A Novel Next-Generation Sequencing Approach without Donor-Derived Material for Acute Rejection and Infection Monitoring in Solid Organ Transplantation

Background: Donor-derived cell free DNA (ddcf DNA) has been reported as a universal noninvasive biomarker for rejection monitoring in heart, kidney, liver, and lung transplantation. Current approaches based on next-generation sequencing for quantification of ddcf DNA, although promising, may be restricted by the requirement for donor material, as donor samples may not be available. Methods: We proposed a novel next-generation sequencing approach without donor-derived material and compared the non-donor-derived approach and the donor-derived approach using simulation testing and 69 clinical specimens. We also evaluated the performance for acute rejection and infection monitoring in lung transplantation. Results: The non-donor-derived approach reached similar efficacy as the donor-derived approach with a significant linear correlation of R2 = 0.98. Subsequent validation in clinical specimens demonstrated significant difference between the acute rejection group (4.83% ± 2.11%, mean ± SD) and the non-rejection group (1.61% ± 0.63%, mean ± SD) (P ’s t test). With the cut-off value of 2.999, our approach had 90.48% sensitivity (95% CI, 69.62% - 98.83%), 100% specificity (95% CI, 91.59% - 100%), and AUC 0.9266 (95% CI, 0.8277 - 1.026). The test also had the ability to simultaneously detect infectious agents, especially cytomegalovirus, as compared with the clinical test. Conclusion: The proposed approach without donor-derived material could potentially be used to monitor acute rejection and infection in lung transplantation and may be applied to other types of solid organ transplantation.

染色体水平的大熊猫基因组揭示其亚种分化及进化特征

现生的大熊猫包含两个亚种——四川亚种和秦岭亚种.本研究利用第三代基因组测序技术在染色体层次上组装了迄今为止最为完整的大熊猫两个亚种的基因组,且秦岭亚种的基因组为首次组装.通过对25只大熊猫的高深度测序和分化时间的估算,发现大熊猫四川亚种和秦岭亚种之间的分化时间在距今约1.0到1.2万年前.进一步的比较基因组分析发现,大熊猫基因组上DACH2基因调控元件的特异性丢失以及SYT6基因的特异性位点突变是大熊猫较其他哺乳动物的繁殖率低的重要原因之一,而四川亚种IQCD基因正选择进化的结果则是四川亚种比秦岭亚种具有较高繁殖率的主要原因之一.最后,本研究发现大熊猫Hippo通路上诸基因的快速进化和一些基因调控元件上的特异性突变位点,可能是导致大熊猫具有较小的内脏器官以应对食性改变和减少能量代谢的适应性进化结果.

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes

The vagina contains at least a billion microbial cells,dominated by lactobacilli.Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age,as well as cervical,fecal,and salivary samples from a second cohort of 632 women.Factors such as pregnancy history,delivery history,cesarean section,and breastfeeding were all more important than menstrual cycle in shaping the microbiome,and such information would be necessary before trying to interpret differences between vagino-cervical microbiome data.Greater proportion of Bifidobacterium breve was seen with older age at sexual debut.The relative abundance of lactobacilli especially Lactobacillus crispatus was negatively associated with pregnancy history.Potential markers for lack of menstrual regularity,heavy flow,dysmenorrhea,and contraceptives were also identified.Lactobacilli were rare during breastfeeding or post-menopause.Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome.Gut and salivary microbiomes,plasma vitamins,metals,amino acids,and hormones showed associations with the vagino-cervical microbiome.Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.

Cervicovaginal microbiome dynamics after taking oral probiotics

The vaginal microbiota is less complex than the gut microbiota,and the colonization of Lactobacillus in the female vagina is considered to be critical for reproductive health.Oral probiotics have been suggested as promising means to modulate vaginal homeostasis in the general population.In this study,60 Chinese women were followed for over a year before,during,and after treatment with the probiotics Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14.Shotgun metagenomic data of 1334 samples from multiple body sites did not support a colonization route of the probiotics from the oral cavity to the intestinal tract and then to the vagina.Our analyses enable the classification of the cervicovaginal microbiome into a stable state and a state of dysbiosis.The microbiome in the stable group steadily maintained a relatively high abundance of Lactobacilli over one year,which was not affected by probiotic intake,whereas in the dysbiosis group,the microbiota was more diverse and changed markedly over time.Data from a subset of the dysbiosis group suggests this subgroup possibly benefited from supplementation with the probiotics,indicating that probiotics supplementation can be prescribed for women in a subclinical microbiome setting of dysbiosis,providing opportunities for targeted and personalized microbiome reconstitution.

Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

The oral cavity of each person is home to hundreds of bacterial species.While taxa for oral diseases have been studied using culture-based characterization as well as amplicon sequencing,metagenomic and genomic information remains scarce compared to the fecal microbiome.Here,using metagenomic shotgun data for 3346 oral metagenomic samples together with 808 published samples,we obtain 56,213 metagenome-assembled genomes(MAGs),and more than 64%of the 3589 species-level genome bins(SGBs)contain no publicly available genomes.The resulting genome collection is representative of samples around the world and contains many genomes from candidate phyla radiation(CPR)that lack monoculture.Also,it enables the discovery of new taxa such as a genus Candidatus Bgiplasma within the family Acholeplasmataceae.Large-scale metagenomic data from massive samples also allow the assembly of strains from important oral taxa such as Porphyromonas and Neisseria.The oral microbes encode genes that could potentially metabolize drugs.Apart from these findings,a strongly male-enriched Campylobacter species was identified.Oral samples would be more user-friendly collected than fecal samples and have the potential for disease diagnosis.Thus,these data lay down a genomic framework for future inquiries of the human oral microbiome.