PDF(Pubmed)
Abstract：
UNASSIGNED: Analyzing bacterial microbiomes consistently using next-generation sequencing (NGS) is challenging due to the diversity of synthetic platforms for 16S rRNA genes and their analytical pipelines. This study compares the efficacy of full-length (V1-V9 hypervariable regions) and partial-length (V3-V4 hypervariable regions) sequencing of synthetic 16S rRNA genes from human gut microbiomes, with a focus on childhood obesity.
UNASSIGNED: In this observational and comparative study, we explored the differences between these two sequencing methods in taxonomic categorization and weight status prediction among twelve children with obstructive sleep apnea.
UNASSIGNED: The full-length NGS method by Pacbio® identified 118 genera and 248 species in the V1-V9 regions, all with a 0% unclassified rate. In contrast, the partial-length NGS method by Illumina® detected 142 genera (with a 39% unclassified rate) and 6 species (with a 99% unclassified rate) in the V3-V4 regions. These approaches showed marked differences in gut microbiome composition and functional predictions. The full-length method distinguished between obese and non-obese children using the Firmicutes/Bacteroidetes ratio, a known obesity marker (p = 0.046), whereas the partial-length method was less conclusive (p = 0.075). Additionally, out of 73 metabolic pathways identified through full-length sequencing, 35 (48%) were associated with level 1 metabolism, compared to 28 of 61 pathways (46%) identified through the partial-length method. The full-length NGS also highlighted complex associations between body mass index z-score, three bacterial species (Bacteroides ovatus, Bifidobacterium pseudocatenulatum, and Streptococcus parasanguinis ATCC 15912), and 17 metabolic pathways. Both sequencing techniques revealed relationships between gut microbiota composition and OSA-related parameters, with full-length sequencing offering more comprehensive insights into associated metabolic pathways than the V3-V4 technique.
UNASSIGNED: These findings highlight disparities in NGS-based assessments, emphasizing the value of full-length NGS with amplicon sequence variant analysis for clinical gut microbiome research. They underscore the importance of considering methodological differences in future meta-analyses.
UNASSIGNED: In this observational and comparative study, we explored the differences between these two sequencing methods in taxonomic categorization and weight status prediction among twelve children with obstructive sleep apnea.
UNASSIGNED: The full-length NGS method by Pacbio® identified 118 genera and 248 species in the V1-V9 regions, all with a 0% unclassified rate. In contrast, the partial-length NGS method by Illumina® detected 142 genera (with a 39% unclassified rate) and 6 species (with a 99% unclassified rate) in the V3-V4 regions. These approaches showed marked differences in gut microbiome composition and functional predictions. The full-length method distinguished between obese and non-obese children using the Firmicutes/Bacteroidetes ratio, a known obesity marker (p = 0.046), whereas the partial-length method was less conclusive (p = 0.075). Additionally, out of 73 metabolic pathways identified through full-length sequencing, 35 (48%) were associated with level 1 metabolism, compared to 28 of 61 pathways (46%) identified through the partial-length method. The full-length NGS also highlighted complex associations between body mass index z-score, three bacterial species (Bacteroides ovatus, Bifidobacterium pseudocatenulatum, and Streptococcus parasanguinis ATCC 15912), and 17 metabolic pathways. Both sequencing techniques revealed relationships between gut microbiota composition and OSA-related parameters, with full-length sequencing offering more comprehensive insights into associated metabolic pathways than the V3-V4 technique.
UNASSIGNED: These findings highlight disparities in NGS-based assessments, emphasizing the value of full-length NGS with amplicon sequence variant analysis for clinical gut microbiome research. They underscore the importance of considering methodological differences in future meta-analyses.
摘要：
■由于16SrRNA基因的合成平台及其分析管道的多样性，使用下一代测序（NGS）始终分析细菌微生物群落具有挑战性。这项研究比较了来自人类肠道微生物组的合成16SrRNA基因的全长（V1-V9高变区）和部分长度（V3-V4高变区）测序的功效，专注于儿童肥胖。
■在这项观察和比较研究中，我们在12名阻塞性睡眠呼吸暂停儿童中,探讨了这两种测序方法在分类分类和体重状态预测方面的差异.
■Pacbio®的全长NGS方法在V1-V9地区确定了118属和248种，全部为0%的未分类率。相比之下,Illumina®的部分长度NGS方法在V3-V4区域检测到142属(未分类率39%)和6种(未分类率99%)。这些方法在肠道微生物组组成和功能预测方面显示出明显的差异。全长方法使用Firmicutes/拟杆菌比率区分肥胖和非肥胖儿童，一个已知的肥胖标记(p=0.046)，而部分长度法的结论较少（p=0.075）。此外,在通过全长测序确定的73个代谢途径中，35(48%)与1级代谢相关，与通过部分长度方法鉴定的61条路径中的28条(46%)相比。全长NGS还强调了体重指数z-score之间的复杂关联，三种细菌(卵形拟杆菌，假双歧杆菌，和副血链球菌ATCC15912)，和17种代谢途径。两种测序技术都揭示了肠道菌群组成与OSA相关参数之间的关系，与V3-V4技术相比，全长测序提供了对相关代谢途径的更全面了解。
■这些发现突出了基于NGS的评估中的差异，强调具有扩增子序列变异分析的全长NGS在临床肠道微生物组研究中的价值。他们强调了在未来的荟萃分析中考虑方法差异的重要性。
■在这项观察和比较研究中，我们在12名阻塞性睡眠呼吸暂停儿童中,探讨了这两种测序方法在分类分类和体重状态预测方面的差异.
■Pacbio®的全长NGS方法在V1-V9地区确定了118属和248种，全部为0%的未分类率。相比之下,Illumina®的部分长度NGS方法在V3-V4区域检测到142属(未分类率39%)和6种(未分类率99%)。这些方法在肠道微生物组组成和功能预测方面显示出明显的差异。全长方法使用Firmicutes/拟杆菌比率区分肥胖和非肥胖儿童，一个已知的肥胖标记(p=0.046)，而部分长度法的结论较少（p=0.075）。此外,在通过全长测序确定的73个代谢途径中，35(48%)与1级代谢相关，与通过部分长度方法鉴定的61条路径中的28条(46%)相比。全长NGS还强调了体重指数z-score之间的复杂关联，三种细菌(卵形拟杆菌，假双歧杆菌，和副血链球菌ATCC15912)，和17种代谢途径。两种测序技术都揭示了肠道菌群组成与OSA相关参数之间的关系，与V3-V4技术相比，全长测序提供了对相关代谢途径的更全面了解。
■这些发现突出了基于NGS的评估中的差异，强调具有扩增子序列变异分析的全长NGS在临床肠道微生物组研究中的价值。他们强调了在未来的荟萃分析中考虑方法差异的重要性。
