Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2014 Aug 3

PMID 25085493

Citations 137

Authors

Christian Milani

Gabriele Andrea Lugli

Sabrina Duranti

Francesca Turroni

Francesca Bottacini

Marta Mangifesta

Borja Sanchez

Alice Viappiani

Leonardo Mancabelli

Bernard Taminiau

Veronique Delcenserie

Rodolphe Barrangou

Abelardo Margolles

Douwe Van Sinderen

Marco Ventura

Affiliations

Soon will be listed here.

Abstract

Bifidobacteria represent one of the dominant microbial groups that are present in the gut of various animals, being particularly prevalent during the suckling stage of life of humans and other mammals. However, the overall genome structure of this group of microorganisms remains largely unexplored. Here, we sequenced the genomes of 42 representative (sub)species across the Bifidobacterium genus and used this information to explore the overall genetic picture of this bacterial group. Furthermore, the genomic data described here were used to reconstruct the evolutionary development of the Bifidobacterium genus. This reconstruction suggests that its evolution was substantially influenced by genetic adaptations to obtain access to glycans, thereby representing a common and potent evolutionary force in shaping bifidobacterial genomes.

Citing Articles

Genomic insights into the beneficial potential of and strains isolated from Cameroonian infants.

Kaktcham P, Kujawska M, Kouam E, Piame L, Tientcheu M, Mueller J Microb Genom. 2025; 11(2).

PMID: 39969280 PMC: 11840169. DOI: 10.1099/mgen.0.001354.

Antioxidant and anti-inflammatory properties of water kefir microbiota and its bioactive metabolites for health promoting bio-functional products and applications.

Papadopoulou D, Chrysikopoulou V, Rampaouni A, Tsoupras A AIMS Microbiol. 2024; 10(4):756-811.

PMID: 39628717 PMC: 11609422. DOI: 10.3934/microbiol.2024034.

Development of Alginate Composite Microparticles for Encapsulation of subsp. .

Vincekovic M, Zivkovic L, Turkeyeva E, Mutaliyeva B, Madybekova G, Segota S Gels. 2024; 10(11).

PMID: 39590108 PMC: 11593877. DOI: 10.3390/gels10110752.

Molecular cross-talk among human intestinal bifidobacteria as explored by a human gut model.

Rizzo S, Alessandri G, Tarracchini C, Bianchi M, Viappiani A, Mancabelli L Front Microbiol. 2024; 15:1435960.

PMID: 39314876 PMC: 11418510. DOI: 10.3389/fmicb.2024.1435960.

From raw milk cheese to the gut: investigating the colonization strategies of .

Longhi G, Lugli G, Tarracchini C, Fontana F, Bianchi M, Carli E Appl Environ Microbiol. 2024; 90(9):e0124424.

PMID: 39150265 PMC: 11409640. DOI: 10.1128/aem.01244-24.

References

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

Pfeiffer T, Schuster S, Bonhoeffer S . Cooperation and competition in the evolution of ATP-producing pathways. Science. 2001; 292(5516):504-7. DOI: 10.1126/science.1058079. View

Segata N, Bornigen D, Morgan X, Huttenhower C . PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013; 4:2304. PMC: 3760377. DOI: 10.1038/ncomms3304. View

Ventura M, Canchaya C, Del Casale A, Dellaglio F, Neviani E, Fitzgerald G . Analysis of bifidobacterial evolution using a multilocus approach. Int J Syst Evol Microbiol. 2006; 56(Pt 12):2783-2792. DOI: 10.1099/ijs.0.64233-0. View

Borisov V, Gennis R, Hemp J, Verkhovsky M . The cytochrome bd respiratory oxygen reductases. Biochim Biophys Acta. 2011; 1807(11):1398-413. PMC: 3171616. DOI: 10.1016/j.bbabio.2011.06.016. View

Ventura M, Turroni F, Lugli G, Van Sinderen D . Bifidobacteria and humans: our special friends, from ecological to genomics perspectives. J Sci Food Agric. 2013; 94(2):163-8. DOI: 10.1002/jsfa.6356. View

Malago J, Tooten P, Koninkx J . Anti-inflammatory properties of probiotic bacteria on Salmonella-induced IL-8 synthesis in enterocyte-like Caco-2 cells. Benef Microbes. 2011; 1(2):121-30. DOI: 10.3920/BM2009.0021. View

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M . Artemis: sequence visualization and annotation. Bioinformatics. 2000; 16(10):944-5. DOI: 10.1093/bioinformatics/16.10.944. View

Ye Y, Wei B, Wen L, Rayner S . BlastGraph: a comparative genomics tool based on BLAST and graph algorithms. Bioinformatics. 2013; 29(24):3222-4. PMC: 5994941. DOI: 10.1093/bioinformatics/btt553. View

10.

Guglielmetti S, Mora D, Gschwender M, Popp K . Randomised clinical trial: Bifidobacterium bifidum MIMBb75 significantly alleviates irritable bowel syndrome and improves quality of life--a double-blind, placebo-controlled study. Aliment Pharmacol Ther. 2011; 33(10):1123-32. DOI: 10.1111/j.1365-2036.2011.04633.x. View

11.

Lin J, Stewart V . Nitrate assimilation by bacteria. Adv Microb Physiol. 1997; 39:1-30, 379. DOI: 10.1016/s0065-2911(08)60014-4. View

12.

Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J . PGAP: pan-genomes analysis pipeline. Bioinformatics. 2011; 28(3):416-8. PMC: 3268234. DOI: 10.1093/bioinformatics/btr655. View

13.

Katoh K, Misawa K, Kuma K, Miyata T . MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30(14):3059-66. PMC: 135756. DOI: 10.1093/nar/gkf436. View

14.

Eberl M, Hintz M, Reichenberg A, Kollas A, Wiesner J, Jomaa H . Microbial isoprenoid biosynthesis and human gammadelta T cell activation. FEBS Lett. 2003; 544(1-3):4-10. DOI: 10.1016/s0014-5793(03)00483-6. View

15.

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

16.

Callister S, McCue L, Turse J, Monroe M, Auberry K, Smith R . Comparative bacterial proteomics: analysis of the core genome concept. PLoS One. 2008; 3(2):e1542. PMC: 2213561. DOI: 10.1371/journal.pone.0001542. View

17.

Loquasto J, Barrangou R, Dudley E, Roberts R . Short communication: the complete genome sequence of Bifidobacterium animalis subspecies animalis ATCC 25527(T) and comparative analysis of growth in milk with B. animalis subspecies lactis DSM 10140(T). J Dairy Sci. 2011; 94(12):5864-70. DOI: 10.3168/jds.2011-4499. View

18.

Heuston S, Begley M, Davey M, Eberl M, Casey P, Hill C . HmgR, a key enzyme in the mevalonate pathway for isoprenoid biosynthesis, is essential for growth of Listeria monocytogenes EGDe. Microbiology (Reading). 2012; 158(Pt 7):1684-1693. DOI: 10.1099/mic.0.056069-0. View

19.

Schmid R, Blaxter M . annot8r: GO, EC and KEGG annotation of EST datasets. BMC Bioinformatics. 2008; 9:180. PMC: 2324097. DOI: 10.1186/1471-2105-9-180. View

20.

Lowe T, Eddy S . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. PMC: 146525. DOI: 10.1093/nar/25.5.955. View