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Rare bacterial strain isolated and sequenced: The new bacterial strain belongs to the group Candidatus phylum Dependentiae, a group of organisms that can only grow inside other cells

The development of the field of metagenomics — the study of genetic material from environmental samples — has revolutionized how we observe and discover new species. Many bacteria cannot be independently cultivated in the lab. Sometimes this is because the medium they are grown in is not suitable, sometimes it is because these bacteria thrive only in multispecies communities (such as many bacteria in our gut!) and sometimes this is because they can only grow in relation to another larger organism. A group of bacteria belonging to the final category are Candidatus phylum Dependentiae. Not much is known about this group because thus far, only three strains belonging to it have been isolated. But in a recent study, published in Microbiology Resource Announcements, Professor Masaharu Takemura from Tokyo University of Science (TUS) has succeeded in isolating the fourth such strain — Noda2021.

“Initially we sampled Risoukai Park in the Noda Campus of TUS with the aim of isolating a giant virus by screening it using a common laboratory host ‘Vermamoeba vermiformis.’ However, in the process of doing so we accidentally discovered this rare bacterium that also infects Vermamoeba,” says Dr. Takemura.

To isolate the new strain, Dr. Takemura first cultured a sample obtained from the pond in Risoukai Park and then added it to a culture of Vermamoeba. After growing the Vermamoeba for a few days, he extracted Noda2021 from this and then performed an analysis of its genetic material.

“We found that the Noda2021 strain consists of 1,222,284 base pairs with approximately 38.3% guanine and cytosine (GC) content and 1,287 genes. We then performed a 16S rRNA molecular phylogenetic analysis of the strain and found that it is relatively close to one of the other Candidatus phylum Dependentiae strains isolated so far, ‘Vermiphilus pyriformis,'” explains Dr. Takemura. He also examined the infected Vermamoeba cells under an electron microscope and found that Noda2021 sometimes exhibited a connected cellular structure within its host cells.

“This discovery is evidence that the pond in the Noda campus is microbiologically diverse and ecologically exciting,” says Dr. Takemura. This is also the first time such a strain has been isolated in Japan.

The isolation of this new strain of Candidatus phylum Dependentiae is sure to further our understanding of this curious bacterial group. According to Dr. Takemura, “This bacterium is located in the border region between giant viruses and microbacteria, so we expect it to provide some useful and unique information on the origin and ecological position of both these groups.”

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Materials provided by Tokyo University of Science. Note: Content may be edited for style and length.

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