The phylum Bacteroidota (synonym Bacteroidetes) is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.
Although some Bacteroides spp. can be opportunistic pathogens, many Bacteroidota are symbiotic species highly adjusted to the gastrointestinal tract. Bacteroides are highly abundant in intestines, reaching up to 1011 cells g−1 of intestinal material. They perform metabolic conversions that are essential for the host, such as degradation of proteins or complex sugar polymers. Bacteroidota colonize the gastrointestinal tract already in infants, as non-digestible oligosaccharides in mother milk support the growth of both Bacteroides and Bifidobacterium spp. Bacteroides spp. are selectively recognized by the immune system of the host through specific interactions.
History
Bacteroides fragilis was the first
Bacteroides species isolated in 1898 as a human pathogen linked to
appendicitis among other clinical cases.
By far, the species in the class
Bacteroidia are the most well-studied, including the genus
Bacteroides (an abundant organism in the
feces of warm-blooded animals including humans), and
Porphyromonas, a group of organisms inhabiting the human
oral cavity. The class
Bacteroidia was formerly called
Bacteroidetes; as it was until recently the only class in the phylum, the name was changed in the of Bergey's
Manual of Systematic Bacteriology.
For a long time, it was thought that the majority of Gram-negative gastrointestinal tract bacteria belonged to the genus Bacteroides, but in recent years many species of Bacteroides have undergone reclassification. Based on current classification, the majority of the gastrointestinal Bacteroidota species belong to the families Bacteroidaceae, Prevotellaceae, Rikenellaceae, and Porphyromonadaceae.
Medical and ecological role
In the gastrointestinal
microbiota Bacteroidota have a very broad metabolic potential and are regarded as one of the most stable part of gastrointestinal microflora. Reduced abundance of the
Bacteroidota in some cases is associated with
obesity. This bacterial group as a whole has conflicting evidence for alteration of abundance in patients with irritable bowel syndrome, though its genus
Bacteroides is likely enriched,
but it may be involved in type 1 and type 2 diabetes pathogenesis.
spp. in contrast to
Prevotella spp. were recently found to be enriched in the metagenomes of subjects with low gene richness that were associated with adiposity, insulin resistance and dyslipidaemia as well as an inflammatory phenotype.
Bacteroidota species that belong to classes
Flavobacteriales and
Sphingobacteriales are typical soil bacteria and are only occasionally detected in the gastrointestinal tract, except
Capnocytophaga spp. and
Sphingobacterium spp. that can be detected in the human oral cavity.
Bacteroidota are not limited to gut microbiota, they colonize a variety of habitats on Earth.
Metabolism
Gastrointestinal
Bacteroidota species produce
succinic acid,
acetic acid, and in some cases
propionic acid, as the major end-products. Species belonging to the genera
Alistipes,
Bacteroides,
Parabacteroides,
Prevotella,
Paraprevotella,
Alloprevotella,
Barnesiella, and
Tannerella are saccharolytic, while species belonging to
Odoribacteraceae and
Porphyromonas are predominantly asaccharolytic. Some
Bacteroides spp. and
Prevotella spp. can degrade complex plant polysaccharides such as
starch,
cellulose,
, and
. The
Bacteroidota species also play an important role in protein metabolism by proteolytic activity assigned to the
linked to the cell. Some "
Bacteroides spp. have a potential to utilize
urea as a nitrogen source. Other important functions of
Bacteroides spp. include the deconjugation of
and growth on
mucus.
Many members of the
Bacteroidota genera (
Flexibacter,
Cytophaga,
Sporocytophaga and relatives) are coloured yellow-orange to pink-red due to the presence of pigments of the
flexirubin group. In some
Bacteroidota strains, flexirubins may be present together with
carotenoid pigments. Carotenoid pigments are usually found in marine and
Halophile members of the group, whereas flexirubin pigments are more frequent in clinical, freshwater or soil-colonizing representatives.
Genomics
Comparative genomic analysis has led to the identification of 27 proteins which are present in most species of the phylum
Bacteroidota. Of these, one protein is found in all sequenced
Bacteroidota species, while two other proteins are found in all sequenced species with the exception of those from the genus
Bacteroides. The absence of these two proteins in this genus is likely due to selective gene loss.
Additionally, four proteins have been identified which are present in all
Bacteroidota species except
Cytophaga hutchinsonii; this is again likely due to selective gene loss. A further eight proteins have been identified which are present in all sequenced
Bacteroidota genomes except
Salinibacter ruber. The absence of these proteins may be due to selective gene loss, or because
S. ruber branches very deeply, the genes for these proteins may have evolved after the divergence of
S. ruber. A conserved signature indel has also been identified; this three-amino-acid deletion in ClpB chaperone is present in all species of the
Bacteroidota phylum except
S. ruber. This deletion is also found in one
Chlorobiota species and one
Archaeum species, which is likely due to horizontal gene transfer. These 27 proteins and the three-amino-acid deletion serve as molecular markers for the
Bacteroidota.
Relatedness of Bacteroidota, Chlorobiota, and Fibrobacterota phyla
Species from the
Bacteroidota and
Chlorobiota phyla branch very closely together in phylogenetic trees, indicating a close relationship. Through the use of comparative genomic analysis, three proteins have been identified which are uniquely shared by virtually all members of the
Bacteroidota and
Chlorobiota phyla.
The sharing of these three proteins is significant because other than them, no proteins from either the
Bacteroidota or
Chlorobiota phyla are shared by any other groups of bacteria. Several conserved signature indels have also been identified which are uniquely shared by members of the phyla. The presence of these molecular signatures supports their close relationship.
Additionally, the phylum
Fibrobacterota is indicated to be specifically related to these two phyla. A clade consisting of these three phyla is strongly supported by phylogenetic analyses based upon a number of different proteins
These phyla also branch in the same position based upon conserved signature indels in a number of important proteins.
Lastly and most importantly, two conserved signature indels (in the RpoC protein and in serine hydroxymethyltransferase) and one signature protein PG00081 have been identified that are uniquely shared by all of the species from these three phyla. All of these results provide compelling evidence that the species from these three phyla shared a common ancestor exclusive of all other bacteria, and it has been proposed that they should all recognized as part of a single "FCB" superphylum.
Phylogeny
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature
See also
-
List of bacteria genera
-
List of bacterial orders
External links
