GENOMICS, TRANSCRIPTOMICS, PROTEOMICS Staying alive: growth and survival of Bifidobacterium animalis subsp. animalis under in vitro and in vivo conditions Muireann Egan 1 & Francesca Bottacini 1 & Mary O’Connell Motherway 1 & Patrick G. Casey 1 & Ruth Morrissey 1 & Silvia Melgar 1 & Jean-Michel Faurie 2 & Christian Chervaux 2 & Tamara Smokvina 2 & Douwe van Sinderen 1 Received: 7 June 2018 /Revised: 8 September 2018 /Accepted: 16 September 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Members of the Bifidobacterium genus are widely used as probiotics in fermented milk products. Bifidobacterium animalis subsp. animalis CNCM I-4602 grows and survives poorly in reconstituted skimmed milk (RSM). Availing of genome and transcriptome information, this poor growth and survival phenotype in milk was substantially improved by the addition of certain compounds, such as yeast extract, uric acid, glutathione, cysteine, ferrous sulfate, and a combination of magnesium sulfate and manganese sulfate. Carbohydrate utilization of CNCM I-4602 was also investigated, allowing the identification of several carbohydrate utilization gene clusters, and highlighting this strain’s inability to utilize lactose, unlike the type strain of this subspecies, B. animalis subsp. animalis ATCC25527 and the B. animalis subsp. lactis subspecies. In addition, the ability of B. animalis subsp. animalis CNCM I-4602 to colonize a murine model was investigated, which showed that this strain persists in the murine gut for a period of at least 4 weeks. Associated in vivo transcriptome analysis revealed that, among other genes, a gene cluster encoding a predicted type IVb tight adherence (Tad) pilus was upregulated, indicating that this extracellular structure plays a role in the colonization/adaptation of the murine gastrointestinal tract by this strain. Keywords Bifidobacteria . Genome sequencing . Reconstituted skimmed milk . Transcriptomics . Probiotic . Gastrointestinal tract Introduction Bifidobacteria are gram-positive, anaerobic, typically Y- shaped bacteria, which are found in the gastrointestinal tract (GIT) of various animals, while also isolated from the human oral cavity and sewage (Milani et al. 2014). The GIT is the natural habitat for a dense and diverse bacterial community, which contributes to human health through a variety of routes, such as metabolic activities to provide energy and nutrients to the host (Ferrario et al. 2017; Holmes et al. 2012; LeBlanc et al. 2013; Milani et al. 2017; Vaughan et al. 2005; Ventura et al. 2018), or development of the immune system and pro- tection against disease (de Almada et al. 2015; Round and Mazmanian 2009; Ventura et al. 2012). Therefore, various members of the Bifidobacterium genus are exploited as probiotics, defined as Blive microorganisms that, when admin- istered in adequate amounts, confer a health benefit on the host^ (FAO/WHO 2001). Strains of Bifidobacterium animalis subsp. lactis are widely used as probiotic ingredients in fermented food products, and their claimed health benefits have been scientifically supported (Agrawal et al. 2009; Eskesen et al. 2015; Guyonnet et al. 2009; Jungersen et al. 2014; Marteau et al. 2013; Martin et al. 2016; Rizzardini et al. 2012; Tillisch et al. 2013). However, as stated in the definition above, for probiotic bac- teria to assert such health benefits, they must be present in adequate amounts and be viable (Boylston et al. 2004; Jay et al. 2012; Ouwehand and Salminen 1998; Phillips et al. 2006; Raeisi et al. 2013; Sanders and in’t Veld 1999). The viability of (probiotic) bacteria in food is dependent on various physicochemical properties of the food matrix, such as pH, Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00253-018-9413-7) contains supplementary material, which is available to authorized users. * Douwe van Sinderen d.vansinderen@ucc.ie 1 APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork, Ireland 2 Danone Nutricia Research, Avenue de la Vauve, 91767 Palaiseau, France Applied Microbiology and Biotechnology https://doi.org/10.1007/s00253-018-9413-7