The Bifidobacteriaceae are the only

family Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is to maintain the well-being of its ...

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 few micrometres in length, bacteria were among ...

in the order '' Bifidobacteriales''. According to the

16S rRNA 16S rRNA may refer to: * 16S ribosomal RNA 16 S ribosomal RNA (or 16 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 g ...

-based

LTP LTP may refer to: Biology and medicine * Lateral tibial plateau, part of a leg bone * Lipid transfer proteins, proteins found in plant tissues * Long-term potentiation (neurophysiology), a long-lasting enhancement in signal transmission between ...

release 106 published by 'The All-Species Living Tree' Project, the order Bifidobacteriales is a clade nested within the suborder

Micrococcineae The Micrococcales are an order of bacteria in the phylum Actinomycetota. 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 ...

, also the genus ''

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 ...

'' is

paraphyletic In taxonomy (general), taxonomy, a group is paraphyletic if it consists of the group's most recent common ancestor, last common ancestor and most of its descendants, excluding a few Monophyly, monophyletic subgroups. The group is said to be pa ...

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

''.

Genomics

In a

phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

for the order ''Bifidobacteriales'', based on

RpoB The ''rpoB'' gene encodes the β subunit of bacterial RNA polymerase and the homologous plastid-encoded RNA polymerase (PEP). It codes for 1342 amino acids in ''E. coli'', making it the second-largest polypeptide in the bacterial cell. It is targe ...

, RpoC, and DNA Gyrase B, ''

Gardnerella vaginalis ''Gardnerella vaginalis'' is a species of Gram-variable-staining facultative anaerobic bacteria. The organisms are small (1.0–1.5 μm in diameter) non-spore-forming, nonmotile coccobacilli. Once classified as ''Haemophilus vaginalis'' an ...

'' branches between different ''

'' species, which makes the genus ''Bifidobacterium''

polyphyletic A polyphyletic group is an assemblage of organisms or other evolving elements that is of mixed evolutionary origin. The term is often applied to groups that share similar features known as homoplasies, which are explained as a result of converg ...

. The genus could be made

monophyletic In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic gro ...

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 is a molecular biology term for an insertion or deletion of bases in the genome of an organism. It is classified among small genetic variations, measuring from 1 to 10 000 base pairs in length, including insertion and deletion events that ...

, a 1

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

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

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 soi ...

'', providing a potential

molecular marker 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 another example, some proteins can be ...

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 catalyzes the chemical reaction : D-glucose 6-phosphate + NADP+ + H2O 6-phospho-D-glucono-1,5-lactone + NADPH + H+ This enzyme participates in the pentose phosph ...

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

clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...

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 ''Gardnerella'' is a genus of Gram-variable-staining facultative anaerobic bacteria. Eponym It is named after Hermann L. Gardner (1912–1982), an American bacteriologist who discovered it in 1955. References

Bifidobacteriales Bacteria ...

'' 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 Nomenclature ...

(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