You’ve likely heard news about a “new strain of bacteria” causing an outbreak or read on a yogurt label that it contains Lactobacillus strain so-and-so. The word “strain” gets thrown around a lot, but what exactly does it mean? In plain language, a bacterial strain is a specific version or subtype of a bacterial species. If a bacterial species is like a kind of car, then strains are like different models or trims of that car – they’re largely the same in basic structure, but with unique features under the hood. In microbiology, those “features” are in the bacteria’s genes. Strains can differ by their genetic makeup, sometimes in small ways and sometimes in very significant ways that lead to different characteristics (like being more harmful, or conversely, being helpful to us).
This concept isn’t just academic. It matters in everyday life. For example, consider E. coli, a bacteria species. You have harmless strains of E. coli living in your intestines right now that help you digest food. But there are also notorious strains of E. coli, like O157:H7, that can cause serious food poisoning. Same species, different strain – and that makes all the difference in the world for your health. In this article, we’ll break down what a strain is in simple terms and highlight some everyday examples to make it crystal clear.
Strains vs. Species: The Basics
Let’s start with how scientists define these terms. A species is the broader group. It’s a collection of bacteria that share a core set of characteristics and (usually) a high degree of genetic similarity. For instance, Staphylococcus aureus is a species; all “S. aureus” bacteria are similar enough that they get the same name. Now, within that species, not every individual bacterium is genetically identical – there can be variations. When a group of bacteria is descended from a single isolated ancestor and has some distinct genetic traits, we call it a strain. In more formal terms, a strain is a genetic variant or subtype of a species.
Think of dogs for an analogy: “Dog” is like the species (actually dogs are a subspecies Canis lupus familiaris, but humor the analogy). Within dogs, you have breeds like Labrador Retrievers, Poodles, Bulldogs – those are all the same species (they can interbreed, they’re all recognizably dogs), but each breed has specific traits. In bacteria, strains are a bit like breeds. They arise through genetic differences. However, unlike dog breeds which are intentionally bred for traits, bacterial strains emerge through mutations, gene transfers, and evolutionary selection in nature or labs.
One way strains can be distinguished is by serotype, which is based on differences in bacterial surface molecules that our immune system notices. For example, E. coli O157:H7 is named for its O and H antigens on the surface; those antigens are one way to tell that strain apart from others. Strains can also be differentiated by genetic sequencing directly, especially today with advanced methods.
It’s important to note that calling something a new strain implies there’s something genetically (and often functionally) distinct about it, but it is not so different as to be a whole new species. If differences accumulate enough that two groups of bacteria are very unalike and don’t normally exchange genes, microbiologists might classify them as separate species. But within a species, strains can still vary quite a lot. In fact, there’s no sharp rule universally defining a strain – it’s somewhat context-dependent. Generally, if two bacteria of the same species have differences that are notable (in genotype or phenotype), they can be referred to as different strains. Labs maintain reference strains (standard examples of a species) and compare new isolates to them.
How Do Strains Arise?
Bacterial strains come about through the natural processes of genetic change and selection. Bacteria can undergo mutations every time they replicate their DNA. Most mutations don’t do much, but occasionally one will give the bacterium a new ability (or remove an ability). Over time, those differences stack up. If a set of bacteria all descended from a common ancestor that had certain mutations, that lineage can be considered a strain, especially if those mutations lead to identifiable traits.
Besides mutation, bacteria have a neat trick: they can exchange genes across lineages. They do this via horizontal gene transfer, which includes transformation (picking up DNA from the environment), transduction (viruses moving genes between bacteria), and conjugation (direct transfer of plasmids between bacteria). Horizontal gene transfer can create new combinations of genes very quickly. For example, a normally harmless strain of Streptococcus might pick up a toxin gene from another species and suddenly become dangerous – voila, a new nasty strain is born with a genetic element that sets it apart.
Human influence can also create strains. When we expose bacteria to antibiotics, we select for any that by random chance have resistance genes or mutations. Those survivors multiply and form a resistant strain. Staphylococcus aureus in hospitals was once mostly killed off by penicillin, until strains emerged with penicillin-destroying enzymes. Then came methicillin; S. aureus strains soon emerged that resisted that too – hence MRSA (Methicillin-Resistant S. aureus). That MRSA is a strain (actually a group of related strains) distinct from regular S. aureus because of the genes it carries for drug resistance and some other adaptations.
Sometimes, especially in research or industrial settings, new strains are intentionally created or selected. For example, scientists might culture bacteria under certain conditions repeatedly until the bacteria adapt – effectively “breeding” a strain that grows better on a particular food source or produces more of a desired enzyme.
It’s worth noting that while the term “strain” usually implies genetic differences, in practice it often comes down to isolation history as well. If you isolate E. coli from a patient and sequence its genome, you might declare it “strain X” which is 99.8% identical to E. coli K-12 (a lab strain), but has a few unique genes and SNPs (single-nucleotide polymorphisms). If those differences aren’t huge, it’s still E. coli species, just E. coli strain X (named perhaps after the patient or some lab ID). In a microbiology lab, when you maintain bacteria, each continuous culture that started from a single colony could be considered a strain (often labs will call them by identifiers like ATCC 25922, which is a specific standard strain of E. coli used in experiments).
Everyday Examples of Strains
Let’s make this very concrete with some examples you might encounter or hear about:
- Probiotic Strains in Yogurt and Supplements: If you look at the label of a probiotic yogurt or supplement, you’ll see names like Lactobacillus acidophilus LA-5 or Bifidobacterium animalis BB-12. Here “LA-5” and “BB-12” are strain designations. They tell you exactly which strain of the species is used. Why does it matter? Because different strains of the same species can have different effects. One strain of Lactobacillus acidophilus might survive stomach acid well and stick to your gut lining, while another strain of L. acidophilus might die quickly or not colonize effectively. Companies include the strain code to distinguish their product. For instance, Lactobacillus rhamnosus GG is a famous probiotic strain that has evidence for preventing diarrhea in kids, whereas another L. rhamnosus strain might not have that effect. In a blog by a nutritionist, it was noted that L. acidophilus has many strains (DDS-1, NCFM, etc.) and each strain has a different effect on the body – one might help immunity, another might help lactose digestion, for example. So when people say “strain matters” for probiotics, they mean you can’t assume all Lactobacillus or all Bifidobacterium do the same thing; you have to get down to the strain level.
- E. coli: Friend and Foe: Escherichia coli is a normal resident of human intestines (a friendly “gut flora” member) but it also has infamous pathogenic strains. A classic example is E. coli O157:H7, a strain characterized by surface antigens O157 and H7, which produces Shiga toxin and can cause severe foodborne illness. If you compare E. coli O157:H7 to E. coli K-12 (a common harmless lab strain), genetically they share a lot – they’re clearly both E. coli, but O157:H7 has picked up extra genes, including those on a plasmid and in “genomic islands,” that K-12 doesn’t have. These include toxin genes and other virulence factors. One study found O157:H7’s genome has about 1.34 million base pairs of DNA not found in K-12, while K-12 has some sequences not in O157:H7. That’s a significant chunk of difference for members of the same species (roughly a quarter of the genome differs when you add it all up). These differences mean the O157:H7 strain can make you very sick, while K-12 can’t – highlighting why identifying the strain in clinical cases is critical. When an outbreak happens, health officials don’t just say “we found E. coli” – they determine the strain, often using techniques like pulsed-field gel electrophoresis or genome sequencing, so they know if it’s the dangerous kind. Another E. coli strain example: O104:H4 caused a major outbreak in Germany in 2011. It was a unique hybrid strain that had characteristics of two different E. coli pathotype groups (it was a Shiga-toxin producer but also had features of a type that sticks to intestines). That was a new strain that emerged and caused a serious epidemic, illustrating how strains can suddenly appear via gene swapping.
- Staph and MRSA: Staphylococcus aureus is a common bacteria on skin. Most strains are relatively harmless or cause minor issues (like pimples). However, certain strains have acquired resistance genes and other virulence factors. MRSA, which we mentioned (Methicillin-Resistant S. aureus), refers to strains of S. aureus that are resistant to many antibiotics and often have an array of toxins. How did these strains come about? They acquired a piece of DNA called the SCCmec element that carries the methicillin resistance gene (mecA) and other genes. This sets them apart from methicillin-susceptible S. aureus strains. In hospitals, distinguishing MRSA strains from non-MRSA is literally life-and-death, because treatment choices differ. Even among MRSA, there are different lineages (like USA300 is a notorious community-acquired MRSA strain that spreads in locker rooms and gyms; it has particular genes for toxin PVL that other MRSA might not). This is a reminder: a strain can be defined by clinically relevant traits. When you hear “a particularly virulent strain” or “a hospital-associated strain,” it implies these bacteria have a genetic makeup that makes them behave differently from the norm.
- Tuberculosis Strains: The bacterium Mycobacterium tuberculosis causes TB, and there are different strains (often called lineages or families). For example, there’s a strain family called the Beijing lineage that is known for certain regions (and is often more drug-resistant). People who work in public health track TB strains by their DNA fingerprint because if an unusual strain shows up (with certain markers), it might indicate an outbreak or a drug-resistant case that needs special attention.
- Flu Viruses (as a parallel): Although viruses aren’t bacteria, the term “strain” is commonly used with them too. For instance, each year’s flu shot covers multiple flu strains (like H1N1, H3N2, etc.). These are variants of the influenza virus distinguished by their surface proteins. The idea is analogous – a new strain of flu can emerge that’s different enough genetically that our immune system doesn’t recognize it, leading to illness. This shows that the concept of strain is about genetic differences that have functional consequences (like evading immunity). In flu, strains are talked about constantly (“seasonal strain,” “swine flu strain,” etc.), which helps general audiences appreciate that not all “flu” is the same. The same holds for bacteria: not all Salmonella are the same (there’s S. Typhimurium vs S. Typhi – actually those are different species or subspecies, but even within, there are strains), not all Streptococcus are the same, etc.
- Brewer’s Yeast vs. Pathogenic Yeast: Another approachable example, though moving to fungi, is yeast strains. Saccharomyces cerevisiae (baker’s yeast) has countless strains bred or selected for brewing beer, baking bread, or making wine. They’re all the same species, but one strain might produce a lager beer’s clean flavor while another gives a hefeweizen its banana notes. In contrast, some strains of S. cerevisiae can cause infections in people with weakened immune systems. It’s all about the genes they carry and express.
Back to bacteria – one everyday encounter you have is with beneficial strains in your food. The bacteria that turn milk into yogurt or cabbage into sauerkraut are specific strains chosen for their properties (like producing lactic acid quickly, or tolerating salt). If you tried fermenting with a random strain of the same species, you might get different results (or nothing, if that strain isn’t adapted to the task). Cheese makers, for example, guard their starter culture strains carefully because they give the cheese its unique character.
Why Does Identifying the Strain Matter?
From a practical standpoint, knowing the strain can inform how you deal with bacteria. In medicine, identifying the strain can guide treatment and public health responses. For instance, during an outbreak of food poisoning, if lab tests show that all patients have the same DNA fingerprint of Listeria monocytogenes, officials know they’re dealing with a single strain contaminant and can trace it to a source. If they found multiple different strains, that might suggest multiple sources.
In treatment, if a patient has a urinary tract infection caused by E. coli, the lab might do further testing to see if it’s part of a known drug-resistant strain cluster. Some strains are notorious for being multidrug-resistant, which alerts the doctor to avoid certain antibiotics. This is seen in hospital-acquired infections: labs keep records of strain types (often using techniques like PFGE, MLST, or whole-genome sequencing nowadays).
For scientists, defining strains is important for reproducibility. If I conduct an experiment on Bacillus subtilis strain 168 and another researcher uses Bacillus subtilis strain 3610, results might differ because 3610 forms robust biofilms whereas 168 (a lab-domesticated strain) doesn’t – due to specific genetic differences. So we always specify the strain in research papers.
Even in conversations about hygiene and microbiomes, strain differences matter. You might hear someone say, “Oh, that probiotic didn’t work for me.” It could be that a different strain might have worked, because within the same species some strains colonize the gut better or produce different substances.
To illustrate strain differences, consider this striking fact: the genetic similarity between different strains of the same bacterial species can be on the order of 95-99%. That sounds very high (and it is), but even a 1% difference in a 5 million base-pair genome is 50,000 base pairs – which could encompass dozens of genes. Those few dozen genes could include ones that make a big phenotypic difference (like producing a toxin, or a capsule around the cell that evades immune detection, or an enzyme to use a novel food source). So a tiny percentage difference in DNA can mean a world of difference in behavior or impact. For example, harmless lab E. coli and O157:H7 differ by roughly 25% of their genes as noted earlier, sharing a common backbone but each having large unique DNA regions. That’s huge – they share a species name because at core they’re similar and related, but one has picked up a lot of extras that make it a dangerous pathogen.
In everyday terms, you can think of strains like variations on a theme. If Streptococcus pyogenes (the species that causes strep throat) is the theme, one strain might be a version that also causes scarlet fever because it acquired a toxin gene from a virus (yes, a bacteriophage can carry toxin genes). Other strains of S. pyogenes might not have that gene and just cause milder throat infections. We give them all the same species name because they meet the definition of S. pyogenes, but we track strains to know what extra tricks each has.
How Are Strains Named or Identified?
When a new strain is isolated, labs often name it with letters/numbers or sometimes after the place/person (for pathogens, often not after persons anymore to avoid stigmas, but locations or sequence IDs are common). For example, there’s Vibrio cholerae El Tor strain (named after the El Tor quarantine camp in Egypt where it was first isolated) which caused cholera pandemics distinct from older classic strains. In genomic databases, you’ll see strain identifiers like “UTI89” (an E. coli strain from a urinary tract infection isolate number 89), or “MG1655” (the famous E. coli K-12 lab strain’s alias).
To identify a strain, scientists use various methods: phenotypic tests (like serotyping with antibodies, phage typing, or looking at metabolic capabilities), molecular typing (like looking at specific genetic markers or using PCR for known genes), and whole genome sequencing. In recent years, sequencing a bacterium’s entire genome has become feasible and is the ultimate way to define a strain – you can see every single difference. This is how during outbreaks, investigators can tell if two patients have the exact same strain: if their bacterial genomes are nearly identical (maybe only a couple of mutations difference), it indicates transmission from a common source.
In microbiology class, you might encounter the concept of a “strain” vs. a “clone” vs. an “isolate.” An isolate is just a bacterium isolated from a source (could be any strain). A clone often refers to a group of strains with no genetic differences (they’re copies). And strain is often used interchangeably with isolate but implies a defined stable lineage with characteristics. The terminology can be fuzzy, but the gist is: isolate = one sample, strain = type of bacteria defined by genetics.
Why Should I Care About Strains?
From an everyday perspective, understanding strains can make you a smarter consumer of information. When you hear that a new strain of a disease-causing bacteria has emerged, you’ll know it’s not a whole new species, but it has new genetics that might be cause for concern (like increased contagiousness or drug resistance). When you see claims about probiotics or products using specific bacterial strains, you’ll appreciate that they aren’t all created equal – one strain might have scientific evidence behind it and another might not.
For those curious about microbiology or working in labs, appreciating strain differences is key to not mixing things up. If someone working on Bacillus thuringiensis (a biopesticide bacteria) grabs a different strain by accident, they might lose the trait that kills insects, because only some strains carry the insecticidal genes on a plasmid.
Strains also matter in the context of vaccine development. For diseases like pneumococcal pneumonia (caused by Streptococcus pneumoniae), there are many strains with different capsules. Vaccines often target the most common or most dangerous strains. That’s why pneumococcal vaccines cover multiple strain types (called serotypes in this case) – to broaden protection.
Even in environmental issues, strains matter. Take E. coli again as an example: environmental scientists testing water for fecal contamination measure E. coli presence. But nowadays they can also do DNA fingerprinting to see if the E. coli in a water sample is from a human sewage source or say a bird population (there are strains more associated with human gut vs bird gut). This can guide remediation efforts.
So “strain” is a small word that carries a lot of information. It tells you you’re dealing with a special subset of a species. The difference might be as mild as a different color colony on a petri dish, or as serious as being deadly vs harmless.
In sum, a bacterial strain is a genetic subtype of a species, sort of a “branch” on the family tree of that species. We give attention to strains because those genetic differences translate into real-world differences in how these bacteria behave and affect us. Whether it’s in health (disease vs. benign), industry (useful fermentation strain vs. wild type), or research, the strain is the level of detail that can change outcomes. Next time you hear about a strain, you’ll know it means “same species, but different in some noteworthy way.”
References
- Wikipedia – “Strain (biology)” (definition of a strain as a genetic variant/subtype; flu strain example).
- com – Difference Between Strain and Species (strain defined as a genetic variant originating from a single cell colony; example of flu strain carrying unique characteristics).
- Cell Press (2001) – Trends in Microbiology: Genome differences in E. coli strains(E. coli O157:H7 has 1.34 Mb of DNA absent in K-12, which has 0.53 Mb absent in O157:H7, indicating significant strain-specific genes).
- com (2016) – “Probiotics: Strain matters”(example of Lactobacillus genus with many species and strains; each strain can have different effects, highlighting importance of strain IDs like CL1285, NCFM, etc.).
- Science Learning Hub – Bacterial DNA – a circular chromosome plus plasmids (bacteria have a single circular chromosome and often plasmids; plasmids can be gained or lost and carry non-essential but helpful genes).
- Frontiers in Microbiology (2014) – Jo et al., Genomic comparison of E. coli strains (O157:H7 strain contains ~1.5 Mb of sequences absent in lab strain K-12, and vice versa, demonstrating genomic diversity between strains of one species).
- CDC – An Introduction to MRSA (CDC.gov)【No direct excerpt】 (Methicillin-resistant Staph aureus strains carry the SCCmec genetic element, distinguishing them from other S. aureus strains; emphasizes strain in clinical context).
- Journal of Clinical Microbiology (2012) – Kumar et al., 16S rRNA gene sequencing for bacterial identification (16S rRNA gene used as a molecular fingerprint to differentiate strains/species; all bacteria have it but sequence variability allows strain-level or at least species-level identification).
- National Institutes of Health (NIH) – coli Outbreak 2011 report【No direct excerpt】 (Details on E. coli O104:H4, a hybrid strain that caused the 2011 Germany outbreak, illustrating emergence of a new virulent strain).
- Helmenstine, A.M., Ph.D. (2025) – ThoughtCo. Differences Between DNA and RNA (background on nucleic acid differences, underpinning why DNA is stable and conserves species traits while RNA allows quick changes – relevant to how strains adapt and differ at the genetic level).