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Botaccini, Francesca et al. ; Bifidobacteria are known as anaerobic/microaerophilic and fermentative microorganisms, which commonly inhabit the gastrointestinal tract of various animals and insects. Analysis of the 2,167,301 bp genome of Bifidobacterium asteroides PRL2011, a strain isolated from the hindgut of Apis mellifera var. ligustica, commonly known as the honey bee, revealed its predicted capability for respiratory metabolism. Conservation of the latter gene clusters in various B. asteroides strains enforces the notion that respiration is a common metabolic feature of this ancient bifidobacterial species, which has been lost in currently known mammal-derived Bifidobacterium species. In fact, phylogenomic based analyses suggested an ancient origin of B. asteroides and indicates it as an ancestor of the genus Bifidobacterium. Furthermore, the B. asteroides PRL2011 genome encodes various enzymes for coping with toxic products that arise as a result of oxygen-mediated respiration. © 2012 Bottacini et al. ; This work was financially supported by the Cariparma Bank Foundation to MV. This work was also financially supported by a Federation European Microbiology society (FEMS) Advanced Fellowship 2011 and an Irish Research Council for Science, Engineering & Technology (IRCSET) Embark postdoctoral fellowship to FT. DV is a member of The Alimentary Pharmabiotic Centre and the Alimentary Glycoscience Research Cluster, both funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan (grant nos. 07/CE/B1368 and 08/SRC/B1393, respectively). ; Peer Reviewed

Bifidobacteria are common and frequently dominant members of the gut microbiota of many animals, including mammals and insects. Carbohydrates are considered key carbon sources for the gut microbiota, imposing strong selective pressure on the complex microbial consortium of the gut. Despite its importance, the genetic traits that facilitate carbohydrate utilization by gut microbiota members are still poorly characterized. Here, genome analyses of 47 representative Bifidobacterium (sub)species revealed the genes predicted to be required for the degradation and internalization of a wide range of carbohydrates, outnumbering those found in many other gut microbiota members. The glycan-degrading abilities of bifidobacteria are believed to reflect available carbon sources in the mammalian gut. Furthermore, transcriptome profiling of bifidobacterial genomes supported the involvement of various chromosomal loci in glycan metabolism. The widespread occurrence of bifidobacterial saccharolytic features is in line with metagenomic and metatranscriptomic datasets obtained from human adult/infant faecal samples, thereby supporting the notion that bifidobacteria expand the human glycobiome. This study also underscores the hypothesis of saccharidic resource sharing among bifidobacteria through species-specific metabolic specialization and cross feeding, thereby forging trophic relationships between members of the gut microbiota. ; We thank GenProbio srl for financial support of the Laboratory of Probiogenomics. This work was financially supported by a FEMS Jensen Award to FT, and by a Ph.D. fellowship (Spinner 2013, Regione Emilia Romagna) to S.D. DvS and FT are members of The APC Microbiome Institute, while DvS is also a member of the Alimentary Glycoscience Research Cluster, both funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan (Grant numbers SFI/12/RC/2273 and 08/SRC/B1393, respectively). This work was also partially supported by Fondazione Caritro, by the EU FP7 (PCIG13- GA-2013-618833), and by MIUR "Futuro in Ricerca" E68C13000500001 to NS. Furthermore, this project has been funded in part with funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900018C. ; Peer Reviewed

Adaptation and tolerance to bile stress are important factors for the survival of bifidobacteria in the intestinal tract. Bifidobacterium animalis is a probiotic microorganism which has been largely applied in fermented dairy foods due to its technological properties and its health-promoting effects for humans. The effect of the presence of bile on the activity and expression of F1F0-ATPase, the pool of ATP and the intracellular pH of B. animalis IPLA 4549 and its mutant with acquired resistance to bile B. animalis 4549dOx was determined. The bile-resistant mutant tolerated the acid pH better than its parent strain. Bile induced the expression of the F1F0-ATPase and increased the membrane-bound H+-ATPase activity, in both parent and mutant strains. In acidic conditions (pH 5.0), the expression and the activity of this enzyme were higher in the mutant than in the parent strain when cells were grown in the absence of bile. Total ATP content was higher for the mutant in the absence of bile, whereas the presence of bile induced a decrease of intracellular ATP levels, which was much more pronounced for the parent strain. At pH 4.0, and independently on the presence or absence of bile, the mutant showed a higher intracellular pH than its parent strain. These findings suggest that the bile-adapted B. animalis strain is able to tolerate bile by increasing the intracellular ATP reserve, and by inducing proton pumping by the F1F0-ATPase, therefore tightly regulating the internal pH, and provide a link between the physiological state of the cell and the response to bile ; This work was financed by European Union FEDER funds and the Spanish Plan Nacional de I + D (AGL2004-06727-C02-01/ALI). B.S. was the recipient of a FPI predoctoral fellowship from the Spanish Ministerio de Educación y Ciencia. ; Peer reviewed

Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease in humans and is characterized by the presence of hyperactive immune cells and aberrant antibody responses to nuclear and cytoplasmic antigens, including characteristic anti–double-stranded DNA antibodies. We performed a cross-sectional study in order to determine if an SLE-associated gut dysbiosis exists in patients without active disease. A group of 20 SLE patients in remission, for which there was strict inclusion and exclusion criteria, was recruited, and we used an optimized Ion Torrent 16S rRNA gene-based analysis protocol to decipher the fecal microbial profiles of these patients and compare them with those of 20 age- and sex-matched healthy control subjects. We found diversity to be comparable based on Shannon's index. However, we saw a significantly lower Firmicutes/Bacteroidetes ratio in SLE individuals (median ratio, 1.97) than in healthy subjects (median ratio, 4.86; P < 0.002). A lower Firmicutes/Bacteroidetes ratio in SLE individuals was corroborated by quantitative PCR analysis. Notably, a decrease of some Firmicutes families was also detected. This dysbiosis is reflected, based on in silico functional inference, in an overrepresentation of oxidative phosphorylation and glycan utilization pathways in SLE patient microbiota. IMPORTANCE: Growing evidence suggests that the gut microbiota might impact symptoms and progression of some autoimmune diseases. However, how and why this microbial community influences SLE remains to be elucidated. This is the first report describing an SLE-associated intestinal dysbiosis, and it contributes to the understanding of the interplay between the intestinal microbiota and the host in autoimmune disorders. © 2014 Hevia et al. ; This study was financed by European Union FEDER funds and the Spanish Plan Nacional de I+D (grant AGL2010-14952). Arancha Hevia was the recipient of an FPI grant, and Borja Sánchez was the recipient of a Juan de la Cierva postdoctoral contract, both from the Spanish Ministerio de Ciencia e Innovación. ; Peer Reviewed

The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome. Bioactivity prediction is based on the global alignment of the automatically processed peptides with experimentally validated immunomodulatory and antiproliferative peptides, in the reference section. MAHMI provides researchers with a comparative tool for inspecting the potential immunomodulatory or antiproliferative bioactivity of new amino acidic sequences and identifying promising peptides to be further investigated. Moreover, researchers are welcome to submit new experimental evidence on peptide bioactivity, namely, empiric and structural data, as a proactive, expert means to keep the database updated and improve the implemented bioactivity prediction method. Bioactive peptides identified by MAHMI have a huge biotechnological potential, including the manipulation of aberrant immune responses and the design of new functional ingredients/foods based on the genetic sequences of the human microbiome. Hopefully, the resources provided by MAHMI will be useful to those researching gastrointestinal disorders of autoimmune and inflammatory nature, such as Inflammatory Bowel Diseases. MAHMI database is routinely updated and is available free of charge. ; This work was funded by the Grant AGL2013-44039-R from the Spanish "Plan Estatal de I + D+I", and the Grant EM2014/046 from the "Plan Galego de investigación, innovación e crecemento 2011-2015". Borja Sánchez was recipient of a Ramón y Cajal postdoctoral contract from the Spanish Ministry of Economy and Competitiveness. This work was also partially funded by the [14VI05] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273) and the European Union's Seventh Framework Programme FP7/REGPOT-2012-2013.1 under grant agreement n° 316265, BIOCAPS. ; Peer reviewed

Bifidobacteria are commensal microoganisms found in the gastrointestinal tract. Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics, and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization, or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota, and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs. ; This research was funded by Grant AGL2013-44039-R from the Spanish "Plan Estatal de I+D+I." LR has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/ under REA grant agreement n°624773. BS was recipient of a Ramón y Cajal postdoctoral contract from the Spanish Ministry of Economy and Competitiveness. SD is hired on a contract supported by BIO2014-55019-JIN project from the Spanish "Plan Estatal de I+D+I." ; Peer Reviewed

Our group has recently shown the existence of a gut microbial dysbiosis in systemic lupus erythematosus (SLE), supporting previous evidence involving intestinal bacteria in the initiation and amplification of autoimmune diseases. While several studies have addressed the use of dietary fibres to modify intestinal microbiota, information about other correlated components, such as polyphenols, is scarce. The aim of this work was to identify dietary components able to influence this altered microbiota in 20 SLE women and 20 age-matched controls. Food intake was recorded by means of a food frequency questionnaire. The intake of fibres was calculated from Marlett tables, and Phenol-Explorer was used for polyphenol consumption. Results showed positive associations between flavone intake and Blautia, flavanones and Lactobacillus, and dihydrochalcones and Bifidobacterium in the SLE group. Regarding the controls, dihydroflavonols were directly associated with Faecalibacterium, whereas flavonol intake was inversely associated with Bifidobacterium. From the food sources of these polyphenols related to microbiota, orange intake was directly associated with Lactobacillus and apple with Bifidobacterium in SLE, whilst red wine was the best contributor to Faecalibacterium variation. The association between common foods and particular microbial genera, reported to be decreased in SLE, could be of great importance for these patients. ; This study was financed by European Union FEDER funds and the Spanish Plan Nacional de I+D (grant AGL2010-14952). We are most grateful to the Asociación Lúpicos Asturias (ALAS) and all the volunteers participating in the study. We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI). ; Peer reviewed

Bifidobacterium animalis ssp. lactis is a probiotic frequently used as adjunct culture in fermented dairy products. In order to ensure its proper function at the intestinal level, this bacterium has to be tolerant to physiological concentrations of bile. This study examined the influence of bile on the fatty acid composition and the membrane characteristics of B. animalis IPLA 4549 and its mutant with acquired resistance to bile, B. animalis 4549dOx. Bile adaptation triggers in B. animalis 4549dOx a decrease in membrane fluidity and in the protein : phospholipid ratio, as well as a shift in the fatty acid composition of the cell. Remarkably, the presence of bile in the growth medium induced similar changes in both B. animalis cells. Furthermore, transmission electron microscopy analysis showed that bile promotes a severe distortion of the cell surface. This study provides new insights of the action of bile on the cell envelope of bifidobacteria ; This work was financed by European Union FEDER funds and the Spanish Plan Nacional de I+D (project AGL2004-06727-C02-01/ALI). Lorena Ruiz was supported by an I3P predoctoral fellowship granted by CSIC and FEDER funds, and Borja Sánchez was the recipient of a FPI predoctoral fellowship from the Spanish Ministry of Education and Science. ; Peer reviewed

This work was supported by European Union FEDER funds, Fondo de Investigación Sanitaria (PI12/00523), Spanish Plan Nacional de I+D (AGL2010-14952 and AGL2013-44039-R) and Fundación para el Fomento en Asturias de la Investigación Científica Aplicada y la Tecnología (EQUIP09-19). J.R.-C. is a recipient of a FPU grant from the Spanish Ministerio de Educación, Cultura y Deporte. B.J. and A.H. are recipients of a Ramón y Cajal postdoctoral contract and a FPI grant, respectively, both from the Spanish Ministerio deEconomía y Competitividad. We thank SLE patients and ALAS (Asociación Lúpicos de Asturias) for their continuous encouragement.

Bacteroides is among the most abundant microorganism inhabiting the human intestine. They are saccharolytic bacteria able to use dietary or host-derived glycans as energy sources. Some Bacteroides fragilis strains contribute to the maturation of the immune system but it is also an opportunistic pathogen. The intestine is the habitat of most Bifidobacterium species, some of whose strains are considered probiotics. Bifidobacteria can synthesize exopolysaccharides (EPS), which are complex carbohydrates that may be available in the intestinal environment. We studied the metabolism of B. fragilis when an EPS preparation from bifidobacteria was added to the growth medium compared to its behavior with added glucose. 2D-DIGE coupled with the identification by MALDI-TOF/TOF evidenced proteins that were differentially produced when EPS was added. The results were supported by RT qPCR gene expression analysis. The intracellular and extracellular pattern of certain amino acids, the redox balance and the a-glucosidase activity were differently affected in EPS with respect to glucose. These results allowed us to hypothesize that three general main events, namely the activation of amino acids catabolism, enhancement of the transketolase reaction from the pentose-phosphate cycle, and activation of the succinate-propionate pathway, promote a shift of bacterial metabolism rendering more reducing power and optimizing the energetic yield in the form of ATP when Bacteroides grow with added EPS. Our results expand the knowledge about the capacity of B. fragilis for adapting to complex carbohydrates and amino acids present in the intestinal environment. © 2015 Rios-covian, Sanchez, Salazar, Martinez, Redruello, Gueimonde and De los Reyes-Gavilan. ; This work was financed by projects AGL2010-16525 and AGL2013-43770-R from Plan Nacional/Plan Estatal de I+D+I (Spanish Ministry of Economy and Competitiveness, MINECO). The activity of Probiotics and Prebiotics Group is being partly supported through the Grant GRUPIN14-043 from Plan Regional de Investigación del Principado de Asturias. Both, national and regional grants received cofounding from European Union FEDER funds. DR-C was the recipient of predoctoral FPI fellowship whereas BS enjoys a Ramon and Cajal contract from MINECO. NS benefits from a Clarin post-doctoral contract (Marie Curie European CoFund Program) cofinanced by Plan Regional de Investigación del Principado de Asturias, Spain. We acknowledge the excellent technical assistance of Lidia Alaez, whose technician contract was partially supported by the project AGL2010-16525 and by Plan Regional de Investigación del Principado de Asturias, through the grant COF 13-020. ; Peer Reviewed

This study was financed by European Union FEDER funds and the Spanish Plan Nacional de I+D (grant AGL2010-14952).

This work was financed by European Union FEDER funds, the Spanish Plan Nacional de I D (projects AGL2007-61805, AGL2009-09445, and AGL2010-14952), and the Consejo Superior de Investigaciones Científicas (CSIC PIE 200870I049)

Extracellular proteins of Bifidobacterium longum may mediate important interactions with the host. Here, we report on a comprehensive analysis of such proteins by using protein-free culture conditions and two-dimensional gel electrophoresis followed by mass spectrometry for protein identification. Seventeen proteins were detected in the culture supernatant, and 14 of them could be identified. Among these were 3 hypothetical solute-binding proteins of ABC transporters, an invasion-associated protein homolog, putative enzymes catalyzing cell wall turnover, several polypeptides with similarity to bacterial conjugation proteins, and 3 proteins of unknown function. Surprisingly, aldolase, usually considered as a cytoplasmic protein, was found in the culture supernatant. All proteins, excluding aldolase, were predicted to contain a signal peptide and a signal peptide cleavage site in their immature form. Some of the excreted proteins are interesting targets for further genetic and physiological studies ; This work was financed by European Union FEDER funds and the Spanish Plan Nacional de I+D (project AGL2004-06727-C02). B.S. was the recipient of a pre-doctoral fellowship from the Spanish Ministerio de Ciencia y Tecnologia and from the MICA Department of the National Institute for Research in Agronomy (INRA) ; Peer reviewed

Metabolic impairments are a frequent hallmark of systemic lupus erythematosus (SLE). Increased serum levels of free fatty acids (FFA) are commonly found in these patients, although the underlying causes remain elusive. Recently, it has been suggested that factors other than inflammation or clinical features may be involved. The gut microbiota is known to influence the host metabolism, the production of short-chain fatty acids (SCFA) playing a potential role. Taking into account that lupus patients exhibit an intestinal dysbiosis, we wondered whether altered FFA levels may be associated with the intestinal microbial composition in lupus patients. To this aim, total and specific serum FFA levels, fecal SCFA levels, and gut microbiota composition were determined in 21 SLE patients and 25 healthy individuals. The Firmicutes to Bacteroidetes (F/B) ratio was strongly associated with serum FFA levels in healthy controls (HC), even after controlling for confounders. However, this association was not found in lupus patients, where a decreased F/B ratio and increased FFA serum levels were noted. An altered production of SCFA was related to the intestinal dysbiosis in lupus, while SCFA levels paralleled those of serum FFA in HC. Although a different serum FFA profile was not found in SLE, specific FFA showed distinct patterns on a principal component analysis. Immunomodulatory omega-3 FFA were positively correlated to the F/B ratio in HC, but not in SLE. Furthermore, divergent associations were observed for pro- and anti-inflammatory FFA with endothelial activation biomarkers in lupus patients. Overall, these findings support a link between the gut microbial ecology and the host metabolism in the pathological framework of SLE. A potential link between intestinal dysbiosis and surrogate markers of endothelial activation in lupus patients is supported, FFA species having a pivotal role. ; This work was funded through the grants GRUPIN14-043 "Microbiota Humana, Alimentación y Salud" from the "Plan Regional de Investigación del Principado de Asturias" and cofounded from European Union FEDER funds, AGL2010-14952 from the Spanish Ministry of Science and Innovation, and PI012/00523 from the "Fondo de Investigaciones Sanitarias, Instituto de Investigación Carlos III." JR-C is supported by a contract from the grant GRUPIN14-043. ; Peer reviewed ; Peer Reviewed

The proteome of the ropy strain Bifidobacterium animalis subsp. lactis A1dOxR, compared to that of its nonropy isogenic strain, showed an overproduction of a protein involved in rhamnose biosynthesis. Results were confirmed by gene expression analysis, and this fact agreed with the high rhamnose content of the ropy exopolysaccharide. © 2013, American Society for Microbiology. ; This work was financed by the Spanish Ministry of Science and Innovation (MICINN) and FEDER European Union funds through project AGL2009-09445. ; Peer Reviewed