Background Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S rRNA gene analysis using the nanopore long-read sequencer MinION™. We compared it to the conventional short-read sequencing method in both a mock bacterial community and human fecal samples. Results We modified our existing protocol for full-length 16S rRNA gene amplicon sequencing by MinION™. A new strategy for library construction with an optimized primer set overcame PCR-associated bias and enabled taxonomic classification across a broad range of bacterial species. We compared the performance of full-length and short-read 16S rRNA gene amplicon sequencing for the characterization of human gut microbiota with a complex bacterial composition. The relative abundance of dominant bacterial genera was highly similar between full-length and short-read sequencing. At the species level, MinION™ long-read sequencing had better resolution for discriminating between members of particular taxa such as Bifidobacterium, allowing an accurate representation of the sample bacterial composition. Conclusions Our present microbiome study, comparing the discriminatory power of full-length and short-read sequencing, clearly illustrated the analytical advantage of sequencing the full-length 16S rRNA gene.

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STUDY QUESTION Can preimplantation genetic testing for aneuploidy (PGT-A) improve the live birth rate and reduce the miscarriage rate in patients with recurrent pregnancy loss (RPL) caused by an abnormal embryonic karyotype and recurrent implantation failure (RIF)? SUMMARY ANSWER PGT-A could not improve the live births per patient nor reduce the rate of miscarriage, in both groups. WHAT IS KNOWN ALREADY PGT-A use has steadily increased worldwide. However, only a few limited studies have shown that it improves the live birth rate in selected populations in that the prognosis has been good. Such studies have excluded patients with RPL and RIF. In addition, several studies have failed to demonstrate any benefit at all. PGT-A was reported to be without advantage in patients with unexplained RPL whose embryonic karyotype had not been analysed. The efficacy of PGT-A should be examined by focusing on patients whose previous products of conception (POC) have been aneuploid, because the frequencies of abnormal and normal embryonic karyotypes have been reported as 40–50% and 5–25% in patients with RPL, respectively. STUDY DESIGN, SIZE, DURATION A multi-centre, prospective pilot study was conducted from January 2017 to June 2018. A total of 171 patients were recruited for the study: an RPL group, including 41 and 38 patients treated respectively with and without PGT-A, and an RIF group, including 42 and 50 patients treated respectively with and without PGT-A. At least 10 women in each age group (35–36, 37–38, 39–40 or 41–42 years) were selected for PGT-A groups. PARTICIPANTS/MATERIALS, SETTING, METHODS All patients and controls had received IVF-ET for infertility. Patients in the RPL group had had two or more miscarriages, and at least one case of aneuploidy had been ascertained through prior POC testing. No pregnancies had occurred in the RIF group, even after at least three embryo transfers. Trophectoderm biopsy and array comparative genomic hybridisation (aCGH) were used for PGT-A. The live birth rate of PGT-A and non-PGT-A patients was compared after the development of blastocysts from up to two oocyte retrievals and a single blastocyst transfer. The miscarriage rate and the frequency of euploidy, trisomy and monosomy in the blastocysts were noted. MAIN RESULT AND THE ROLE OF CHANCE There were no significant differences in the live birth rates per patient given or not given PGT-A: 26.8 versus 21.1% in the RPL group and 35.7 versus 26.0% in the RIF group, respectively. There were also no differences in the miscarriage rates per clinical pregnancies given or not given PGT-A: 14.3 versus 20.0% in the RPL group and 11.8 versus 0% in the RIF group, respectively. However, PGT-A improved the live birth rate per embryo transfer procedure in both the RPL (52.4 vs 21.6%, adjusted OR 3.89; 95% CI 1.16–13.1) and RIF groups (62.5 vs 31.7%, adjusted OR 3.75; 95% CI 1.28–10.95). Additionally, PGT-A was shown to reduce biochemical pregnancy loss per biochemical pregnancy: 12.5 and 45.0%, adjusted OR 0.14; 95% CI 0.02–0.85 in the RPL group and 10.5 and 40.9%, adjusted OR 0.17; 95% CI 0.03–0.92 in the RIF group. There was no difference in the distribution of genetic abnormalities between RPL and RIF patients, although double trisomy tended to be more frequent in RPL patients. LIMITATIONS, REASONS FOR CAUTION The sample size was too small to find any significant advantage for improving the live birth rate and reducing the clinical miscarriage rate per patient. Further study is necessary. WIDER IMPLICATION OF THE FINDINGS A large portion of pregnancy losses in the RPL group might be due to aneuploidy, since PGT-A reduced the overall incidence of pregnancy loss in these patients. Although PGT-A did not improve the live birth rate per patient, it did have the advantage of reducing the number of embryo transfers required to achieve a similar number live births compared with those not undergoing PGT-A. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by the Japan Society of Obstetrics and Gynecology and grants from the Japanese Ministry of Education, Science, and Technology. There are no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A

33Species-level genetic characterization of complex bacterial communities has important 34 clinical applications. In the present study, we assessed the performance of full-length 35 16S rRNA gene analysis of human gut microbiota using the nanopore long-read 36 sequencer MinION™. A new strategy for library construction with an optimized primer 37 set overcame PCR-associated bias and produced accurate taxonomic classifications of a 38 broad range of bacterial species. Our present microbiome study, comparing the 39 discriminatory power of full-length and short-read sequencing, clearly illustrated the 40 analytical advantage of sequencing the full-length 16S rRNA gene, which provided 41 higher species-level resolution and accuracy. 42 43 Keywords: 44 16S rRNA, gut microbiota, metagenome, MinION™, nanopore sequencing 45 46 4 Background 47 Recent advances in DNA sequencing technology have had a revolutionary impact on 48 clinical microbiology [1]. Next-generation sequencing (NGS) technology enables 49 parallel sequencing of DNA on a massive scale to generate vast quantities of accurate 50 data. NGS platforms are now increasingly used in the field of clinical research [2]. 51 Metagenomic sequencing offers numerous advantages over traditional culture-based 52 techniques that have long been the standard test for detecting pathogenic bacteria. This 53 method is particularly useful for characterizing uncultivable bacteria and novel 54 pathogens [3].55 Among the metagenomic sequencing strategies, amplicon sequencing of the 16S 56 ribosomal RNA (rRNA) gene has proven to be a reliable and efficient option for 57 taxonomic classification [4, 5]. The bacterial 16S rRNA gene contains nine variable 58 regions (V1 to V9) that are separated by highly conserved sequences across different 59 taxa. For bacterial identification, the 16S rRNA gene is first amplified by polymerase 60 chain reaction (PCR) with primers annealing to conserved regions and then sequenced.61 The sequencing data are subjected to bioinformatic analysis in which the variable 62 regions are used to discriminate between bacterial taxa [6]. 63 Since the conventional parallel-type short-read sequencer cannot yield reads covering 64 the full length of the 16S rRNA gene [7], several regions of it have been targeted for 65 sequencing, which often causes ambiguity in taxonomic classification [8]. New 66 sequencing platforms have overcome these technical restrictions, particularly those 67 affecting read length. A prime example is the MinION™ sequencer from Oxford 68Nanopore Technologies, which is capable of producing long sequences with no 69 theoretical read length limit [9][10][11]. MinION™ sequencing targets the entire 16S rRNA 70 gene, allowing the identification of bacteria with more accuracy and sensitivity [12, 13]. 71Furthermore, MinION™ produces sequencing data in real time, which reduces 72 turnaround time for data processing [14, 15]. 73 5Given these features of MinION™ sequencing, we had previously conducted full-length 74 16S amplicon sequencing analyse...

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