Wednesday 22 March 2023

Exploring bacterial dark matter: The case of Omnitrophota

Image by NASA -, Public Domain,


Bacteria are everywhere and they play a big role in almost every facet of life on Earth. Despite their abundance, surprisingly little is known about many microorganisms that have existed for billions of years.


This includes an entire lineage of nano-sized bacteria of the phyla Omnitrophota. These organisms, first discovered based on short fragments of DNA 25 years ago, are common in many environments around the world. Yet they have been poorly understood.


An international research team produced the first large-scale analysis of more than 400 newly sequenced and existing Omnitrophota genomes, uncovering new details about their biology and behaviour. 



The complexity with Omnitrophota is that they're still largely considered microbial dark matter, which means they exist in nature but they cannot yet be cultivated as single species in laboratory studies. Just two species have been microscopically observed to date.


Omnitrophota have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes, novel lineages and novel metabolic traits have been identified.


The first species to be identified was Candidatus Omnitrophus magneticus SKK-01 was described as a large, ovoid putatively free-living magnetic bacterium containing sulphur inclusions.


To present a comprehensive picture of their biology, scientists compared 349 existing and 72 newly mapped genomes of Omnitrophota. This included a review of publicly available data and new samples collected from geothermal environments, freshwater lakes, wastewater, groundwater, and springs located around the world.


The team observed that, in most cases, Omnitrophota measure less than 450 nanometers, which places them among the smallest of all known organisms. The bacterium also displayed genetic markers consistent with symbiosis - possibly as predators or parasites of other microorganisms - which suggested they would have high metabolic rates.


The more researchers learn about their energy conservation pathways and possible lifestyles, the closer they will get to the goal of cultivating them in the lab and bringing them into ‘the light’.


The presence of nanobacteria is of potential concern. The pharmaceutical industry is urged to look for nanobacteria, and to invest in their elimination; vaccines, blood, and blood derivates should be guaranteed nanobacterium-free.


The research appears in the journal Nature Microbiology, titled “Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota.”


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

No comments:

Post a Comment

Pharmaceutical Microbiology Resources

Special offers