The Bifidobacteriaceae are the only

family Family (from ) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). It forms the basis for social order. Ideally, families offer predictabili ...

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

in the

order Order, ORDER or Orders may refer to: * A socio-political or established or existing order, e.g. World order, Ancien Regime, Pax Britannica * Categorization, the process in which ideas and objects are recognized, differentiated, and understood ...

Bifidobacteriales The Bifidobacteriaceae are the only family (biology), family of bacteria in the order (biology), order ''Bifidobacteriales''. According to the 16S rRNA-based 'The All-Species Living Tree' Project, LTP release 106 published by 'The All-Species Liv ...

''. According to the

16S rRNA 16S ribosomal RNA (or 16Svedberg, S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as ...

-based LTP release 106 published by 'The All-Species Living Tree' Project, the order

is a clade nested within the suborder Micrococcineae, also the genus '' Bifidobacterium'' is

paraphyletic Paraphyly is a taxonomic term describing a grouping that consists of the grouping's last common ancestor and some but not all of its descendant lineages. The grouping is said to be paraphyletic ''with respect to'' the excluded subgroups. In co ...

to the other genera within the family, i.e. the other genera are nested within '' Bifidobacterium''.

Genomics

In a

phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...

for the order ''Bifidobacteriales'', based on RpoB, RpoC, and DNA Gyrase B, '' Gardnerella vaginalis'' branches between different '' Bifidobacterium'' species, which makes the genus ''Bifidobacterium''

polyphyletic A polyphyletic group is an assemblage that includes organisms with mixed evolutionary origin but does not include their most recent common ancestor. The term is often applied to groups that share similar features known as Homoplasy, homoplasies ...

. The genus could be made

monophyletic In biological cladistics for the classification of organisms, monophyly is the condition of a taxonomic grouping being a clade – that is, a grouping of organisms which meets these criteria: # the grouping contains its own most recent co ...

if ''G. vaginalis'' were placed within ''Bifidobacterium''. Comparative analysis of aligned protein sequences has led to the discovery of two

conserved signature indels 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 ...

which are specific for the order ''Bifidobacteriales''. The first

indel Indel (insertion-deletion) is a molecular biology term for an insertion or deletion of bases in the genome of an organism. Indels ≥ 50 bases in length are classified as structural variants. In coding regions of the genome, unless the lengt ...

, a 1

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

deletion in ribosomal protein L13, is found in all ''Bifidobacteriales'' species and no other ''

Actinomycetota The Actinomycetota (or Actinobacteria) are a diverse phylum of Gram-positive bacteria with high GC content. They can be terrestrial or aquatic. They are of great importance to land flora because of their contributions to soil systems. In soil t ...

'', providing a potential

molecular marker In molecular biology and other fields, a molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. ...

for the entire ''Bifidobacteriales'' order. The second indel that has been identified is a 1 amino acid insertion in

glucose-6-phosphate dehydrogenase Glucose-6-phosphate dehydrogenase (G6PD or G6PDH) () is a cytosolic enzyme that catalysis, catalyzes the chemical reaction : Glucose 6-phosphate, D-glucose 6-phosphate + NADP+ + 6-Phosphogluconolactone, 6-phospho-D-glucono-1,5-lactone + NADPH ...

found in all ''Bifidobacterium'' species and ''G. vaginalis'', but not in any other ''Actinomycetota''. This indel is thus characteristic of the

clade In biology, a clade (), also known as a Monophyly, monophyletic group or natural group, is a group of organisms that is composed of a common ancestor and all of its descendants. Clades are the fundamental unit of cladistics, a modern approach t ...

consisting of ''Bifidobacterium'' species and ''G. vaginalis'' and can be used to distinguish these genera from the rest of the order ''Bifidobacteriales''. 16 conserved signature proteins have also been identified which are unique to the order ''Bifidobacteriales'' and can be used as molecular markers for this order. Additionally, 6 conserved signature proteins which are unique to ''Bifidobacterium'' and '' Gardnerella'' have been identified, providing further evidence that species from these two genera are closely related and providing molecular markers for the clade consisting of these genera.

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 naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...

(LPSN). The phylogeny is based on whole-genome analysis.

Notes

References

External links

Systema Naturae 2000 / Classification - Family Bifidobacteriaceae
{{Taxonbar, from=Q4904765 Bifidobacteriales Bacteria families Bacteria described in 1997