Thursday 27 January 2022

Ultrasmall bacteria from the environment have adapted to live inside humans


The microbes that live inside our mouths (the oral microbiome) impact our overall health in many ways that are not yet fully understood. Some bacteria cause inflammation, leading to periodontitis and other systemic diseases, such as cardiovascular disease and diabetes. Other oral organisms have been associated with certain types of cancer.


Scientists are working to understand how these microbes interact with one another and our bodies to tease out their individual roles in health and disease.


Among the diverse bacterial species living within our mouths is a group belonging to the Candidate Phyla Radiation (CPR) – which may become the Patescibacteria. These organisms are ultra-small, adopt a unique symbiotic lifestyle with their host bacteria. 



ultrasmall cell size (200 to 300 nm), and a reduced genome of only 705 genes”.


The only bacteria within the CPR to be examined in-depth are a group called TM7, which were cultivated for the first time by Forsyth Institute researcher Dr. Xuesong He in 2014.


Researchers have developed a new model system using the first isolated human oral TM7 strain, TM7x, and its host bacterium, Actinomyces odontolyticus. Researchers used the model system to experimentally study these tiny bacteria, testing a hypothesis for how TM7 adapted to live inside humans, and providing empirical data to confirm previous genomic studies.


Scientists have found TM7 in many different environments, including soil, groundwater, and the bodies of other mammals. Studies have shown that while maintaining a remarkably similar genome overall, the TM7 found in human mouths are unique from those in other environments because they have acquired a gene cluster encoding the arginine deiminase system (ADS).


Researchers hypothesized that TM7 acquired ADS as an evolutionary advantage to help them adapt and survive in the human oral cavity.


It was established that ADS helped TM7x break down arginine, a process that produces the compounds Adenosine triphosphate (ATP) and ammonia. The increased abundance of ATP and ammonia benefitted TM7x by increasing its infectivity, or ability to multiply. It also protected TM7x and its host bacterium from acid stress, a condition that microbes frequently encounter in the human oral cavity due to the acid created when bacteria feed on and metabolize dietary carbohydrates.


This study also adds to a growing body of evidence that TM7 bacteria may play a more protective role in oral health than researchers initially thought. For example, abundance of TM7 is found to increase drastically in the mouths of patients with periodontal disease, which led scientists to assume the bacteria contributed to the disease.




Jing Tian, Daniel R. Utter, Lujia Cen et al. Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment. Proceedings of the National Academy of Sciences, 2022; 119 (2): e2114909119 DOI: 10.1073/pnas.2114909119


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

Wednesday 26 January 2022

Climate change increases microbial diversity


Rising temperatures are causing a "growing diversity" of Vibrio bacteria in the sea around the UK, new research shows.


The study found two Vibrio species -- Vibrio rotiferianus and Vibrio jasicida - that have never been recorded in UK waters before. These species can harm sea creatures such as shellfish, but the increasing range of Vibrio species also raises concerns for human health.


Some Vibrio bacteria can cause gastroenteritis when eaten in raw or undercooked shellfish, and the bacteria can also cause skin infections. The researchers say the spread of Vibrio species has resulted in a "worldwide surge" of Vibriosis infections in humans and aquatic animals.



The key pattern for this is with sea-surface temperatures rising due to climate change. Understanding how these changes will affect ecologically and commercially important species and the people that rely on them will be crucial moving forward, in order to mitigate against them.


Journal Reference:


Jamie Harrison, Kathryn Nelson, Helen Morcrette, Cyril Morcrette, Joanne Preston, Luke Helmer, Richard W. Titball, Clive S. Butler, Sariqa Wagley. The increased prevalence of Vibrio species and the first reporting of Vibrio jasicida and Vibrio rotiferianus at UK shellfish sites.. Water Research, 2021; 117942 DOI: 10.1016/j.watres.2021.117942


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

Tuesday 25 January 2022

New framework to understand biological systems


Despite the fundamental role networks play in how scientists understand the dynamics and properties of complex systems, reconstructing networks from large-scale experimental data is a challenge.


In systems biology and microbial ecology -- the study of microbes in the environment and their interactions with each other -- the challenges of reconstructing these networks can be compounded by difficulty unraveling direct and indirect interactions, or the ability of one element in a system to impact another, either with or without direct interaction.


Researchers have devised a new conceptual framework for disentangling direct and indirect relationships in association networks. The framework is called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity).


The researchers tested on the framework on synthetic gene expression and microbial community data.


Specifically, the iDIRECT framework reduces mathematical challenges to network reconstruction, including ill-conditioning, self-looping and interaction strength overflow. Using simulation data to benchmark results, the researchers demonstrated high prediction accuracies using the iDIRECT framework.




Naijia Xiao, Aifen Zhou, Megan L. Kempher, Benjamin Y. Zhou, Zhou Jason Shi, Mengting Yuan, Xue Guo, Linwei Wu, Daliang Ning, Joy Van Nostrand, Mary K. Firestone, Jizhong Zhou. Disentangling direct from indirect relationships in association networks. Proceedings of the National Academy of Sciences, 2022; 119 (2): e2109995119 DOI: 10.1073/pnas.2109995119


Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (

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