How a Mislabeled Microbe Revealed a New Species
Genetic analysis reveals that what scientists classified as a single species actually comprises multiple distinct organisms
For two long years, a 12-year-old girl suffered from persistent abdominal pain with no clear cause 1 . When doctors isolated what appeared to be the well-known bacterium Clostridium difficile from her stool sample, the mystery seemed solved. But something didn't add up—the standard identification methods had caught an impostor.
Through advanced genetic detective work, scientists would eventually discover this was no ordinary C. difficile, but rather a member of the enigmatic Hungatella genus, with a genetic makeup so distinct it revealed an entirely new understanding of bacterial classification 1 5 8 .
This diagnostic mystery, solved through cutting-edge genomic analysis, would uncover a fundamental truth: what scientists had historically classified as a single species, Hungatella hathewayi, actually comprised multiple genetically distinct organisms with important implications for human health and disease 1 5 8 .
Hungatella hathewayi is a normal resident of the human gut microbiome, the complex community of microorganisms living in our digestive tracts 1 6 . For years, it was considered a harmless commensal bacterium, quietly coexisting with its human host. However, emerging evidence began to link this microbe to serious infections, including septicemia and bacteremia—dangerous bloodstream infections that can be fatal 1 6 .
Gut microbiome studies revealed that high levels of H. hathewayi were associated with severe COVID-19 cases 1 .
Research has found this bacterium approximately fivefold more abundant in colorectal cancer tissues compared to healthy tissues 6 .
The taxonomic history of Hungatella reveals why understanding these bacteria has proven so challenging. Initially classified as Clostridium hathewayi, the organism was later reclassified into the Hungatella genus in 2014 when scientists recognized it was more closely related to Hungatella effluvii than to other clostridia 6 . This reclassification highlights the ongoing evolution of microbial taxonomy as genetic analysis techniques become more sophisticated.
At the heart of this story lies a powerful biological concept: genetic distance—a measure of the genetic divergence between species or populations 3 . Think of it as a molecular clock that ticks as mutations accumulate over time; the more differences in DNA sequences between two organisms, the longer ago they diverged from a common ancestor 3 .
Genetic distance provides crucial insights into evolutionary relationships that often can't be determined through physical characteristics alone, especially for microorganisms that look nearly identical under a microscope 3 .
Visualization: Genetic distance between Hungatella strains showing clear separation into distinct groups
When scientists applied genetic distance measures to Hungatella genomes, they made a startling discovery: strains historically classified as H. hathewayi displayed such significant genetic differences that they likely represented multiple distinct species 1 5 8 .
| Measure | Key Principle | Application in Microbiology |
|---|---|---|
| Average Nucleotide Identity (ANI) | Compares overall DNA sequence similarity between genomes | Species demarcation (strains with >95% ANI typically belong to same species) |
| Genome-to-Genome Distance (GGDC) | Calculates overall genomic similarity using multiple features | Complementary to ANI for species boundary determination |
| Nei's Standard Distance | Assumes genetic differences arise from mutation and genetic drift | Works well when divergence time is proportional to genetic change |
| Cavalli-Sforza Chord Distance | Geometric approach representing populations on a hypersphere | Visualizing population relationships without biological assumptions |
The groundbreaking study that uncovered the true nature of Hungatella began with the puzzling case of the 12-year-old girl with chronic abdominal pain 1 . Here's how the scientific detective work unfolded, step by step:
When the patient's stool sample arrived at the laboratory, researchers used standard clinical methods, culturing it on selective medium specifically designed for C. difficile 1 . The colonies that grew displayed characteristics suspiciously similar to C. difficile—similar morphology, odor, and Gram stain characteristics 1 .
The researchers performed additional tests, including cytotoxicity assays on human cervical cancer cells (HeLa cells) and antibiotic susceptibility testing 1 . While the isolate was a strict anaerobe and produced spores—both characteristics of C. difficile—something didn't align perfectly with typical C. difficile behavior, prompting the team to dig deeper.
Scientists extracted DNA from the bacterial isolate and performed whole-genome sequencing using Illumina technology 1 2 . This process involved breaking the DNA into fragments, sequencing them, and then computationally reassembling the pieces into a complete genomic picture—much like solving a complex jigsaw puzzle 1 .
The research team then compared their isolate's genome against 22 publicly available H. hathewayi genomes and one H. effluvii genome 1 . They employed multiple analysis methods to ensure robustness:
The genetic evidence revealed a striking pattern: the historical reference strain (DSM-13479) and the clinical isolate represented two genetically distinct groups, despite both being classified as H. hathewayi 1 . The data clearly showed that some genomes labeled as H. hathewayi actually belonged to entirely different genera, including Clostridium and Faecalicatena 1 .
| Genomic Characteristic | Finding | Interpretation |
|---|---|---|
| Pan-genome structure | Open | High genomic diversity with many unique genes |
| Species groups identified | Two clear groups | One containing reference H. hathewayi strain, another classified as H. effluvii |
| Misclassified genomes | Multiple instances | Some H. hathewayi genomes belonged to Clostridium and Faecalicatena genera |
| Overall genomic diversity | Larger than previously appreciated | Previous taxonomic definitions were inadequate |
The findings from this genetic detective work were profound. The researchers demonstrated that:
The original H. hathewayi reference strain was not representative of the diversity within the species 1
Two clearly differentiated groups existed—one containing the reference strain, and a second representing H. effluvii 1
The Hungatella species possess an open pan-genome with high genomic diversity 1
Perhaps most importantly, the study highlighted that conventional laboratory identification methods can be misleading, potentially resulting in misdiagnosis and inappropriate treatment 1 . The isolate that initially appeared to be C. difficile was in fact a different organism with potentially different virulence properties and antibiotic susceptibilities.
| Aspect | Impact of Accurate Identification | Consequences of Misidentification |
|---|---|---|
| Patient Treatment | Appropriate antibiotic selection | Potential treatment failure |
| Understanding Virulence | Accurate assessment of disease potential | Misattribution of pathogenicity |
| Epidemiological Tracking | Correct monitoring of infection sources | Inaccurate public health data |
| Therapeutic Development | Targeted drug and vaccine design | Wasted resources on incorrect targets |
Unraveling this bacterial mystery required sophisticated tools and techniques. Here are the key components of the microbial forensics toolkit:
The story of Hungatella illustrates a fundamental shift occurring throughout microbiology: we're moving beyond classifying microorganisms based solely on their appearance or simple biochemical tests to understanding them through their genetic blueprints. As the research team concluded, "This study highlights the importance of correctly assigning taxonomic identification, particularly in disease-associated strains, to better understand virulence and therapeutic options" 1 .
This genetic detective work has opened new avenues for understanding how our microbiome influences health and disease. The revelation that H. hathewayi actually comprises multiple genetically distinct species may explain why some strains remain harmless gut residents while others become dangerous pathogens—a difference that could lie in their unique genetic makeup.
As sequencing technologies become faster and more accessible, we're likely to discover more cases of microbial mistaken identity throughout the bacterial world, each discovery potentially opening new possibilities for diagnosing, treating, and preventing disease. The quiet revolution in microbial classification is just beginning, promising to transform our relationship with the invisible world within and around us.