The phylum Bacteroidota (synonym Bacteroidetes) is composed of three large classes of

Gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wa ...

, nonsporeforming, anaerobic or aerobic, and rod-shaped

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...

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 An opportunistic infection is an infection caused by pathogens (bacteria, fungi, parasites or viruses) that take advantage of an opportunity not normally available. These opportunities can stem from a variety of sources, such as a weakened immune ...

, 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

oligosaccharide An oligosaccharide (/ˌɑlɪgoʊˈsækəˌɹaɪd/; from the Greek ὀλίγος ''olígos'', "a few", and σάκχαρ ''sácchar'', "sugar") is a saccharide polymer containing a small number (typically two to ten) of monosaccharides (simple sug ...

s in mother milk support the growth of both ''

Bacteroides ''Bacteroides'' is a genus of Gram-negative, obligate anaerobic bacteria. ''Bacteroides'' species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unus ...

'' and ''

Bifidobacterium ''Bifidobacterium'' is a genus of gram-positive, nonmotile, often branched anaerobic bacteria. They are ubiquitous inhabitants of the gastrointestinal tract though strains have been isolated from the vagina and mouth ('' B. dentium'') of mammal ...

'' spp. ''Bacteroides'' spp. are selectively recognized by the

immune system The immune system is a network of biological processes that protects an organism from diseases. It detects and responds to a wide variety of pathogens, from viruses to parasitic worms, as well as cancer cells and objects such as wood splint ...

of the host through specific interactions.

History

Bacteroides fragilis ''Bacteroides fragilis'' is an anaerobic, Gram-negative, pleomorphic to rod-shaped bacterium. It is part of the normal microbiota of the human colon and is generally commensal, but can cause infection if displaced into the bloodstream or surrou ...

'' was the first ''Bacteroides'' species isolated in 1898 as a human pathogen linked to

appendicitis Appendicitis is inflammation of the appendix. Symptoms commonly include right lower abdominal pain, nausea, vomiting, and decreased appetite. However, approximately 40% of people do not have these typical symptoms. Severe complications of a ru ...

among other clinical cases. By far, the species in the

class Class or The Class may refer to: Common uses not otherwise categorized * Class (biology), a taxonomic rank * Class (knowledge representation), a collection of individuals or objects * Class (philosophy), an analytical concept used differentl ...

Bacteroidia Bacteroidales is an order of bacteria. Notably it includes the genera ''Prevotella'' and ''Bacteroides'' , which are commonly found in the human gut microbiota. Phylogeny The currently accepted taxonomy is based on the List of Prokaryotic names ...

'' are the most well-studied, including the genus ''

'' (an abundant organism in the feces of warm-blooded animals including humans), and ''

Porphyromonas ''Porphyromonas'' is a Gram-negative, non-spore-forming, obligately anaerobic and non-motile genus from the family of Porphyromonadaceae. There were 16 different Porphyromonas species documented as of 2015 which reside in both animal and human ...

'', a group of organisms inhabiting the human

oral cavity In animal anatomy, the mouth, also known as the oral cavity, or in Latin cavum oris, is the opening through which many animals take in food and issue vocal sounds. It is also the cavity lying at the upper end of the alimentary canal, bounded on t ...

. The class ''Bacteroidia'' was formerly called ''Bacteroidetes''; as it was until recently the only class in the phylum, the name was changed in the fourth volume 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''. This phylum is sometimes grouped with ''

Chlorobiota The green sulfur bacteria are a phylum of obligately anaerobic photoautotrophic bacteria that metabolize sulfur. Green sulfur bacteria are nonmotile (except ''Chloroherpeton thalassium'', which may glide) and capable of anoxygenic photosynthes ...

'', ''

Fibrobacterota Fibrobacterota is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus '' Fibrobac ...

'', ''

Gemmatimonadota The Gemmatimonadota are a phylum of bacteria established in 2003. The phylum contains two classes Gemmatimonadetes and Longimicrobia. Species The type species '' Gemmatimonas aurantiaca'' strain T-27T was isolated from activated sludge in a sewa ...

'', ''

Calditrichota ''Caldithrix'' is a genus of thermophilic and anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anae ...

'', and marine group A to form the

FCB group FCB may refer to: Banks * Fairfield County Bank, in the United States * Farm Credit Bank, part of the Farm Credit System in the United States * Florida Community Bank, in the United States * First Community Bank, in Kenya * First Consolidated B ...

or superphylum. In the alternative classification system proposed by

Cavalier-Smith Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (21 October 1942 – 19 March 2021), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford. His research has led to disc ...

, this taxon is instead a class in the phylum Sphingobacteria.

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 Obesity is a medical condition, sometimes considered a disease, in which excess body fat has accumulated to such an extent that it may negatively affect health. People are classified as obese when their body mass index (BMI)—a person's ...

. This bacterial group appears to be enriched in patients with

irritable bowel syndrome Irritable bowel syndrome (IBS) is a "disorder of gut-brain interaction" characterized by a group of symptoms that commonly include abdominal pain and or abdominal bloating and changes in the consistency of bowel movements. These symptoms may ...

and involved in type 1 and

type 2 diabetes Type 2 diabetes, formerly known as adult-onset diabetes, is a form of diabetes mellitus that is characterized by high blood sugar, insulin resistance, and relative lack of insulin. Common symptoms include increased thirst, frequent urinatio ...

. ''

'' spp. in contrast to ''

Prevotella ''Prevotella'' is a genus of Gram-negative bacteria. ''Prevotella'' spp. are members of the oral, vaginal, and gut microbiota and are often recovered from anaerobic infections of the respiratory tract. These infections include aspiration pn ...

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 The order Flavobacteriales comprises several families of environmental bacteria. Comparative genomics and molecular signatures ''Flavobacteriales'' is of one of the orders from the phylum ''Bacteroidota''. Comparative genomic studies have identi ...

'' and '' Sphingobacteriales'' are typical soil bacteria and are only occasionally detected in the gastrointestinal tract, except ''

Capnocytophaga ''Capnocytophaga'' is a genus of Gram-negative bacteria. Normally found in the oropharyngeal tract of mammals, they are involved in the pathogenesis of some animal bite wounds and periodontal diseases. Taxonomy The term ''Capnocytophaga'' come ...

spp.'' and ''

Sphingobacterium ''Sphingobacterium'' is a genus in the family Sphingobacteriaceae. The genus ''Sphingobacterium'' is characterized by the high concentrations of sphingolipid, sphingophospholipids as lipid components. ''Bacteroidota'' are not limited to gut microbiota, they colonize a variety of habitats on Earth. For example, ''Bacteroidota'', together with " Pseudomonadota", "

Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...

", and "

Actinomycetota The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to s ...

", are also among the most abundant bacterial groups in

rhizosphere The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microo ...

. They have been detected in soil samples from various locations, including cultivated fields, greenhouse soils and unexploited areas. ''Bacteroidota'' also inhabit freshwater lakes, rivers, as well as oceans. They are increasingly recognized as an important compartment of the bacterioplankton in marine environments, especially in pelagic oceans.

Halophilic The halophiles, named after the Greek word for "salt-loving", are extremophiles that thrive in high salt concentrations. While most halophiles are classified into the domain Archaea, there are also bacterial halophiles and some eukaryotic species, ...

''Bacteroidota'' genus '' Salinibacter'' inhabit hypersaline environments such as salt-saturated brines in hypersaline lakes. ''Salinibacter'' shares many properties with halophilic '' Archaea'' such as '' Halobacterium'' and ''

Haloquadratum ''Haloquadratum'' (common abbreviation: ''Hqr.'') is a genus of archaean, belonging to the family Haloferacaceae. The first species to be identified in this group, ''Haloquadratum walsbyi'', is unusual in that its cells are shaped like square, ...

'' that inhabit the same environments. Phenotypically, ''Salinibacter'' is remarkably similar to ''Halobacterium'' and therefore for a long time remained unidentified.

Metabolism

Gastrointestinal ''Bacteroidota'' species produce

succinic acid Succinic acid () is a dicarboxylic acid with the chemical formula (CH2)2(CO2H)2. The name derives from Latin ''succinum'', meaning amber. In living organisms, succinic acid takes the form of an anion, succinate, which has multiple biological ro ...

, acetic acid, and in some cases propionic acid, as the major end-products. Species belonging to the genera '' Alistipes'', ''

'', ''

Parabacteroides ''Parabacteroides'' is a Gram-negative, anaerobic, non-spore-forming genus from the family ''Tannerellaceae''. First isolated from fecal specimen in 1933, type strain '' Parabacteroides distasonis'' was originally classified under the name ''Bac ...

'', ''

'', ''Paraprevotella'', ''Alloprevotella'', '' Barnesiella'', and '' Tannerella'' are saccharolytic, while species belonging to '' Odoribacter'' and ''

'' are predominantly asaccharolytic. Some ''Bacteroides spp.'' and ''Prevotella spp.'' can degrade complex plant polysaccharides such as starch,

cellulose Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units. Cellulose is an important structural component of the primary cell w ...

xylan Xylan (; ) ( CAS number: 9014-63-5) is a type of hemicellulose, a polysaccharide consisting mainly of xylose residues. It is found in plants, in the secondary cell walls of dicots and all cell walls of grasses. Xylan is the third most abundan ...

s, and pectins. The ''Bacteroidota'' species also play an important role in protein metabolism by proteolytic activity assigned to the

protease A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the ...

s linked to the cell. Some "''Bacteroides'' spp. have a potential to utilize

urea Urea, also known as carbamide, is an organic compound with chemical formula . This amide has two amino groups (–) joined by a carbonyl functional group (–C(=O)–). It is thus the simplest amide of carbamic acid. Urea serves an important ...

as a nitrogen source. Other important functions of ''Bacteroides'' spp. include the deconjugation of bile acids and growth on

mucus Mucus ( ) is a slippery aqueous secretion produced by, and covering, mucous membranes. It is typically produced from cells found in mucous glands, although it may also originate from mixed glands, which contain both serous and mucous cells. It ...

. Many members of the ''Bacteroidota'' genera (''

Flexibacter ''Flexibacter'' is a genus of bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a f ...

'', ''

Cytophaga ''Cytophaga'' is a genus of Gram-negative, gliding, rod-shaped bacteria. This bacterium is commonly found in soil, rapidly digests crystalline cellulose ''C. hutchinsonii'' is able to use its gliding motility to move quickly over surfaces. A ...

'', ''Sporocytophaga'' and relatives) are coloured yellow-orange to pink-red due to the presence of pigments of the

flexirubin Flexirubin is the main pigment in the bacteria genera '' Flexibacter'', ''Flavobacterium'', ''Chryseobacterium'', and ''Cytophaga''.Reichenbach, H., W. Kohl, et al. (1980). ''FLEXIRUBIN-TYPE PIGMENTS IN FLAVOBACTERIUM''. Archives of Microbiology 1 ...

group. In some ''Bacteroidota'' strains, flexirubins may be present together with carotenoid pigments. Carotenoid pigments are usually found in marine and

halophilic The halophiles, named after the Greek word for "salt-loving", are extremophiles that thrive in high salt concentrations. While most halophiles are classified into the domain Archaea, there are also bacterial halophiles and some eukaryotic species, ...

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 ''

''. 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 Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers ...

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 Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...

. 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 ''

'' 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 Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) (Vitamin B6) dependent enzyme () which plays an important role in cellular one-carbon pathways by catalyzing the reversible, simultaneous conversions of L-serine to glycine ...

) 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 List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the nomenclature, naming and Taxonomy (biology), taxonomy of prokaryotes, following the taxonomy requirements and rulings of the In ...

References

External links

Phylogenomics and Evolutionary Studies on Bacteriodetes, Chlorobi and Fibrobacteres Species
Bacterial (Prokaryotic) Phylogeny Webpage {{Taxonbar, from=Q1061265 Bacteria phyla Gram-negative bacteria

History

Medical and ecological role

Metabolism

Genomics

Relatedness of ''Bacteroidota'', ''Chlorobiota'', and ''Fibrobacterota'' phyla

Phylogeny

See also

References

External links