基于基因组的假小链双歧杆菌与卷曲乳杆菌代谢互作分析

The Genome-Scale Analysis of Metabolic Interaction Between Bifidobacterium pseudocatenulatum and Lactobacillus crispatus

肠道菌群是一个复杂的微生态系统。肠道内的不同微生物之间相互作用,以功能群(guild)的形式响应环境的扰动,但其互作关系仍不明确。一名小胖威利综合征(prader-willi syndrome,PWS)儿童在接受了一种高膳食纤维食谱的营养干预后,肥胖表型改善,肠道内假小链双歧杆菌和卷曲乳杆菌被富集,两类菌丰度变化呈现正相关关系。针对这一现象,我们对假小链双歧杆菌和卷曲乳杆菌之间的互作关系进行了探究。假小链双歧杆菌C95分离自该名PWS儿童干预后的粪便样品,该菌基因组上拥有丰富的碳水化合物利用基因、胆汁酸抗性及粘附性功能因子相关基因和编码产生胞外多糖的基因簇。本研究中,我们从相同样本中分离到一株卷曲乳杆菌B4,该菌基因组上拥有丰富的碳水化合物利用基因、S层蛋白基因、细菌素分泌基因和乙酸合成的关键基因。然后,我们利用Netcooperate对C95菌株与B4菌株之间的代谢互补关系进行预测。结果表明,C95菌株能够为B4菌株提供57%的代谢底物,拓宽B4菌株的碳水化合物和核苷酸代谢通路。本研究利用菌株全基因组信息,寻找到假小链双歧杆菌C95与卷曲乳杆菌B4之间的代谢互作证据,为这种数学模型找到的微生物共变化关系赋予实际的生物学意义。

Gut microbiota is a complicated micro-ecosystem,in which bacteria interact with each other and form as functional groups(guilds)to respond to environmental perturbations.However,the interaction between different microorganisms remains unclear.After one child with prader-willi syndrome(PWS)received a high-fiber dietary intervention,his bioclinical parameters related to obesity were improved.Furthermore,Bifidobacterium pseudocatenulatum and Lactobacillus crispatus in the child’s gut were enriched,and there was a positive correlation between their abundance.Based on this phenomenon,we attempted to explore the interaction between Bifidobacterium pseudocatenulatum and Lactobacillus crispatus.Bifidobacterium pseudocatenulatum C95 was isolated from the post-intervention fecal sample of the PWS child and harbored abundant carbohydrate utilization genes,genes related to bile acid resistance and adhesion as well as gene cluster encoding exopolysaccharide.In this study,we obtained Lactobacillus crispatus B4 from the same fecal sample.The genome analysis showed that B4harbors abundant carbohydrate utilization genes as well as genes related to S-layer protein,bacteriocin production and acetate production.Then,we used Netcooperate to predict the metabolic interaction between C95 and B4strains.The results showed that C95 can provide 57%metabolic substrates for B4 and broaden the pathways for carbohydrate and nucleotide metabolism of B4.This study provided a clue for metabolic interaction between Bifidobacterium pseudocatenulatum C95 and Lactobacillus crispatus B4 based on the genomes of the strains,and gave this co-abundance relationship between different microorganisms found by mathematical model the real biological significance.