Aujoulat Fabien, Roudière Laurent, Picaud Jean-Charles, Jacquot Aurélien, Filleron Anne, Neveu Dorine, Baum Thierry-Pascal, Marchandin Hélène, Jumas-Bilak Estelle
Université Montpellier 1, UMR 5119 ECOSYM, Equipe Pathogènes et Environnements Unité de Bactériologie, U.F.R. des Sciences pharmaceutiques et biologiques, 15, Avenue Charles Flahault, BP 14491, Montpellier, Cedex 5, 34093, France.
Centre Hospitalier de Fréjus, Laboratoire de bactériologie, 240 avenue de Saint-Lambert BP 110 83608, Fréjus, France.
BMC Microbiol. 2014 Dec 31;14:325. doi: 10.1186/s12866-014-0325-0.
BACKGROUND: The very-preterm infant gut microbiota is increasingly explored due to its probable role in the development of life threatening diseases. Results of high-throughput studies validate and renew the interest in approaches with lower resolution such as PCR-Temporal Temperature Gel Electrophoresis (TTGE) for the follow-up of dominant microbiota dynamics. We report here an extensive longitudinal study of gut colonization in very preterm infants. We explored by 16S rDNA-based PCR-TTGE a total of 354 stool specimens sampled during routine monitoring from the 1(st) to the 8(th) week of life in 30 very pre-term infants born before 30 weeks of gestational age. RESULTS: Combining comparison with a diversity ladder and sequencing allowed affiliation of 50 Species-Level Operational Taxonomic Units (SLOTUs) as well as semi-quantitative estimation of Operational Taxonomic Units (OTUs). Coagulase-negative staphylococci, mainly the Staphylococcus epidermidis, was found in all the infants during the study period and was the most represented (75.7% of the SLOTUs) from the first days of life. Enterococci, present in 60% of the infants were early, highly represented and persistent colonizers of the premature gut. Later Enterobacteriaceae and the genus Clostridium appeared and were found in 10 (33%) and 21 infants (70%), respectively. We showed a high representation of Veillonella in more than a quarter of the infants and being able to persistently colonize premature gut. The genera Anaerococcus, Aquabacterium, Bacillus, Bifidobacterium, Corynebacterium, Micrococcus, Oceanobacillus, Propionibacterium, Pseudomonas, Rothia, Sarcina, Sneathia and Streptococcus were observed as transient or persistent colonizers, each genus being found in a minority of infants. CONCLUSIONS: Despite low resolution, PCR-TTGE remains complementary to high-throughput sequencing-based approaches because it allows the follow-up of dominant bacteria in gut microbiota in a large longitudinal cohorts of preterm neonates. We described the development of pre-term gut microbiota that should be now replaced regarding the functional role of major OTUs.
背景：极早产儿的肠道微生物群因其在危及生命疾病发展中可能发挥的作用而受到越来越多的研究。高通量研究的结果证实并重新激发了人们对低分辨率方法（如聚合酶链反应-时间温度凝胶电泳（TTGE））的兴趣，用于追踪主要微生物群的动态变化。我们在此报告一项关于极早产儿肠道定植的广泛纵向研究。我们通过基于16S rDNA的PCR-TTGE对30例孕周小于30周的极早产儿在出生后第1周至第8周常规监测期间采集的354份粪便标本进行了研究。 结果：将与多样性阶梯的比较和测序相结合，确定了50个物种水平的操作分类单元（SLOTUs），并对操作分类单元（OTUs）进行了半定量估计。在研究期间，所有婴儿中均发现凝固酶阴性葡萄球菌，主要是表皮葡萄球菌，并且从出生第一天起就是最主要的（占SLOTUs的75.7%）。肠球菌存在于60%的婴儿中，是早产儿肠道的早期、高度占优势且持续存在的定植菌。后来肠杆菌科和梭菌属出现，分别在10例（33%）和21例婴儿（70%）中被发现。我们发现韦荣球菌在超过四分之一的婴儿中占比很高，并且能够持续定植于早产儿肠道。厌氧球菌属、水生杆菌属、芽孢杆菌属、双歧杆菌属、棒状杆菌属、微球菌属、海洋芽孢杆菌属、丙酸杆菌属、假单胞菌属、罗氏菌属、八叠球菌属、斯内特菌属和链球菌属被观察到是短暂或持续的定植菌，每个属仅在少数婴儿中被发现。 结论：尽管分辨率较低，但PCR-TTGE仍是基于高通量测序方法的补充，因为它能够在大量极早产新生儿纵向队列中追踪肠道微生物群中的主要细菌。我们描述了早产儿肠道微生物群的发展情况，现在应根据主要OTU的功能作用对其进行更新。
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