Microbes and Infection 17 (2015) 1e5 www.elsevier.com/locate/micinf

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To Serve Man*,** Food is on everybody's tongue, at least in the developed, slightly bored countries. Radical nutritional convictions are sprouting and blooming more than ever, and vehement debates about protein and vitamin B12 sources are carried out by every available communication tool, with an ardor once reserved to more spiritual issues. Within the scope of the ongoing gluten-, lactose- and GMO-hysteria and the constantly reshaped insights from nutritionists about the contested superiority of vegetal oils and cow milk [2], the members of the different alimentary beliefs battle fervently for their convictions. The spectrum ranges from raw-vegans over vegetarians, high-protein partisans and bio-food addicts to those who extol the hunter-gatherer paleo-diet [3], as the decadence of humanity obviously initiated with sedentariness, agriculture and stock farming. Books, blogs, conferences, camps, festivals and specialized journals and media - they all convey the persuasion that the right food is the right solution for pretty everything, from smooth skin to curing cancer. It was only a question of time before the intense navelgazing led a focal plane further, into the universe within us. “If you don't like bacteria, you're on the wrong planet”, said the scientist and writer Stewart Brand. Bacteria are everywhere and bacteria have been already everywhere 3.5 billion years before the first multicellular organism appeared [4]. Maybe things started about 2 billion years ago, when an eukaryotic cell swallowed an archaea which subsequently became a mitochondria [5]. For sure, eukaryotic organisms co-evolved over millennia in the constant presence of prokaryotes [4,6]. Actually, 90% of cells of the human body are not human at all and our intestines hold 200 times more noneukaryotic protein-coding genes than our human genome [7]. Bacteria cover nearly every surface of our body and crowd our guts [8], profoundly changing the perception of the human organism from a defined individual to a walking, super-complex ecosystem [4,9]. Thus, from a democratic point of view, it seems quite legitimate for them to have their

* Article highlight based on “Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes” by Guillaume Le Bihan et al. [1]. ** In allusion to: D. Knight, “To serve Man”, Galaxy Science Fiction (1950), 1(2):91e97.

say in the various processes of decision making of their host and comfortable habitat, and in keeping the latter in good shape [1,4]. Consequently, the gut microbiota is by now considered a symbiont part of ourselves [5], hay an organ in its own right, both metabolic and endocrine [10,11], and the extent of its acknowledged influence over the human species grows constantly. Following a combination of the modern fixation on our bowels and the recent metagenomics-euphoria, allowing us to sequence mostly everything we can lay our hands on [12,13], the microbiota and its metabolic products [8] are now responsible of a long list of tasks, either as friend or foe [4]. Some are essential for the correct development and operating of the human body e the anatomical development of the intestinal epithelium, vasculature and nervous system [10,14], teaching tolerance to the immune system [9,15], drug metabolism [10], breaking down inaccessible complex plant polysaccharides [7], energy balance [16], vitamin production [8] and excluding pathogens [9,15]. Others correlate with a large panel of diseases e autoimmune diseases [10,14], metabolic disorders [6,8], muscle wasting [16], and even autism-spectrum disorders (ASD), depression and anxiety [15,17]. Nevertheless, the most intriguing and recent assertions are those affirming that the gut microbiota modulate our brain chemistry along the so called gut-microbiota-brain axis, thus substantially influencing cognitive functions such as learning, memory and decision making and behavioral outputs like emotional states, motivation and stress processing [4e6,17]. The prosaic insight that the human being is technically no more than a huge, hormone-steered organic machine and that all our noble feelings finally boil down to a finite number of chemical reactions is already rather bad for our self-esteem. The idea of them being moreover orchestrated by a bunch of bacteria might by all means trigger the next existential crisis. Allowedly, considering social interactions, such as kissing and food-sharing, and traditions, like the touching of religious objects, simply as a way to horizontally transfer beneficial microbiota [4,6] somehow lacks the minimal amount of romantic embellishment the human mind requires for operating. Or at least how the bacteria want us to perceive things. What relativizes the conspiratorial theories is the fact that most observations to date stem from rodent animal models

http://dx.doi.org/10.1016/j.micinf.2014.11.005 1286-4579/© 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

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[4,9]. Germ-free mice are indeed more stressed and display ASD-like social-cognitive defects but are less anxious, and conversely, depressed and autistic mice harbor altered microbiota [6,10,17]. Remains to prove that humans are as influenceable as mice. Anyhow, several animal models have provided solid arguments that disadvantageous modifications of the bacterial gut population, or dysbioses, can be the cause rather than the consequence of pathologies: for example, the microbiota of obese mice make lean mice put on weight and vice versa [7]. However, the exact quantitative or qualitative alterations responsible of the dysbiotic state remain unclear and controversial. The current consensus is that disease correlates with a loss of diversity and stability of the microbial community [9,10] and rather a shift in the proportions than the appearance or disappearance of different bacterial phyla [5,8,18]. The main question is, how exactly do the bacteria talk to brain and body? There is certainly no shortage of plausible theoretical explanations [4,15,17]. Apart from being in direct contact with the epithelial cells of the intestines and members of the immune system, signaling mainly through pattern recognition receptors (PRRs) such as Toll-like receptors (TLRs) and nucleotide binding oligomerization domains (NODs) [9,10], the microbiota sits at the source and the control center of a plethora of diffusible signaling molecules which can reach virtually any cell of the organism via the blood stream and the lymphatic system [15,16]. Among the metabolites of gut bacteria feature GABA, tryptophan, serotonin, histamine and dopamine, all wellknown neurotransmitters or precursors of the latter [4,6]. After supervising the nutrient uptake, are bacteria also restricting the availability of neurotransmitters, thus directly influencing behavior and cognition [10,14]? It remains however unclear, to what extend the microbial metabolites diffuse and which section of the nervous system is primarily targeted. Some claim that they affect mainly the neurons of the enteric nervous system (ENS), including the vagus nerve [6,17], others that they smoothly cross the blood brain barrier [8]. The other main powerful tool in the imaginary hands of gut bacteria are called short fatty acids (SCFAs), the principal end products of their metabolism after the fermentation of dietary fibers [4,10]. SCFAs, such as acetate, propionate and butyrate, diffuse passively and bind to PRRs and G protein-coupled receptors [7,8], subsequently inducing immune tolerance [14], modulating the release of neuropeptides including serotonin and peptide YY [10] and decreasing inflammation through inhibition of NF-kB activation [8]. On the host side, the molecular crosstalk [5] seems to involve two currently quite popular domains e noncoding RNAs and epigenetics. The previous issue of this column already dealt with the key role of microRNAs (miRNAs) in the interaction of the host organism and various pathogens [19]. In the special case of the gut microbiota, bacteria-

induced host miRNAs are probably essential to fine-tune and buffer the otherwise binary response of the immune system in order to balance tolerance with barrier function [15]. Epigenetics, the adjustment of gene expression and cell fate without modifying the DNA sequence, in turn, are essential for the diversification of the immune system. It turns out that some gut microbes deliver some epigenetic effector proteins, carrying the fancy name of nucleomodulins, starting with the SCFA butyrate, a potent inhibitor of histone deacetylases (HDACs) [6,8]. Remembering the part of the microbiota in educating the host immune system, the theoretically possible link is quickly established [14]. Epigenetic mechanisms also underlie the plastic changes in the brain, shaping cognition and behavior. Theoretically, HDAC inhibition and the control of histone acetylase substrates by the gut bacteria could favor transcription in neurons, memory consolidation and neuroprotection [6]. Theoretically. Needless to say that mankind in turn claims the control over its inhabitants. After providing our bodies with the right diet, it is now time to provide them with the right bacteria. In 1908, Elie Metchnikoff got the Nobel Prize for correlating the longevity of Bulgarians with their penchant for fermented milk and showing that Lactobacillus-containing yogurt reduced the number of toxin-producing bacteria in the gut [8,9]. 105 years later, we got Shakira suggestively shaking her hips for the football World Cup and the Activia® advertising clip. An individual's initial microbiota seems to be a matter both of genes and environment. On the one hand, a recent study on twin pairs highlighted the existence of the gene-dependent, highly heritable taxa Christensenellaceae and their link with body-mass index [20], on the other hand, factors like the mode of delivery, breast milk versus formula feeding [10,14], the use of antibiotics, geographical origin, stress and infections [5,8] further modulate the composition of our intestinal inhabitants. Now, an entire business is growing around their manipulation, including prebiotics, probiotics, antibiotics and even psychobiotics [6,16,17], despite that the European Food Safety Authority (EFSA) just refused the health claims of marketed probiotics for lack of substantial proof of effectiveness. At least, Lactobacilli & Co. obtained the curious title of organisms “Generally Regarded as Safe” (GRAS) [9]. Even the 2000-year old technique of fecal microbiota transplantation is gaining in popularity and has proven to be quite efficient in treating recurrent Clostridium difficile infection and multiple sclerosis [11,21], as well as in avoiding, in form of an ostensively read article, any attempt of conversation from your train or plane neighbor. Beyond doubt, our microbes, spectators of evolution and ontogeny, have still a lot to tell, if they agree. In order to tell apart causality from the secondary effect of sociality, larger metagenome-wide association studies (MGWAS) are needed [4,5,10], larger cohorts and the inclusion of differences in the microbial population according to their location in the gastrointestinal tract into analyses [9,10,17]. Among the countless

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possible actions, experimental proof has to settle what the around 2 kg of microbes in our body are up to. Speaking of that, dear microbes, the next time we go climbing, we seriously need to talk. Biosketch e Gr
egory Jubelin Gr
egory Jubelin got his PhD in microbiology in 2005 at the National Institute of Applied Sciences (INSA, France). He then did two postdoctoral positions at the National Institute for Agricultural Research (INRA, France), working on the functions of virulence factors as well as their regulation networks from several pathogenic bacteria. Since 2010, he occupies a research fellow position at INRA unit UR454 in ClermontFerrand (France). Dr Jubelin's research focuses on enterovirulent E. coli, especially EHEC, and their multiple interactions inside the gut with microbiota and mucosa.

Biosketch e Jos
ee Harel Jos
ee Harel received her Master of Science from the University of Montral (Department of Microbiology and Immunity), her PhD. from the McGill University (Department of Microbiology and Immunology) and did her postdoctoral training at Stanford University Medical School, working on the genetics of Campylobacter jejuni. Jos.e Harel is a professor at the Faculty of Veterinary Medicine at the University of Montral. She recently completed her term as the director of the Research Centre on Swine and Avian Infectiology. She is the co-director of the Laboratory of Molecular Diagnostic of Infectious Diseases. Presently, Dr Harel's research focuses on the mechanisms of regulation of pathogenic E. coli as well as on the development of Streptococcus suis vaccines.

Interview with Gr
egory JUBELIN and Jos
ee HAREL What triggered your interest in the effect of human microbiota on pathogenic enterobacteria?

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G.J.: Since the beginning of my career, I am fascinated by the ability of bacteria to adapt to their environment, owing to their status of single cell organism. Exploring the ability of pathogenic bacteria to adapt to a very complex ecosystem such as the human gut is now possible with the knowledge and methods we've got to study gut microbiota. It was also the opportunity to keep on and develop a great collaboration with the laboratory of Jos
ee Harel. J.H.: I must add that the complicity between our two laboratories is beneficial to our research (for sure to mine). This collaboration is highly valuable for students who are exposed to different concepts and technologies. What was your first reaction when you faced the results? Did you expect them? G.J.: As we evaluated the influence of the microbiota on enterohemorrhagic E. coli by measuring the overall transcript abundance, it was essential to rationalize the large set of data using bioinformatics tools. Transcripts identified in the pathogenic E. coli showed characteristic profiles which correlated with the microbiota environment. In addition, the expression of genes associated with pathogenicity was also shown to be influenced. This was an important first step for further analyses. How will the project go on? G.J.: Yes, our study provided the foundation to further characterize some of the mechanisms by which some microbiota signals influence the pathogenesis mediated by intestinal bacteria. Our preliminary results are quite exciting. What is the take-home message of the article? J.H.: The human gut microbiota, through its composition and metabolic activities, modulates the expression level of hundreds of genes in intestinal pathogens such as EHEC. From these data and others, an emerging open question is to know if differences in gut microbiota between individuals can explain why only 5e10% of EHEC infected patients develop a hemolytic uremic syndrome during an outbreak. Do you have a personal motto, quote or leading sentence? G.J.: “The science of today is the technology of tomorrow” from Edward Teller. The government and funding agencies should keep this in mind for a better future. J.H.: “The first principle is that you must not fool yourself and you are the easiest person to fool”, by Richard Feynman. This motto is very import when analyzing the results! What advice would you give to the young next-generation scientists? G.J.: I'm still a young scientist and it's hard to give some advice to the next generation. I would say: science is moving fast, so stay informed about new technologies that will help you to get answers and, above all, work hard! J.H.: “Study hard what interests you the most in the most undisciplined, irreverent and original manner possible”, from Richard Feynman. What is your favourite hang-out method after a tough day at the lab?

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G.J.: I like to relax after work by discussing with my children to know what they've done during the day. Practice my favorite sports, badminton and volley ball, is also a way to unwind and feel better. J.H.: I need to read books not necessarily related to science, and when I can, I go walking through the woods and enjoy nature. In your opinion, what are the three most important (scientific) discoveries of the last decade? G.J.: The decoding of the human genome, the development of synthetic biology and the discovery of small RNA that has changed our vision of regulatory mechanisms in bacteria. J.H.: I would add: the microbiome contributions to health and disease. If you could travel back in time e what historical personality would you like to meet and what scientific discovery to assist to? G.J.: I would appreciate to travel back to the 17th century and be there when Antony Van Leeuwenhoek saw bacteria for the first time under a magnifying glass. J.H.: I would have like to meet Barbara McClintock 1983 Nobel laureate in Physiology and Medicine and assist the discovery of transposition she did by studying the genetics of maize plants in the forties. I am impressed by her clearsightedness. If you could travel forth in time e what eventual invention would you like to check out? G.J.: Definitely, I would like to improve the ways to prevent, diagnose and treat all forms of cancer in human. J.H.: Exploring our gut microbial communities is allowing us to envision exciting new ways for addressing global health problems. I would like to check out inventions that would modulate the microbiota to prevent and treat diseases such as infectious diseases, also intestinal diseases such as Crohn's disease but also neurodevelopemental diseases such as autism.

In A Nutshell
The authors compared the transcriptome of pathogenic E. coli cultured in the cecal content of germfree (GFC) or human microbiota-containing (HMC) rats
20% of the genome were differently expressed in the 2 conditions
In the HMC profile compared to the GFC context, genes implicated in a glycolytic metabolic profile were downregulated and genes encoding enzymes required for the degradation of alternative carbon sources were upregulated
Moreover, in the HMC context, a large number of virulence genes involved in lesion formation was inhibited / Pathogenic bacteria efficiently adapt to the gut environment via transcriptomic reorganization / The human microbiota and their molecular products impact on the metabolism and the virulence of pathogens

Background
The human gastrointestinal tract harbors between 1013 and 1014 microorganisms, about 10 times more than cells in our body, and 4 to 5 million nonredundant non-human genes, about 200 times the number of human protein-coding genes
The intestinal microbes belong to around 2000 bacterial species but only several hundred species are present in one individual
The “microbiota” is the sum of all micro-organisms of one given host, the “microbiome” or “metagenome” is the sum of all genes of the microbiota
The “enterotype” refers to the inter-individual variation in gut microbiota composition based on the relative abundance of genes with shared molecular functions. To date 3 enterotypes were identified: Bacteroides, Prevotella and Ruminococcus

References [1] Le Bihan G, Jubelin G, Garneau P, Bernalier-Donadille A, Martin C, Beaudry F, et al. Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes. Microbes Infect 2015;17(1):23e33. [2] Micha€elsson K, Wolk A, Langenski€old S, Basu S, Warensj€o Lemming E, Melhus H, et al. Milk intake and risk of mortality and fractures in woman and men: cohort studies. BMJ 2014;349:g6015. [3] www.paleomagonline.com.

Highlight / Microbes and Infection 17 (2015) 1e5 [4] Montiel-Castro AJ, Gonz
alez-Cervantes RM, Bravo-Ruiseco G, Pacheco-L
opez G. The microbiota- gut-brain axis: neurobehavioural correlates, health and sociality. Front Integr Neurosci 2013;7:70. [5] Burcelin R, Serino M, Chabo C, Garidou L, Pomi
e C, Courtney M, et al. Metagenome and metabolism: the tissue microbiota hypothesis. Diabetes Obes Metab 2013;(Suppl. 3):61e70. [6] Stilling RM, Dinan TG, Cryan JF. Microbial genes, brain & behaviour e epigenetic regulation of the gut-brain axis. Genes Brain Behav 2014;13(1):69e86. [7] Tsai YT, Cheng PC, Pan TM. Anti-obesity effects of gut microbiota are associated with lactic acid bacteria. Appl Microbiol Biotechnol 2014;98(1):1e10. [8] Ferreira CM, Vieira AT, Vinolo MA, Oliveira FA, Curi R, Martins Fdos S. The central role of the gut microbiota in chronic inflammatory diseases. J Immunol Res 2014;2014. 689492. [9] Butel MJ. Probiotics, gut microbiota and health. Med Mal Infect 2014;44(1):1e8. [10] Kennedy PJ, Cryan JF, Dinan TG, Clarke G. Irritable bowel syndrome: a microbiome-gut-brain axis disorder? World J Gastroenterol 2014;20(39):14105e25. [11] Borody TJ, Brandt LJ, Paramsothy S. Therapeutic faecal microbiota transplantation: current status and future developments. Curr Opin Gastroenterol 2014;30(1):97e105. [12] http://www.hmpdacc.org/[NIH funded Human Microbiome Project)]. [13] http://www.metahit.eu/[European-based Metagenomics of the Human Intestinal Tract)]. [14] Arrieta MC, Stiemsma LT, Amenyogbe N, Brown EM, Finlay B. The intestinal microbiome in early life: health and disease. Front Immunol 2014;5:427.

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[15] Runtsch MC, Round JL, O'Connell RM. MicroRNAs and the regulation of intestinal homeostasis. Front Genet 2014;5:347. [16] Bindels LB, Delzenne NM. Muscle wasting: the gut microbiota as a new target? Int J Biochem Cell Biol 2013;45(10):2186e90. [17] Dinan TG, Cryan JF. Melancholic microbes: a link between gut microbiota and depression? Neurogastroenterol Motil 2013;25(9):713e9. [18] Ley RE, B€ackhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Sci U S A 2005;102(31):11070e5. [19] H€afner S. The odds of small things. Microbes Infect 2014;16:881e4. [20] Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell 2014;159(4):789e99. [21] http://www.openbiome.org/.

Sophia H€afner* Univ. Paris Diderot, Sorbonne Paris Cit
e, UMR 7216 CNRS, Epigenetics and Cell Fate, 75013 Paris, France *UMR7216 Epigenetics and Cell Fate, Claire Rougeulle Team, Inactivation of the X Chromosome, 35 Rue H
elene Brion, B^atiment Lamarck, Room 422, 75205 Paris Cedex 13, France. Tel./fax: þ33 (0)1 57 27 89 30. E-mail address: [email protected] 20 November 2014 Available online 2 December 2014