Bacillota (formerly Firmicutes): the 'fat bacteria' that aren't

If you have ever had a stool test come back with a bar chart, the biggest bar was probably labelled Firmicutes. The report may have told you it means you are "wired for weight gain." Here is what the actual studies say about that bar, and about the phylum that now goes by a new name.

What Bacillota is

Bacillota is a phylum of bacteria: a top-level branch of the bacterial family tree, the same rank at which "chordates" sits among animals. Most of its members have a thick, single-layer cell wall (they stain Gram-positive) — the Negativicutes, which stain Gram-negative, are the standing exception — and a genome relatively poor in the DNA letters G and C, which is why older textbooks call them "low G+C Gram-positives."

The name is new. For decades the phylum was Firmicutes, from the Latin for "tough skin." In 2021 ¹ the International Committee on Systematics of Prokaryotes brought the rank of phylum under its naming code, and Oren and Garrity validly published standardized names for 42 phyla ¹, each built on a type genus. Firmicutes became Bacillota, the new name built on the type genus Bacillus. Nothing about the organisms changed; only the label did. You will still meet the old name on almost every consumer test and in every paper written before the switch, so this entry uses both.

Where it lives in you

Mostly in the large intestine. When Eckburg and colleagues at Stanford sequenced 13,355 ² ribosomal gene sequences from the colon lining and stool of healthy adults in 2005 ², the two dominant phyla were the Firmicutes and the Bacteroidetes, and most of the sequences belonged to species no one had ever grown in a lab ². That picture has held. The Human Microbiome Project, sampling healthy adults across many body sites, found that even healthy people differ remarkably in which microbes they carry, with strong niche specialization from one site to the next ³. The MetaHIT catalogue put numbers on the scale: 3.3 million ⁴ non-redundant microbial genes in the stool of 124 ⁴ Europeans, roughly 150 times ⁴ the human gene count, and at least 160 ⁴ prevalent bacterial species in every single person.

Bacillota do not stop at the gut. Lactobacilli, which belong to this phylum, dominated four of the five ⁸ community types Ravel and colleagues found when they sequenced the vaginal microbiome of 396 ⁸ asymptomatic women. And Staphylococcus aureus, another member, lives chiefly in the nose: Wertheim's review in The Lancet Infectious Diseases calls the nose its main ecological niche in humans ¹³.

What it does for us

Start with the mechanism, because the benefit follows from it. Fibre and resistant starch reach the colon undigested. Gut bacteria ferment them into short-chain fatty acids, and two of those, butyrate and propionate, are the ones Louis and Flint's review credits with a range of health-promoting functions, butyrate being the preferred fuel of the cells lining the colon ⁵. The major butyrate producers they describe, Faecalibacterium prausnitzii, Eubacterium rectale and the Roseburia group, are all Bacillota, and they depend on cross-feeding: one species' lactate or succinate becomes another's raw material ⁵.

The best-studied of those producers has its own evidence. Sokol and colleagues followed Crohn's disease patients after surgical resection and found that a lower share of F. prausnitzii on the gut lining predicted recurrence 6 months ⁶ later. In the lab, the bacterium made human blood cells produce significantly less IL-12 and IFN-gamma and more IL-10, and its culture supernatant blocked NF-kappaB activation, a central inflammation switch ⁶. The caveat, said out loud: the treatment arm of that study was mice with chemically induced colitis, not people. It shows a plausible mechanism, not a proven therapy.

There is also a survival trick. Browne and colleagues at the Sanger Institute managed to culture 137 ⁷ species from healthy human stool that had been written off as unculturable, and their genomes suggested that at least 50–60 % ⁷ of gut bacterial genera make resilient spores. Most of those spore-formers are Bacillota. Spores let oxygen-hating gut bacteria survive the trip between one person and the next, which is likely how much of this community is shared in the first place ⁷.

What it does against us

The same phylum holds some of the most serious pathogens we carry. Clostridioides difficile is a spore-forming Bacillota member that takes over the colon after antibiotics clear its competitors. In active surveillance across 10 ¹² US regions, Lessa and colleagues estimated 453,000 ¹² infections and about 29,000 ¹² deaths in 2011 ¹² alone; 65.8 % ¹² of cases were healthcare-associated, and people 65 ¹² or older had a rate ratio of 8.65 ¹² compared with younger adults. Staphylococcus aureus is the other everyday example: the Wertheim review notes that nasal carriers have a higher risk of going on to infection with their own strain, and that the pathogen's rising antibiotic resistance complicates treatment worldwide ¹³.

Note what these two have in common with the helpful members above: the spore, the thick wall, the persistence. The traits that make Bacillota resilient allies also make its pathogens hard to clear.

The obesity ratio, honestly

Now the bar chart. In 2006 ⁹ Ley, Turnbaugh, Klein and Gordon reported in Nature that 12 ⁹ obese volunteers carried a lower share of Bacteroidetes than lean people, and that the share rose as they lost weight on two ⁹ low-calorie diets. The companion mouse study found that an "obese" microbiome extracted more energy from food and that the trait transferred to germ-free mice ¹⁰. From those papers the Firmicutes/Bacteroidetes ratio entered popular culture as a fat-versus-thin dial.

The evidence since has not cooperated. Magne and colleagues reviewed the literature in 2020 ¹¹ and found the results across studies contradictory, with differences explained as easily by sample handling, sequencing method and poorly described lifestyle as by body weight. Their conclusion, in their own terms: it is currently difficult to associate the ratio with a determined health status, and more specifically to consider it a hallmark of obesity ¹¹. So a high Bacillota bar on a test report is not a diagnosis. It is a snapshot of a phylum that contains both the butyrate producers your colon lining runs on and the pathogens your hospital worries about, and the bar cannot tell you which ones you have.