title: Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia.
abstract: One of the fundamental methods for cultivating bacterial strains is conventional plating on solid media, but this method does not reveal the true diversity of the bacterial community. In this study, we develop a new technique and introduce a new device we term, I-tip. The I-tip was developed as an in situ cultivation device that allows microorganisms to enter and natural chemical compounds to diffuse, thereby permitting the microorganisms to grow utilizing chemical compounds in their natural environment. The new method was used to cultivate microorganisms from Baikalian sponges, and the results were compared with conventional plating as well as a pyrosequencing-based molecular survey. The I-tip method produced cultures of 34 species from five major phyla, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Firmicutes, and Gammaproteobacteria, 'missing' only two major phyla detected by pyrosequencing. Meanwhile, standard cultivation produced a smaller collection of 16 species from three major phyla, Betaproteobacteria, Firmicutes, and Gammaproteobacteria, failing to detect over half of the major phyla registered by pyrosequencing. We conclude that the I-tip method can narrow the gap between cultivated and uncultivated species, at least for some of the more challenging microbial communities such as those associated with animal hosts.
authors: Department of Environmental Science, Kangwon National University, Chuncheon, Korea.
authors: Dawoon
authors: D
authors: Jung
authors: Eun-Young
authors: EY
authors: Seo
authors: Slava S
authors: SS
authors: Epstein
authors: Yochan
authors: Y
authors: Joung
authors: Jaemin
authors: J
authors: Han
authors: Valentina V
authors: VV
authors: Parfenova
authors: Olga I
authors: OI
authors: Belykh
authors: Anna S
authors: AS
authors: Gladkikh
authors: Tae Seok
authors: TS
authors: Ahn
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development; D001431:Bacteriological Techniques; D004269:DNA, Bacterial / Q000235:genetics; D060106:Lakes / Q000382:microbiology*; D010802:Phylogeny; D011161:Porifera / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012426:Russia
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: culturing device; in situ cultivation; microbial trap; pyrosequencing; unculturable microorganism