Bifidobacteriaceae

Genomics

All Bifidobacteraceae contain a metabolic pathway to catabolise six-carbon sugars (hexoses) which involves the key enzyme fructose-6-phosphate phosphoketolase. This pathway is known as the fructose-6-phosphate pathway or the 'bifid shunt'.

Comparative analysis of aligned protein sequences has led to the discovery of two conserved signature indels which are specific for the order Bifidobacteriales. The first indel, a one amino acid deletion in ribosomal protein L13, is found in all Bifidobacteriales species and no other Actinomycetota, providing a potential molecular marker for the entire Bifidobacteriales order. The second indel that has been identified is a 1 amino acid insertion in glucose-6-phosphate dehydrogenase found in all Bifidobacterium species and G. vaginalis, but not in any other Actinomycetota. This indel is thus characteristic of the clade 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.

• Aeriscardovia Simpson et al. 2004
• Alloscardovia Huys et al. 2007
• Bifidobacterium Orla-Jensen 1924 (Approved Lists 1980)
• Bombiscardovia Killer et al. 2014
• Galliscardovia Pechar et al. 2017
• Gardnerella Greenwood and Pickett 1980
• Neoscardovia García-Aljaro et al. 2015
• Parascardovia Jian and Dong 2002
• Pseudoscardovia Killer et al. 2014
• Scardovia Jian and Dong 2002

The Bifidobacteriaceae are the only family of bacteria in the order Bifidobacteriales.

The Bifidobacteriaceae family is divided into ten genera ( Bifidobacterium, Aeriscardovia, Alloscardovia, Bombiscardovia, Galliscardovia,Gardnerella, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia with three candidate genera Candidatus Ancillula, Candidatus Opitulatrix, and Candidatus Servula.

Genomics

All Bifidobacteraceae contain a peculiar metabolic pathway to catabolise six-carbon sugars (hexoses) involving the key enzyme Fructose-6-phosphate phosphoketolase (EC 4.1.2.2), known as the fructose-6-phosphate pathway or the 'bifid shunt'.

Comparative analysis of aligned protein sequences has led to the discovery of two conserved signature indels which are specific for the order Bifidobacteriales. The first indel, a 1 amino acid deletion in ribosomal protein L13, is found in all Bifidobacteriales species and no other Actinomycetota, providing a potential molecular marker for the entire Bifidobacteriales order. The second indel that has been identified is a 1 amino acid insertion in glucose-6-phosphate dehydrogenase found in all Bifidobacterium species and G. vaginalis, but not in any other Actinomycetota. This indel is thus characteristic of the clade 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 (LPSN). The phylogeny is based on whole-genome analysis.

Notes

References

Notes

References

References

1. (1997). "Proposal for a new hierarchic classification system, ''Actinobacteria'' classis nov.". Int. J. Syst. Bacteriol..
2. "''Bifidobacteriaceae''". [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN).
3. Alessandri G, van Sinderen D, Ventura M.. (2021). "The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host.". Comput Struct Biotechnol J..
5. Ludwig, W., Euzéby, J.P. and Whitman, W.B.. (2015). "Taxonomic outline of the phylum Actinobacteria". Bergey's Manual of Systematics of Archaea and Bacteria.
6. Silva JK, Herve V, Mies US, Platt K, Brune A.. (2025). "A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.". Environ Microbiol.
7. https://pubchem.ncbi.nlm.nih.gov/pathway/BioCyc:META_P124-PWY
8. Turroni F, Milani C, Duranti S, Mahony J, van Sinderen D, Ventura M.. (2018). "Glycan Utilization and Cross-Feeding Activities by Bifidobacteria.". Trends Microbiol..
9. (2012). "Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria". Microbiology and Molecular Biology Reviews.
10. (February 2009). "Association between Bifidobacteriaceae and the clinical severity of root caries lesions". Oral Microbiol. Immunol..
11. Ludwig, W., Euzéby, J.P. and Whitman, W.B.. (2015). "Taxonomic outline of the phylum Actinobacteria". Bergey's Manual of Systematics of Archaea and Bacteria.
12. Silva JK, Herve V, Mies US, Platt K, Brune A.. (2025). "A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.". Environ Microbiol.
13. (2012). "Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria". Microbiology and Molecular Biology Reviews.
14. (2018). "Genome-Based Taxonomic Classification of the Phylum ''Actinobacteria''". Front. Microbiol..