Scientists Discover a New “Secret Resident” in Our Microbiome

Mysterious RNA “Obelisks” in the Human Microbiome: Do They Reshape Our View of Infection and Health?

Imagine discovering a new class of genetic entities hiding quietly in our guts and mouths—neither classic viruses nor known bacteria, but something altogether different. That is precisely what some cutting-edge research has uncovered. In this article, I walk you through what we currently know about these enigmatic “obelisks,” what they might mean for microbiology and medicine, and why physicians and scientists should pay attention—even before we have definitive proofs.

From Newspaper Rumors to Scientific Revelation
The story begins with news articles that caught public attention: reports that scientists had discovered strange new “life forms” lurking in the human digestive system. Some news outlets poorly defined or sensationalized them, calling them “mysterious entities.” But the deeper scientific account comes from microbiology research, not sensational journalism.

The credible account describes that researchers mining vast RNA sequence databases identified rod-shaped RNA fragments found in gut and mouth microbial communities. These fragments do not match any known virus or RNA element. Because of their shape and novel structure, the researchers named them “obelisks.”

In lab and computational analyses, they found these obelisks in a subset of human microbiome samples—suggesting that they are neither extremely rare nor ubiquitous, but intriguingly present across individuals. These features make them a fascinating subject of inquiry.

What Are Obelisks? A Closer Look at the Evidence
The Discovery Strategy
Instead of isolating a suspicious pathogen, the researchers turned to existing RNA transcriptome datasets obtained from human stool and saliva (i.e. from microbiome sequencing efforts). They looked for RNA sequences that are:

1. Looped or circular in secondary structure (a hallmark of some noncoding RNA elements).
   
   
2. Noncoding (i.e. sequences that do not match any known protein-coding genes).
   
   
3. Unassigned to any known viral or microbial genome.
   

They found nearly 30,000 distinct candidate segments fitting these criteria. Some of them appear to exist within bacterial cells themselves.

Structural Features

• Circular RNA with rod-like folding: Unlike many viroids (plant infecting agents that are circular RNAs), the obelisks’ predicted 3D folding is elongated—hence the name “obelisks.”
  
  
• Small genome size (~1,000 base pairs): They are modest in length compared to many viruses.
  
  
• Potential protein-coding capacity: Interestingly, unlike classic viroids, several obelisks seem to carry short open reading frames (ORFs) that could encode small proteins (called “oblins” in preliminary reports).
  
  
• Lack of conventional viral shell genes: They do not appear to code for capsid or envelope proteins typical of viruses.
  

These features place them in a gray zone: more complex than simple viroids but lacking the full machinery of viruses.

Prevalence in Human Samples

• In stool (gut) microbiome samples, obelisks were detected in about 7% of metatranscriptomes.
  
  
• In saliva (oral) microbiomes, their presence was more frequent—detected in around 50% of samples examined.
  
  
• Some individual datasets from past studies (over 400 people) showed obelisk sequences in nearly 10% of participants.
  

One particular host bacterium identified is Streptococcus sanguinis (a common oral microbe). In that species, some obelisk sequences matched DNA reads suggesting integration or carriage within the bacterial cell.

Why Obelisks Are Scientifically Intriguing (and Confounding)
A New Domain of Genetic Agents?
Classic biological taxonomy divides life into cell-based organisms (bacteria, archaea, eukaryotes) and non-cellular agents (viruses, plasmids, viroids). Obelisks may fall somewhere between these categories—neither clearly a virus, nor simply RNA debris. They represent a possible new class of mobile genetic elements or “virus-like agents.”

Host Interaction and Impact
Because they appear to reside inside bacterial hosts, obelisks might exert influence via:

• Modulation of bacterial gene expression (e.g. via RNA interference, promoter interference).
  
  
• Horizontal transfer between microbial species (if transmissible).
  
  
• Indirect effects on the human host through alteration of microbiome dynamics (e.g. altering bacterial metabolism, immune interactions, or microbial competition).
  

If obelisks can alter host bacteria behavior or gene expression, then their downstream influence might extend to human physiology, immunity, or disease states.

Evolutionary Implications

• Origin: Are obelisks descended from ancient viroids, or do they represent diverged plasmid-like elements?
  
  
• Evolutionary relationships: They show no close homology to known viruses or viroids, implying a distinct evolutionary lineage.
  
  
• Role in the RNA world?: Some scientists speculate that obelisks might preserve relics of ancient RNA-based systems.
  

Challenges and Caveats: Why We Must Be Cautious
Because this field is so new, many questions remain unresolved. As a clinician or researcher, it is vital to balance excitement with skepticism.

Lack of Experimental Validation
So far, obelisks have been inferred via computational analysis. No isolated obelisk particle has been physically purified, cultured, or visualized. Their replication cycle, mechanism of cell entry (if any), and life stage remain hypothetical.

Contamination or Artifacts?
When mining massive sequence databases, there is always risk of contamination, misassembly, or artifacts—RNA fragments from diet, technical noise, or lab reagents. Robust controls are needed to rule out these possibilities.

Effects Unknown
We don’t yet know whether obelisks are harmless “passengers,” beneficial symbionts, or potential pathogens (for bacteria or even indirectly for humans). Associations with disease are purely speculative at this point.

Host Range Unclear
While S. sanguinis is one confirmed host, the full host spectrum is unknown. Many obelisks are detected in microbial communities without clear host assignment.

Clinical Relevance Still Unproven
From a medical standpoint, it is far too early to salt obelisks into diagnostic or therapeutic models. But they represent a frontier worth watching.

Implications for Microbiome Science and Medicine
Even though obelisks remain speculative in many respects, their discovery touches on several key domains in modern microbiome research and medicine.

Enriching the Concept of the Microbiome
Our current view of the microbiome includes bacteria, archaea, fungi, viruses (bacteriophages, viruses that infect human cells), and mobile genetic elements (plasmids, transposons). The addition of obelisks suggests we still have blind spots in our understanding of microbial “dark matter” — genetic entities we do not yet fully appreciate.

Potential Biomarker Role
If future studies find that specific obelisk sequences correlate with disease states (e.g. inflammatory bowel disease, dysbiosis, colorectal cancer, periodontal disease), they could become biomarkers of microbial imbalance or early disease.

Therapeutic Modulation of Microbiome
If we learn how obelisks interact with bacterial hosts, it may become possible to modulate them—either by suppressing pathogenic obelisks or engineering beneficial ones to deliver therapeutic RNA functions (a form of synthetic microbiome gene therapy).

Microbiome Stability and Resilience
The presence of obelisks may affect microbiome resilience to perturbations (e.g. antibiotics, diet shifts, infections). Their dynamics could underlie “memory” or hysteresis in microbial communities.

Helping to Define Non-Cellular Life
From a fundamental biology perspective, the existence of obelisks blurs boundaries between living and nonliving systems. They push us to refine definitions of infection, replication, and genomic autonomy.

How Physicians and Researchers Should Think About Obelisks Now
Here are some guiding principles and recommended next steps:

1. Treat obelisks as a “known unknown”: Be open to their existence, but avoid jumping to conclusions about disease causality.
   
   
2. In clinical microbiome studies, consider mining existing sequencing datasets for obelisk-like sequences as exploratory research.
   
   
3. Integrate multi-omics: Combine metagenomic DNA data, metatranscriptomics (RNA), and metabolomics to see whether obelisk presence associates with functional shifts in microbiome.
   
   
4. Design in vitro validation: Attempt to isolate obelisk-bearing bacteria, purify RNA, and validate replication or transmission in controlled cultures.
   
   
5. Correlate with clinical phenotypes: In cohorts of patients with gut or oral disease (e.g. IBD, periodontitis), test whether obelisks are enriched or correlated with biomarkers.
   
   
6. Collaborate with computational biologists: The discovery of obelisks relies heavily on custom algorithms and large-scale data mining. Clinicians interested in this space should partner with experts in bioinformatics and RNA structure modeling.
   
   
7. Monitor the literature: Because the foundational work is still in preprint stage, we should watch for peer-reviewed validation, follow-up studies, and critiques.
   

A Thought Experiment: Could Obelisks Contribute to Disease?
To make the discussion more concrete, let’s imagine hypothetical scenarios in which obelisks might affect human health.

Scenario A: Obelisk-Driven Bacterial Virulence Shift
An obelisk integrates into a commensal gut bacterium and upregulates a bacterial toxin gene under stress conditions, tipping the microbe toward pathogenic behavior. This could manifest clinically as increased intestinal inflammation or a flare of Crohn’s disease.

Scenario B: Microbiome Destabilization after Antibiotics
Following broad-spectrum antibiotic use, residual obelisks in surviving bacteria help those strains regrow preferentially by modulating transcription. The result: altered microbial community composition that persists longer than expected.

Scenario C: Therapeutic RNA Delivery via Obelisk Vectors
In the future, scientists might repurpose obelisks as vectors—by engineering their small RNA cargo to deliver regulatory RNAs into gut bacteria, suppressing harmful pathways or boosting beneficial ones.

These are speculative, yet they anchor the importance of probing obelisks experimentally, not dismissing them as curiosities.

Summary Themes (for Quick Recall)

• RNA fragments called obelisks have been discovered computationally in human gut and mouth microbiomes.
  
  
• They are circular RNAs with rod-like predicted folding and some appear to encode small proteins (oblins).
  
  
• Detected in ~7% of gut, ~50% of oral microbiome datasets, with Streptococcus sanguinis as one putative host.
  
  
• Obelisks challenge traditional boundaries between viruses, viroids, plasmids, and novel mobile elements.
  
  
• Their functional impact on bacteria and on human health remains unproven.
  
  
• A cautious but open approach is warranted: combine computational mining, wet-lab validation, and clinical correlation.
  
  
• Obelisks could, if validated, reshape microbiome science, open new biomarker or therapeutic directions, and expand our definitions of infection and life.