Bacteriophage Species

A team of biologists from the Wellcome Sanger Institute, the European Bioinformatics Institute and the Universidad de los Andes has identified 142,809 species of bacteriophages — viruses that infect and replicate in bacteria — living in the human gut.

Camarillo-Guerrero et al. introduce the Gut Phage Database, a collection of 142,809 non-redundant viral genomes (10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Image credit: Camarillo-Guerrero et al., doi: 10.1016/j.cell.2021.01.029.

Using a DNA-sequencing method called metagenomics, Wellcome Sanger Institute’s Dr. Luis Camarillo-Guerrero and colleagues explored and catalogued the biodiversity of the viral species found in 28,060 public human gut metagenomes and 2,898 bacterial isolate genomes cultured from the human gut.

“It’s important to remember that not all viruses are harmful, but represent an integral component of the gut ecosystem,” said co-author Dr. Alexandre Almeida, a postdoctoral researcher at the European Bioinformatics Institute and the Wellcome Sanger Institute.

“For one thing, most of the viruses we found have DNA as their genetic material, which is different from the pathogens most people know, such as SARS-CoV-2 or Zika, which are RNA viruses.”

“Secondly, these samples came mainly from healthy individuals who didn’t share any specific diseases.”

“It’s fascinating to see how many unknown species live in our gut, and to try and unravel the link between them and human health.”

The researchers also identified a previously unknown clade of bacteriophages, named Gubaphage.

This was found to be the second most prevalent virus clade in the human gut, after crAssphage, which was discovered in 2014.

“An important aspect of our work was to ensure that the reconstructed viral genomes were of the highest quality,” Dr. Camarillo-Guerrero said.

“A stringent quality control pipeline coupled with a machine learning approach enabled us to mitigate contamination and obtain highly complete viral genomes.”

“High-quality viral genomes pave the way to better understand what role viruses play in our gut microbiome, including the discovery of new treatments such as antimicrobials from bacteriophage origin.”

The team’s results form the basis of the Gut Phage Database, a highly curated database of phage genomes that will be an invaluable resource for those studying bacteriophages and the role they play on regulating the health of both our gut bacteria and ourselves.

“Bacteriophage research is currently experiencing a renaissance,” said Dr. Trevor Lawley, a researcher at the Wellcome Sanger Institute.

“This high-quality, large-scale catalogue of human gut viruses comes at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future virome studies.”

The results appear in the journal Cell.

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Luis F. Camarillo-Guerrero et al. 2021. Massive expansion of human gut bacteriophage diversity. Cell 184 (4): 1098-1109; doi: 10.1016/j.cell.2021.01.029