Bacteroidota

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Bacteroidota
Bacteroides biacutis 01.jpg
Bacteroides biacutis
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Domain: Bacteria
Clade: FCB group
(unranked): Bacteroidetes-Chlorobi group
Phylum: Bacteroidota
Krieg et al. 2021 [1]
Classes [2]
Synonyms
  • "Bacteroidaeota" Oren et al. 2015
  • "Bacteroidetes" Krieg et al. 2010 [3]
  • "Bacteroidota" Whitman et al. 2018
  • "Saprospirae" Margulis and Schwartz 1998
  • "Sphingobacteria" Cavalier-Smith 2002

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.

Contents

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. [4]

History

Bacteroides fragilis was the first Bacteroides species isolated in 1898 as a human pathogen linked to appendicitis among other clinical cases. [4] 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 fourth volume[ clarify ] of Bergey's Manual of Systematic Bacteriology. [5]

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.  [4] This phylum is sometimes grouped with Chlorobiota , Fibrobacterota , Gemmatimonadota , Calditrichota , and marine group A to form the FCB group or superphylum. [6] In the alternative classification system proposed by Cavalier-Smith, 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. 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, [7] but it may be involved in type 1 and type 2 diabetes pathogenesis. [4] Bacteroides 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. [4]

Bacteroidota are not limited to gut microbiota, they colonize a variety of habitats on Earth. [8] For example, Bacteroidota, together with "Pseudomonadota", "Bacillota", and "Actinomycetota", are also among the most abundant bacterial groups in rhizosphere. [9] They have been detected in soil samples from various locations, including cultivated fields, greenhouse soils and unexploited areas. [8] 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. [8] Halophilic 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 that inhabit the same environments. Phenotypically, Salinibacter is remarkably similar to Halobacterium and therefore for a long time remained unidentified. [10]

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 Odoribacter and Porphyromonas are predominantly asaccharolytic. Some Bacteroides spp. and Prevotella spp. can degrade complex plant polysaccharides such as starch, cellulose, xylans, and pectins. The Bacteroidota species also play an important role in protein metabolism by proteolytic activity assigned to the proteases 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 bile acids and growth on mucus. [4] 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 halophilic members of the group, whereas flexirubin pigments are more frequent in clinical, freshwater or soil-colonizing representatives. [11]

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. [6] 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. [6]

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. [6] 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. [6] [12] 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 [12] These phyla also branch in the same position based upon conserved signature indels in a number of important proteins. [13] 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. [6] [12]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature [2]

Whole-genome based phylogeny [14] 16S rRNA based LTP_08_2023 [15] [16] [17] 120 single copy marker proteins based GTDB 08-RS214 [18] [19] [20]

See also

Related Research Articles

<span class="mw-page-title-main">Gram-positive bacteria</span> Bacteria that give a positive result in the Gram stain test

In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.

<span class="mw-page-title-main">Gram-negative bacteria</span> Group of bacteria that do not retain the Gram stain used in bacterial differentiation

Gram-negative bacteria are bacteria that unlike gram-positive bacteria do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is their cell envelope, which consists of a thin peptidoglycan cell wall sandwiched between an inner (cytoplasmic) membrane and an outer membrane. These bacteria are found in all environments that support life on Earth.

The Aquificota phylum is a diverse collection of bacteria that live in harsh environmental settings. The name Aquificota was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

The Thermotogota are a phylum of the domain Bacteria. The phylum contains a single class, Thermotogae. The phylum Thermotogota is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.

<i>Chlorobium</i> Genus of bacteria

Chlorobium is a genus of green sulfur bacteria. They are photolithotrophic oxidizers of sulfur and most notably utilise a noncyclic electron transport chain to reduce NAD+. Photosynthesis is achieved using a Type 1 Reaction Centre using bacteriochlorophyll (BChl) a. Two photosynthetic antenna complexes aid in light absorption: the Fenna-Matthews-Olson complex, and the chlorosomes which employ mostly BChl c, d, or e. Hydrogen sulfide is used as an electron source and carbon dioxide its carbon source.

<span class="mw-page-title-main">Gut microbiota</span> Community of microorganisms in the gut

Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.

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 Fibrobacter was removed from the genus Bacteroides in 1988.

<i>Bacteroides</i> Genus of bacteria

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. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.

<span class="mw-page-title-main">PVC superphylum</span> Superphylum of bacteria

The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell.

Prevotellaceae is a family of bacteria from the order Bacteroidales. As a member of the phylum Bacteroidota, its species are gram negative – meaning their outer cell wall contains lipopolysaccharides. Since they are anaerobes, members of Prevotellaceae can live in areas where there is little to no oxygen – such as the guts of mammals.

<span class="mw-page-title-main">Flavobacteriales</span> Order of bacteria

The order Flavobacteriales comprises several families of environmental bacteria.

Fibrobacter succinogenes is a cellulolytic bacterium species in the genus Fibrobacter. It is present in the rumen of cattle. F. succinogenes is a gram negative, rod-shaped, obligate anaerobe that is a major contributor to cellulose digestion. Since its discovery in the 1950s, it has been studied for its role in herbivore digestion and cellulose fermentation, which can be utilized in biofuel production.

Prevotella is a genus of Gram-negative bacteria.

<span class="mw-page-title-main">SAM-Chlorobi RNA motif</span>

The SAM-Chlorobi RNA motif is a conserved RNA structure that was identified by bioinformatics. The RNAs are found only in bacteria classified as within the phylum Chlorobiota. These RNAs are always in the 5' untranslated regions of operons that contain metK and ahcY genes. metK genes encode methionine adenosyltransferase, which synthesizes S-adenosyl methionine (SAM), and ahcY genes encode S-adenosylhomocysteine hydrolase, which degrade the related metabolite S-Adenosyl-L-homocysteine (SAH). In fact all predicted metK and ahcY genes within Chlorobiota bacteria as of 2010 are preceded by predicted SAM-Chlorobi RNAs. Predicted promoter sequences are consistently found upstream of SAM-Chlorobi RNAs, and these promoter sequences imply that SAM-Chlorobi RNAs are indeed transcribed as RNAs. The promoter sequences are commonly associated with strong transcription in the phyla Chlorobiota and Bacteroidota, but are not used by most lineages of bacteria. The placement of SAM-Chlorobi RNAs suggests that they are involved in the regulation of the metK/ahcY operon through an unknown mechanism.

<span class="mw-page-title-main">Sphingobacteria (phylum)</span> Phylum of bacteria

The FCB group is a superphylum of bacteria named after the main member phyla Fibrobacterota, Chlorobiota, and Bacteroidota. The members are considered to form a clade due to a number of conserved signature indels.

<span class="mw-page-title-main">Bacterial phyla</span> Phyla or divisions of the domain Bacteria

Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.

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 that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.

<i>Bacteroides thetaiotaomicron</i> Species of bacterium

Bacteroides thetaiotaomicron is a gram-negative, rod shaped obligate anaerobic bacterium that is a prominent member of the normal gut microbiome in the distal intestines. Its proteome, consisting of 4,779 members, includes a system for obtaining and breaking down dietary polysaccharides that would otherwise be difficult to digest. B. thetaiotaomicron is also an opportunistic pathogen, meaning it may become virulent in immunocompromised individuals. It is often used in research as a model organism for functional studies of the human microbiota.

Cytophagales is an order of non-spore forming, rod-shaped, Gram-negative bacteria that move through a gliding or flexing motion. These chemoorganotrophs are important remineralizers of organic materials into micronutrients. They are widely dispersed in the environment, found in ecosystems including soil, freshwater, seawater and sea ice. Cytophagales is included in the Bacteroidota phylum.

<span class="mw-page-title-main">Cetacean microbiome</span> Group of communities of microorganisms that reside within whales

The cetacean microbiome is the group of communities of microorganisms that reside within whales.

References

  1. ↑ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi: 10.1099/ijsem.0.005056 . PMID   34694987. S2CID   239887308.
  2. 1 2 Euzéby JP, Parte AC. ""Bacteroidetes"". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved June 23, 2021.
  3. ↑ Krieg NR, Ludwig W, Euzéby J, Whitman WB (2010). "Phylum XIV. Bacteroidetes phyl. nov.". In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds.). Bergey's Manual of Systematic Bacteriology. Vol. 4 (2nd ed.). New York, NY: Springer. p. 25.
  4. 1 2 3 4 5 6 Rajilić-Stojanović, Mirjana; de Vos, Willem M. (2014). "The first 1000 cultured species of the human gastrointestinal microbiota". FEMS Microbiology Reviews. 38 (5): 996–1047. doi:10.1111/1574-6976.12075. ISSN   1574-6976. PMC   4262072 . PMID   24861948.
  5. ↑ Krieg, N.R.; Ludwig, W.; Whitman, W.B.; Hedlund, B.P.; Paster, B.J.; Staley, J.T.; Ward, N.; Brown, D.; Parte, A. (November 24, 2010) [1984(Williams & Wilkins)]. George M. Garrity (ed.). The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Bergey's Manual of Systematic Bacteriology. Vol. 4 (2nd ed.). New York: Springer. p. 908. ISBN   978-0-387-95042-6. British Library no. GBA561951.
  6. 1 2 3 4 5 6 Gupta, R. S.; Lorenzini, E. (2007). "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species". BMC Evolutionary Biology. 7 (1): 71. Bibcode:2007BMCEE...7...71G. doi: 10.1186/1471-2148-7-71 . PMC   1887533 . PMID   17488508.
  7. ↑ Pittayanon R, Lau JT, Yuan Y, Leontiadis GI, Tse F, Surette M, Moayyedi P (2019). "Gut Microbiota in Patients With Irritable Bowel Syndrome-A Systematic Review". Gastroenterology. 157 (1): 97–108. doi:10.1053/j.gastro.2019.03.049. PMID   30940523.
  8. 1 2 3 Thomas, François; Hehemann, Jan-Hendrik; Rebuffet, Etienne; Czjzek, Mirjam; Michel, Gurvan (2011). "Environmental and Gut Bacteroidetes: The Food Connection". Frontiers in Microbiology. 2: 93. doi: 10.3389/fmicb.2011.00093 . ISSN   1664-302X. PMC   3129010 . PMID   21747801.
  9. ↑ Mendes, Rodrigo; Garbeva, Paolina; Raaijmakers, Jos M. (2013). "The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms". FEMS Microbiology Reviews. 37 (5): 634–663. doi: 10.1111/1574-6976.12028 . ISSN   1574-6976. PMID   23790204.
  10. ↑ Oren, Aharon (2013). "Salinibacter: An extremely halophilic bacterium with archaeal properties". FEMS Microbiology Letters. 342 (1): 1–9. doi: 10.1111/1574-6968.12094 . PMID   23373661.
  11. ↑ Jehlička, Jan; Osterrothová, Kateřina; Oren, Aharon; Edwards, Howell G. M. (2013). "Raman spectrometric discrimination of flexirubin pigments from two genera of Bacteroidetes". FEMS Microbiology Letters. 348 (2): 97–102. doi: 10.1111/1574-6968.12243 . PMID   24033756.
  12. 1 2 3 Gupta, R. S. (2004). "The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes". Critical Reviews in Microbiology. 30 (2): 123–140. doi:10.1080/10408410490435133. PMID   15239383. S2CID   24565648.
  13. ↑ Griffiths, E; Gupta, RS (2001). "The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: Evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga–Flavobacterium–Bacteroides division". Microbiology. 147 (Pt 9): 2611–22. doi: 10.1099/00221287-147-9-2611 . PMID   11535801.
  14. ↑ García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M (2019). "Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes". Front Microbiol. 10: 2083. doi: 10.3389/fmicb.2019.02083 . PMC   6767994 . PMID   31608019.
  15. ↑ "The LTP" . Retrieved 20 November 2023.
  16. ↑ "LTP_all tree in newick format" . Retrieved 20 November 2023.
  17. ↑ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  18. ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
  19. ↑ "bac120_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
  20. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.
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