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In recent years, bifidobacterial populations in the gut of various monkey species have been assessed in several ecological surveys, unveiling a diverse, yet unexplored ecosystem harbouring novel species. In the current study, we investigated the species distribution of bifidobacteria present in 23 different species of primates, including human samples, by means of 16S rRNA microbial profiling and internal transcribed spacer bifidobacterial profiling. Based on the observed bifidobacterial‐host co‐phylogeny, we found a statistically significant correlation between the Hominidae family and particular bifidobacterial species isolated from humans, indicating phylosymbiosis between these lineages. Furthermore, phylogenetic and glycobiome analyses, based on 40 bifidobacterial species isolated from primates, revealed that members of the Bifidobacterium tissieri phylogenetic group, which are typical gut inhabitants of members of the Cebidae family, descend from an ancient ancestor with respect to other bifidobacterial taxa isolated from primates., Joint Programming Initiative A healthy diet for a healthy life. Grant Number: 15/JP‐HDHL/3280. Science Foundation Ireland. Grant Numbers: SFI/12/RC/2273a, SFI/12/RC/2273b

Initial establishment of the human gut microbiota is generally believed to occur immediately following birth, involving key gut commensals such as bifidobacteria that are acquired from the mother. The subsequent development of this early gut microbiota is driven and modulated by specific dietary compounds present in human milk that support selective colonization. This represents a very intriguing example of host-microbe co-evolution, where both partners are believed to benefit. In recent years, various publications have focused on dissecting microbial infant gut communities and their interaction with their human host, being a determining factor in host physiology and metabolic activities. Such studies have highlighted a reduction of microbial diversity and/or an aberrant microbiota composition, sometimes referred to as dysbiosis, which may manifest itself during the early stage of life, i.e., in infants, or later stages of life. There are growing experimental data that may explain how the early human gut microbiota affects risk factors related to adult health conditions. This concept has fueled the development of various nutritional strategies, many of which are based on probiotics and/or prebiotics, to shape the infant microbiota. In this review, we will present the current state of the art regarding the infant gut microbiota and the role of key commensal microorganisms like bifidobacteria in the establishment of the first microbial communities in the human gut., This work was primarily funded by the EU Joint Programming Initiative – A Healthy Diet for a Healthy Life (JPI HDHL, http://www.healthydietforhealthylife.eu/) to DvS (in conjunction with Science Foundation Ireland [SFI], Grant number 15/JP-HDHL/3280) and to MV (in conjunction with MIUR, Italy). D.v.S. is member of APC microbiome Ireland which is funded by SFI through the Irish Government’s National Development Plan (Grant Numbers SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2). The study is supported by Fondazione Cariparma, under TeachInParma Project (DV).

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease., This work was funded by the EU Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL, http://www.healthydietforhealthylife.eu/) and MIUR to M.V. and by the Spanish MINECO to M.G. (project PCIN-2015-233). A.M. and S.D.P. are partially funded by grants from the Instituto Danone and by the Spanish Plan Estatal de I+D+I (reference AGL2016-78311-R). D.V.S. is a member of the APC Microbiome Institute funded by Science Foundation Ireland (SFI) through the Irish Government's National Development Plan (grant number SFI/12/RC/2273). J.M.R. is in receipt of AGL2016-75476-R (Ministerio de Economía y Competitividad (Spain). J.M. is in receipt of a Starting Investigator Research Grant (SIRG) (no. 15/SIRG/3430) funded by Science Foundation Ireland (SFI).

We report the complete genome sequence of Bifidobacterium longum W11 (LMG P-21586) isolated from the intestinal microbiota of a healthy man. The analysis of the sequence may provide insights into the microbiological characteristics and the functional activity of this probiotic strain.

Bifidobacteria are members of the human gut microbiota, being numerically dominant in the colon of infants, while also being prevalent in the large intestine of adults. In this study, we determined and analyzed the pan-genome of Bifidobacterium adolescentis, which is one of many bacteria found in the human adult gut microbiota. In silico analysis of the genome sequences of eighteen B. adolescentis strains isolated from various environments, such as human milk, human feces and bovine rumen, revealed a high level of genetic variability, resulting in an open pan-genome. Compared to other bifidobacterial taxa such as Bifidobacterium bifidum and Bifidobacterium breve, the more extensive B. adolescentis pan-genome supports the hypothesis that the genetic arsenal of this taxon expanded so as to become more adaptable to the variable and changing ecological niche of the gut. These increased genetic capabilities are particularly evident for genes required for dietary glycan-breakdown, This work was financially supported by a PostDoc fellowship (Fondazione Caritro) to SD. DvS is member of The APC Microbiome Institute funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan (Grant number SFI/12/RC/2273).

Trabajo presentado en el 4th International Symposium on Propionibacteria and Bifidobacteria (PropioBifido 2016), celebrado en la Universidad de Cork (Irlanda) del 21 al 23 de septiembre de 2016, Bacteria are able to synthesize a variety of polysaccharides with different functions that can be classified according to their sugar composition (homo- or hetero-polysaccharides) and their location on the cell surface. In this context, capsular polysaccharides are bound to the cell surface, while exopolysaccharides or EPS are secreted and released in the environment. In gut commensals, these macromolecules are claimed to protect bacterial cells against gastrointestinal challenges and to be involved in modulating the cross talk with the host. Bifidobacteria are indigenous inhabitants of the human gastro intestinal tract and are one of the first bacterial colonizers following birth. The predicted EPS arsenal of the Bifidobacterium genus, which we designate here as the eps-ome, consists of nine eps gene clusters conserved among different bifidobacterial species and a further 44 unique eps loci, together representing a large proportion of the inter(sub)species variability identified among bifidobacterial genomes. Moreover, phenotypic analyses highlighted not a consensus phenotype of EPS production. Co-cultivations of bifidobacterial species in media simulating adult and infant human gut environments was shown to prompt an enhancement of the number of genes transcribed in all strains tested in monoassociation and multi-associations. Transcription of eps genes was enhanced in fecal media, compared to reference condition in both mono- or multi- associations experiments. In particular, transcriptomic analyses resulted in an increased transcription of key genes for EPS biosynthesis, including glycosyltransferaseencoding genes, as well as genes specifying EPS transporter and polysaccharide biosynthesis protein.