Original Article

The ISME Journal advance online publication 22 August 2017; doi: 10.1038/ismej.2017.138

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life

Christian Milani1, Marta Mangifesta1,2, Leonardo Mancabelli1, Gabriele A Lugli1, Kieran James3, Sabrina Duranti1, Francesca Turroni1, Chiara Ferrario1, Maria C Ossiprandi4, Douwe van Sinderen3 and Marco Ventura1

  1. 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
  2. 2GenProbio srl, Parma, Italy
  3. 3APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
  4. 4Department of Medical-Veterinary Science, University of Parma, Parma, Italy

Correspondence: M Ventura, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy. E-mail: marco.ventura@unipr.it

Received 6 April 2017; Revised 29 May 2017; Accepted 14 July 2017
Advance online publication 22 August 2017

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Abstract

Internally transcribed spacer (ITS) rRNA profiling is a novel tool for detailed analysis of microbial populations at low taxonomic ranks. Here we exploited this approach to explore species-level biogeography of the Bifidobacterium genus across 291 adult mammals. These include humans and 13 other primates, domesticated animals, such as dogs, cats, cows, sheep, goats, horses and pigs, and 46 additional species. The collected profiles revealed the presence of 89 putative novel bifidobacterial taxa in addition to 45 previously described species. Remarkably, in contrast to what is currently known for many gut commensals, we did not observe host-specialization among bifidobacterial species but rather their widespread distribution across mammals. Moreover, ITS rRNA profiling of wild relatives of domesticated dogs, rabbits and pigs clearly indicates that domestication and close contact with humans have impacted on the composition of the fecal bifidobacterial population. These data were complemented by analysis of bifidobacterial communities in milk of eight mammalian families, showing that bifidobacteria represent prototypical early gut microbiota members which are inherited by newborns from their lactating mother. Thus this study highlights the role of bifidobacteria as pioneering gut colonizers of a wide range of mammals.