Understanding the chain of bacteria discovery

Thanks to next generation gene sequencing, knowledge of bacteria, including probiotics, has exploded. But the pace of knowledge acquisition makes it hard to keep up. Here’s what you need to know.

Can’t keep up with all the news about bacteria? You’re not alone.

As a healthcare professional, using knowledge about bacteria is part of your everyday working life. And while specific bacteria may feel like the bane of your existence, you must also have noticed that there are many more bacteria to be aware of than before. In 1980, there were 1,971 known microbial species.¹Fast forward 40 years, and there are now over 45,000 validated species of bacteria.²

How could that happen? It’s because we’re now able to better differentiate these single celled organisms. Previously, limited differences could be observed for bacteria. For example, we could see their shape, which is why bacteria names containing “coccus” are round and those containing “bacillus” are rod shaped. We could also see how they organized, so bacteria that like to cluster can contain “staphylo” in their names, while bacteria that link as a chain can have “strepto” in their names. But it wasn’t possible to observe the minute differences between single cells.

Molecular biology is a relatively new science that became well-known in the 1950’s and 1960’s when the DNA double helix structure was discovered, and we realized DNA held the blueprint to life. DNA sequencing technology has gotten faster and cheaper, allowing scientists to study and identify more of the bacteria around us. Even now with a whopping 45,000 “validated” species of bacteria, it’s estimated that there are between 2.2 to 4.3 million species in all.³Bacteria are everywhere, making up about 75% of all living species on earth.⁴One scientist who studies taxonomy, Dr. Kostas Konstantinidis of Georgia Institute of Technology, Atlanta, GA, USA, has said, “If we were to classify primates using the same standards that are used to classify E. coli, then all primates – from lemurs to humans to chimpanzees – would belong to a single species.” ⁴So there is still much to learn and discover, and some scientists believe the new knowledge will also lead to an improved taxonomy system.

Fact

Proper nomenclature, or naming, is known as the Bacteriological Code, created by the ICSP. A bacterium’s name normally consists of two parts: the genus and the species. The grammatical protocol for naming is as follows ⁶

Example	Explanation
Lactobacillus acidophilus	A species is identified with its genus + species. Only the genus is spelled with capital letter. Both names are usually Italicized or underlined. (Some protocols want the species to be in plain text.)
L. acidophilus	After the first mention, it is permissible to shorten the genus name to just the capital letter.
Lactobacillus sp.	Use “sp.” In plain text when referring to an unnamed species.
Lactobacillus spp.	Use “spp.” when referring to more than one unnamed species.
Bifodobacterium longum subsp. Infantis	There are many words that can be used to refer to a subspecies, such as biovar, chemovar and pathovar. We use “subsp.” The subspecies indicator is in plain text
Bifodobacterium longum subsp. Infantis Bifin02 (DSM33361) B. longum subsp. Infantis Bifin02 (DSM33361) Bifidobacterium infantis(DSM 33361) “…hereafter referred to as ISTILOS^™”	The ICSP doesn’t give specific guidelines for strain designation. It’s common to write a strain capitalized in plain text. Strain collection accession numbers should be preserved to ensure “chain of custody.” Genus can be shortened. If it is a member of a subspecies, sometimes either the species or subspecies is omitted, in this case species longum Commercial names can also be used after the scientific name has been used once.

The importance of next generation sequencing (NGS)

It's well-known that the Human Genome Project began in 1988 and was completed in 2013, even though only about 92% of the human genome was sequenced at that time. The remaining 8% couldn’t be deciphered until new tools and computational approaches were developed. The complete human genome sequence was finally published in 20228 at a total cost was almost $3 billion USD.⁹ The cost was high, but the value was enormous. Now, next generation sequencing (NGS) and third generation sequencing (TGS) can do the job much faster and cheaper, using the original human genome baseline for comparison.

The same is true when studying bacteria and the microbiome. The earliest bacteria genomes were fully sequenced back in 19952, providing baselines for further study. And since then, next generation sequencing (NGS) has provided massive insights into bacteria and the human microbiome, resulting in the explosion of the number of the number of validated species. In the past, scientists tended to focus studies on bacterial species that contained toxic strains. It wasn’t that long ago that all bacteria were thought to be bad for our health and should be combatted. Healthcare curriculums advocated for liberal antibiotic use. Read about antibiotics and antibiotic resistance here .

Why are probiotics getting new names?

Now that we know the vast majority of bacteria are either harmless or beneficial for health, studies have broadened beyond toxic strains with a new focus on beneficial strains, also called probiotics.

Not only have new bacteria been validated, but molecular biology has enabled us to learn more about bacteria’s homology. So much so that in some instances, earlier classifications no longer make sense and can even become a hindrance. In those cases, project groups can be established to reclassify bacteria based on current knowledge with the goal to leave enough room in the new hierarchy for future discoveries.

Another reason for name changes is that since probiotic strains are now sold as dietary supplements, the strain names tend to change as the bacteria moves from scientific identification to commercial manufacturing. When discovered, the strain name is often a series of letters and numbers, which is good for cataloging but hard to remember. As the strain moves towards commercialization, manufacturing companies often assign commercial names to strains so they are more readily identifiable to consumers. LLG^® and BB-12^® are two of the most well-known probiotic commercial names that refer directly to specific strains, namely Lacticaseibacillus rhamnosus, LGG (previously known as Lactobacillus rhamnosus, LLG^®) and Bifidobacterium animalis subsp. lactis, BB-12^®. Commercial names can also be completely different from scientific names, such as the name ISTILOS^™ for the probiotic strain Bifidobacterium longum subsp. infantis Bifin02 (DSM33361).

Occasionally two companies can sell the same probiotic bacterial strain, but it’s unlikely the strains retain the exact same genetic constellation. That’s because bacteria are ever evolving and easily gain new genetic material via horizontal gene transfer. It requires strict protocols to reproduce a single bacterial strain over time. A genetic test of Chr. Hansen (now Novonesis) probiotic bacteria LGG^® has proven that this strain has retained identical genetic material since it was first isolated in 1985.¹⁰

Reclassifying 42 bacterial phyla
The largest recent taxonomical name change was published in 2022 and includes 42 phyla. While the changes will help standardize science, it has caused dismay among the scientific community who see a big chunk of their work becoming difficult to access, thereby losing the chain of scientific discovery to anyone who isn’t a scholar of taxonomy. Some of the names have simply been updated to align with the new rule that all phyla must be named based on one of its genus but with the same suffix ending in “ota.” But others have received completely new names, for example “Bacillota” replaces “Firmicutes.” Here are name changes of some phyla that have been heavily researched. See the full list here.¹²

Former name	New name as of February 2021	Comments
Firmicutes	Bacillota	Dominates the gut microbiome together with Bacteroidota. Probiotics from the family of lactic acid bacteria Lactobacillaceae belong here.
Bacteroidetes	Bacteroidota	Dominates the gut microbiome together with Bacillota.
Proteobacteria	Pseudomonadota	Includes bacteria such as E. coli, known to cause food poisoning
Actinobacteria	Actinomycetota	Probiotics from the family Bifidobacteriaceae belong here.

Reclassifying 42 bacterial phyla
The genus Lactobacillus was first described in 1901 with Lactobacillus dulbrueckii, a species used in yogurt production. By March 2020, there were 261 species validated under the genus Lactobacillus. Gene sequencing showed large heterogeneity between them – so much so that their homology was unfounded. It took several years to reclassify these bacteria based on genetic markers, and their new classification was released in April 2020. Lactobacillus wasn’t the only genus affected; Paralactobacillus, Pediococcus and 23 novel genera within the Lactobacillaceae family were also reclassified. These microorganisms seem to exist wherever there is fermentation, from fermented mustard and stinky tofu of Taiwan, kimchi in Korea, fermented cabbage in China, kefir from the Caucaus, to sourdough and fermented spirits from around the world, like beer, wine and sake. As well, some of the species originated from the lungs of beaked whales, wild gorillas, jaguars, birds, bees and more.¹³

The Microbiome Times published the below extensive overview of new genera and species names of bacteria commonly studied as probiotics.¹³If you’re interested in seeing all the changes made, here is a tool to quickly search for the new names.

Former name (basonym)	New Name as of April 2020	What this tells us
Lactobacillus delbrueckii subsp. Delbrueckii Lactobacillus delbrueckii subsp. Bulgaricus Lactobacillus Acidophilus Lactobacillus crispatus Lactobacillus gasseri Lactobacillus helveticus Lactobacillus iners Lactobacillus jensenii Lactobacillus johnsonii	No change	These are host adapted organisms (to vertebrates on the one hand and to bees on the other), homofermentative and thermophilic
Lactobacillus casei	Lacticaseibacillus casei	From lacti and casei, derived from milk and cheese.
Lactobacillus paracasei	Lacticaseibacillus paracasei
Lactobacillus rhamnosus	Lacticaseibacillus rhamnosus
Lactobacillus salivarius	Ligilactobacillus salivarius	Ligi=unite; bacteria in a host-adapted lifestyle (for salivarius, in different vertebrate hosts)
Lactobacillus plantarum	Lactiplantibacillus plantarum	Lacti, planti: milk and plant-derived. Plantarum is found in dairy, humans, fermented foods, sourdough… Pentosus was isolated from corn silage, fermented olives, tea, dough, dairy, humans, sewage
Lactobacillus pentosus	Lactiplantibacillus pentosus
Lactobacillus fermentum	Limosilactobacillus fermentum	Limosi: slimy, from the strains ability to produce exopolysaccharides. Fermentum is found in fermented cereals, dairy and humans. Reuteri in birds, rodents, swine, cereal fermentation and sourdough.
Lactobacillus reuteri	Limosilactobacillus reuteri
Lactobacillus brevis	Levilactobacillus brevis	Levi from leavening and relief. L. brevis is isolated from dairy, different foods and animals.
Lactobacillus kefiri	Lentilactobacillus kefiri	Lentilacto: slow growth with lactate. L. kefiri is from the core kefir microbiota.

Reclassifying 42 bacterial phyla
Bifidobacterium were first discovered from the feces of a breastfed infant in 1899 and is one of the major genera inhabiting the gut microbiome. Its form is a Y-shaped rod, hence the term “bifid.”¹⁴Members of the order Bifidobacteriales have a unique ability to metabolize carbohydrates.¹⁵The most well-documented probiotic is the Bifidobacterium animalis subsp. lactis, BB-12^®. It was deposited in the cell culture bank of Chr. Hansen (now Novonesis) in 1983.¹⁶ At that time, it was known as Bifidobacterium bifidum. Scientists later reclassified it as Bifidobacterium animalis, and later gave it a new species name Bifidobacterium lactis. Lactis was then determined not to fulfill the criteria for a species, so it became a subspecies, and the scientific name for BB-12 is now Bifidobacterium animalis subsp. lactis, BB-12.¹⁶ So in the past 40 years the strain has not changed, but its species name has been changed four times. This is just one example of how difficult it can be as a healthcare professional to keep up on the literature about probiotics.

Currently the genus Bifidobacterium comprises 82 species and 12 subspecies.¹⁴ It’s been isolated from the gastrointestinal tracts of humans and non-human mammals, insects and birds, as well as from human blood, sewage, the oral cavity, and fermented milk. Originally thought to be adapted to specific hosts, it’s now known that they are not particularly host specific.¹⁴All of this, together with the fact that there is intense research on strains from the genus Bifidobacterium since they are well-known probiotics, points to the conclusion that a major reclassification of Bifidobacterium may be on the way.

What’s next for probiotic research?
It’s well known that various strains of the same species react differently to stimuli in the microbiome. Even so, most scientific literature doesn’t usually specify strains for the simple reason that scientists aren’t able to do so with confidence.

Next generation sequencing (NGS) has given us massive insights into the world of bacteria. It analyzes the ~1500 bp16S rRNA gene at nine variable regions interspersed throughout the highly conserved 16S sequence. It’s much faster than Sanger sequencing (first generation sequencing), but since the technology produces short sequences, most studies only sequence part of the gene, for example choosing variable 4 or up to three variable regions, such as V3-V5.9 As a result, NGS is not always able to identify on a strain level, nor can it always differentiate closely related species.⁹

This is obviously problematic, as the beneficial effects of probiotics are only reliable on a strain level. While it’s known that every person’s microbiome is unique and therefore it’s unlikely that one probiotic strain will generate the same benefit for every person, it’s curious that some studies use the same bacterial species in nearly identical circumstances and achieve quite different results. One reason for this could be that the studies were unable to identify and study individual strains.

Third generation sequencing (TGS) maps the entire gene sequence.⁹ As it becomes more common, we would expect to see greater predictability and accuracy in studies. And don’t be surprised if bacterial taxonomy experiences new re-alignments.

Strains and names

- keeping track of beneficial bacteria

Thanks to next generation gene sequencing, knowledge of bacteria, including probiotics, has exploded. But the pace of knowledge acquisition makes it hard to keep up. Here’s what you need to know.

Proper nomenclature, or naming, is known as the Bacteriological Code, created by the ICSP. A bacterium’s name normally consists of two parts: the genus and the species. The grammatical protocol for naming is as follows ⁶

Related Articles

Reference list

What are

probiotics?

What to

look for

Our
strains

Strains and names

- keeping track of beneficial bacteria

Thanks to next generation gene sequencing, knowledge of bacteria, including probiotics, has exploded. But the pace of knowledge acquisition makes it hard to keep up. Here’s what you need to know.

Proper nomenclature, or naming, is known as the Bacteriological Code, created by the ICSP. A bacterium’s name normally consists of two parts: the genus and the species. The grammatical protocol for naming is as follows 6

Related Articles

Reference list

What are

probiotics?

What to

look for

Our strains

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Proper nomenclature, or naming, is known as the Bacteriological Code, created by the ICSP. A bacterium’s name normally consists of two parts: the genus and the species. The grammatical protocol for naming is as follows ⁶

Our
strains