotype of essential thrombocythemia and chronic idiopathic myelofibrosis to more "erythremic" and less "thrombocythemic": a molecular, histologic, and clinical study.

We investigated the prevalence of the JAK2 V617F gain-of-function mutation in patients with Philadelphia chromosome-negative chronic myeloproliferative disorders (Ph- MPD) and explored the links between JAK2 mutational status and the clinicopathologic picture of essential thrombocythemia (ET), chronic idiopathic myelofibrosis (CIMF), and polycythemia vera (PV). Allele-specific polymerase chain reaction results for 59 ET, 18 CIMF, and 9 PV cases were compared with values for clinical variables at presentation and last follow-up and with the diagnostic trephine bone marrow biopsy pictures. JAK2 V617F was found in 38 (64%) of ET cases, 7 (39%) of CIMF cases, and 9 (100%) of PV cases. The ET patients with the mutant JAK2 showed significantly higher (although not overtly polycythemic) red blood cell parameter values, lower platelet counts, and higher white blood cell counts. Similar trends were found in CIMF. Megakaryocyte clustering was much less pronounced in the CIMF cases with mutant JAK2, with an analogous trend occurring in the ET cases. Bone marrow cellularity values and the numbers of CD34+ and CD117+ blasts in the ET and CIMF groups did not differ. Fibrosis was slightly less marked in the ET cases with mutant JAK2. The mutation did not significantly influence the clinical course during the follow-up in either disease in the short term (median follow-up, 22 months). The JAK2 V617F mutation is prevalent in all Ph- MPD and may skew their presenting phenotype, including bone marrow histology, toward a more "erythremic" and less "thrombocythemic" phenotype.

Clonal lymphocytic populations in Philadelphia-negative chronic myeloproliferative disorders: is the T-cell clonality of 'undetermined' significance (TCUS) linked to a worse clinical outcome?

This study examined the clonality of B- and T-cells by PCR in 83 patients with Philadelphia-negative myeloproliferative disorders (Ph-MPD), to investigate its clinical and morphological correlates. Clonal lymphocytic populations were found in 23% of patients (T: n = 20, B: n = 3), with no frequency differences between ET, CIMF and PV. At the presentation, patients with clonal bands were older (58.1+/-13.8 vs 47.5+/-14.6, p = 0.0039), but did not differ in other clinical parameters. After the median follow-up of 21 months they were less likely to be asymptomatic (11.8% vs 41.1%, p = 0.029). The T-cell clonality was the strongest predictor of the symptomatic last follow-up by discriminant function analysis, surpassing the patient's age. This surprising negative prognostic impact of lymphocyte clonality in Ph-MPD may result from this phenomenon to be a better measure of the 'hematopoietic biologic age' than the metrical age itself.