Comparative Genomic Analysis Reveals Ecological Differentiation in the GenusCarnobacterium.
Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study,Carnobacteriumwas used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed thatC. maltaromaticumfollowed byC. divergensare the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified inC. maltaromaticumandC. divergenswith genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast,Carnobacteriumspecies belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalistCarnobacterium.
Laboratoire d'Ingénierie des Biomolécules, École Nationale Supérieure d'Agronomie et des Industries Alimentaires - Université de Lorraine Vandoeuvre-lès-Nancy, France.
Christelle F
CF
Iskandar
Laboratoire d'Ingénierie des Biomolécules, École Nationale Supérieure d'Agronomie et des Industries Alimentaires - Université de Lorraine Vandoeuvre-lès-Nancy, France.
Frédéric
F
Borges
Laboratory of Food Microbiology, Department of Food Science, Fundamental and Applied Research for Animal and Health, University of Liège Liège, Belgium.
Bernard
B
Taminiau
Laboratory of Food Microbiology, Department of Food Science, Fundamental and Applied Research for Animal and Health, University of Liège Liège, Belgium.
Georges
G
Daube
UMR1014 SECALIM, INRA, Oniris Nantes, France.
Monique
M
Zagorec
UMR1014 SECALIM, INRA, Oniris Nantes, France.
Benoît
B
Remenant
Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark.
Jørgen J
JJ
Leisner
Molecular Microbial Ecology Group, University of Copenhagen Copenhagen, Denmark.
Martin A
MA
Hansen
Molecular Microbial Ecology Group, University of Copenhagen Copenhagen, Denmark.
Søren J
SJ
Sørensen
Laboratoire d'Ingénierie des Biomolécules, École Nationale Supérieure d'Agronomie et des Industries Alimentaires - Université de Lorraine Vandoeuvre-lès-Nancy, France.
Cécile
C
Mangavel
Laboratoire d'Ingénierie des Biomolécules, École Nationale Supérieure d'Agronomie et des Industries Alimentaires - Université de Lorraine Vandoeuvre-lès-Nancy, France.
Catherine
C
Cailliez-Grimal
Laboratoire d'Ingénierie des Biomolécules, École Nationale Supérieure d'Agronomie et des Industries Alimentaires - Université de Lorraine Vandoeuvre-lès-Nancy, France.
Anne-Marie
AM
Revol-Junelles
16S meta-barcoding; Carnobacterium; comparative genomic analyses; ecological differentiation; lactic acid bacteria