School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia.
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
PLoS One. 2020 May 22;15(5):e0233557. doi: 10.1371/journal.pone.0233557. eCollection 2020.
Intestinal bacterial dysbiosis is evident in children with cystic fibrosis (CF) and intestinal viruses may be contributory, given their influence on bacterial species diversity and biochemical cycles. We performed a prospective, case-control study on children with CF and age and gender matched healthy controls (HC), to investigate the composition and function of intestinal viral communities. Stool samples were enriched for viral DNA and RNA by viral extraction, random amplification and purification before sequencing (Illumina MiSeq). Taxonomic assignment of viruses was performed using Vipie. Functional annotation was performed using Virsorter. Inflammation was measured by calprotectin and M2-pyruvate kinase (M2-PK). Eight CF and eight HC subjects were included (50% male, mean age 6.9 ± 3.0 and 6.4 ± 5.3 years, respectively, p = 0.8). All CF subjects were pancreatic insufficient. Regarding the intestinal virome, no difference in Shannon index between CF and HC was identified. Taxonomy-based beta-diversity (presence-absence Bray-Curtis dissimilarity) was significantly different between CF and HC (R2 = 0.12, p = 0.001). Myoviridae, Faecalibacterium phage FP Taranis and unclassified Gokushovirinae were significantly decreased in CF compared with HC (q<0.05). In children with CF (compared to HC), the relative abundance of genes annotated to (i) a peptidoglycan-binding domain of the peptidoglycan hydrolases (COG3409) was significantly increased (q<0.05) and (ii) capsid protein (F protein) (PF02305.16) was significantly decreased (q<0.05). Picornavirales, Picornaviridae, and Enterovirus were found to positively correlate with weight and BMI (r = 0.84, q = 0.01). Single-stranded DNA viruses negatively correlated with M2-PK (r = -0.86, q = 0.048). Children with CF have an altered intestinal virome compared to well-matched HC, with both taxonomic and predicted functional changes. Further exploration of Faecalibacterium phages, Gokushovirinae and phage lysins are warranted. Intestinal viruses and their functions may have important clinical implications for intestinal inflammation and growth in children with CF, potentially providing novel therapeutic targets.
肠道细菌失调在囊性纤维化 (CF) 患儿中很明显，肠道病毒也可能是一个促成因素，因为它们会影响细菌物种多样性和生化循环。我们对 CF 患儿和年龄、性别匹配的健康对照 (HC) 进行了一项前瞻性病例对照研究，以研究肠道病毒群落的组成和功能。通过病毒提取、随机扩增和纯化 (Illumina MiSeq) 对粪便样本进行病毒 DNA 和 RNA 富集。使用 Vipie 对病毒进行分类分配。使用 Virsorter 进行功能注释。通过钙卫蛋白和 M2-丙酮酸激酶 (M2-PK) 测量炎症。纳入 8 例 CF 和 8 例 HC 受试者（50%为男性，平均年龄分别为 6.9 ± 3.0 岁和 6.4 ± 5.3 岁，p = 0.8）。所有 CF 患者均存在胰腺功能不全。关于肠道病毒组，CF 和 HC 之间的 Shannon 指数无差异。基于分类的 beta 多样性（存在-不存在 Bray-Curtis 不相似性）在 CF 和 HC 之间存在显著差异（R2 = 0.12，p = 0.001）。与 HC 相比，CF 中肌尾病毒科、拟杆菌噬菌体 FP Taranis 和未分类的 Gokushovirinae 显著减少（q<0.05）。与 HC 相比，CF 患儿（与 HC 相比）中注释为（i）肽聚糖水解酶的肽聚糖结合域的基因相对丰度显著增加（q<0.05）和（ii）衣壳蛋白（F 蛋白）（PF02305.16）显著减少（q<0.05）。小核糖核酸病毒科、小核糖核酸病毒科和肠道病毒与体重和 BMI 呈正相关（r = 0.84，q = 0.01）。单链 DNA 病毒与 M2-PK 呈负相关（r = -0.86，q = 0.048）。与匹配良好的 HC 相比，CF 患儿的肠道病毒组发生了改变，在分类和预测功能上均发生了变化。进一步探索拟杆菌噬菌体、Gokushovirinae 和噬菌体溶素是值得的。肠道病毒及其功能可能对 CF 患儿的肠道炎症和生长具有重要的临床意义，可能为新的治疗靶点提供依据。
