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The gastrointestinal microbiome comprises trillions of bacteria, and is a vitally important organ with wide ranging effects on pet health
Food impacts the composition and metabolism of the microbiome, as well as the production of postbiotics, which are bioactive end products of microbial consumption of prebiotics. Postbiotics include metabolites of nutrients like fatty acids, amino acids, vitamins and polysaccharides. Also gut bacteria can produce postbiotics from plant antioxidants like polyphenols. A growing body of evidence has shown that influencing postbiotic production may have beneficial effects on pet health. Soluble and insoluble fibers are commonly used sources of prebiotics in the pet food industry, some of these fibers have polyphenols bound to them. Understanding the impact of each fiber type on the microbiome composition, metabolism and postbiotic production provides insights into formulating foods that are optimal for pet health.

Changes in the human gastrointestinal microbiome are associated with several diseases. To infer causality, experiments in representative models are essential, but widely used animal models exhibit limitations. Here we present a modular, microfluidics-based model (HuMiX, human-microbial crosstalk), which allows co-culture of human and microbial cells under conditions representative of the gastrointestinal human-microbe interface. We demonstrate the ability of HuMiX to recapitulate in vivo transcriptional, metabolic and immunological responses in human intestinal epithelial cells following their co-culture with the commensal Lactobacillus rhamnosus GG (LGG) grown under anaerobic conditions. In addition, we show that the co-culture of human epithelial cells with the obligate anaerobe Bacteroides caccae and LGG results in a transcriptional response, which is distinct from that of a co-culture solely comprising LGG. HuMiX facilitates investigations of host-microbe molecular interactions and provides insights into a range of fundamental research questions linking the gastrointestinal microbiome to human health and disease. ; We thank the scientists and technical staff of the Luxembourg Centre for Systems Biomedicine and Center for Applied Nanobioscience and Medicine, particularly Matthew Barrett and Brett Duane for their excellent technical assistance and engineering support. We are grateful to Francois Bernardin, Nathalie Nicot and Laurent Vallar for the microarray analysis; Aidos Baumuratov for imaging support; Linda Wampach for HuMiX illustrations; and Anna Heintz-Buschart for fruitful discussions. This work was supported by an ATTRACT programme grant (ATTRACT/A09/03), a CORE programme grant (CORE/11/BM/1186762), a European Union Joint Programming in Neurodegenerative Diseases grant (INTER/JPND/12/01) and a Proof-of-Concept grant (PoC-15/11014639) to P.W., Accompany Measures mobility grant (12/AM2c/05) to P.W. and P.S., an INTER mobility grant to P.S. (INTER/14/7516918), and an Aide a la Formation Recherche (AFR) postdoctoral grant (AFR/PDR 2013-1/BM/5821107) as well as a CORE programme grant (CORE/14/BM/8066232) to J.V.F., all funded by the Luxembourg National Research Fund (FNR). This work was further supported by a grant attributed to C.S.-D. by the 'Fondation Recherche sur le SIDA du Luxembourg'. Bioinformatics analyses presented in this paper were carried out in part using the HPC facilities of the University of Luxembourg (http://hpc.uni.lu). ; This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.

Background/Aims: Current models of Crohn's disease (CD) describe an inappropriate immune response to gut microbiota in genetically susceptible individuals. NOD2 variants are strongly associated with development of CD, and NOD2 is part of the innate immune response to bacteria. This study aimed to identify differences in fecal microbiota in CD patients and non-IBD controls stratified by NOD2 genotype. Methods: Patients with CD and non-IBD controls of known NOD2 genotype were identified from patients in previous UK IBD genetics studies and the Cambridge bioresource (genotyped/phenotyped volunteers). Individuals with known CD-associated NOD2 mutations were matched to those with wild-type genotype. We obtained fecal samples from patients in clinical remission with low fecal calprotectin (<250 µg/g) and controls without gastrointestinal disease. After extracting DNA, the V1-2 region of 16S rRNA genes were polymerase chain reaction (PCR)-amplified and sequenced. Analysis was undertaken using the mothur package. Volatile organic compounds (VOC) were also measured. Results: Ninety-one individuals were in the primary analysis (37 CD, 30 bioresource controls, and 24 household controls). Comparing CD with nonIBD controls, there were reductions in bacterial diversity, Ruminococcaceae, Rikenellaceae, and Christensenellaceae and an increase in Enterobacteriaceae. No significant differences could be identified in microbiota by NOD2 genotype, but fecal butanoic acid was higher in Crohn's patients carrying NOD2 mutations. Conclusions: In this well-controlled study of NOD2 genotype and fecal microbiota, we identified no significant genotype-microbiota associations. This suggests that the changes associated with NOD2 genotype might only be seen at the mucosal level, or that environmental factors and prior inflammation are the predominant determinant of the observed dysbiosis in gut microbiota. ; Funding was supported by CORE, the Digestive Diseases Foundation and the Wellcome Trust [grant number 097943 to NAK, 093885 to CAL and 098051 to Alan W Walker and Julian Parkhill . Dr. Walker receives core funding support from the Scottish Government Rural and Environmental Science and Analysis Service (RESAS). We also acknowledge the NIHR Biomedical Research Centre awards to Addenbrooke's Hospital/University of Cambridge School of Clinical Medicine and acknowledge the NIHR Newcastle Biomedical Research Centre.

Sepsis is a life-threatening condition in preterm infants. Neonatal microbiota plays a pivotal role in the immune system maturation. Changes in gut microbiota have been associated to inflammatory disorders; however, a link with sepsis in the neonatal period has not yet been established. We aimed to analyze gut microbiota and mucosal gene expression using non-invasively obtained samples to provide with an integrative perspective of host-microbe interactions in neonatal sepsis. For this purpose, a prospective observational case-control study was conducted in septic preterm dizygotic twins and their non-septic twin controls. Fecal samples were used for both microbiota analysis and host genome-wide expression using exfoliated intestinal cells. Gene expression of exfoliated intestinal cells in septic preterm showed an induction of inflammatory and oxidative stress pathways in the gut and pro-oxidant profile that caused dysbiosis in the gut microbiota with predominance of Enterobacteria and reduction of Bacteroides and Bifidobacterium spp.in fecal samples, leading to a global reduction of beneficial anaerobic bacteria. Sepsis in preterm infants induced low-grade inflammation and oxidative stress in the gut mucosa, and also changes in the gut microbiota. This study highlights the role of inflammation and oxidative stress in neonatal sepsis on gut microbial profiles. ; M.C. acknowledges a Research Grant Fellowship "Rio Hortega" and M.V. a RD12/0022/0012 (Red SAMID) and FIS PI14/0443 grants from the Instituto Carlos III (Spanish Ministry of Economy and Competitiveness) and Fondos FEDER from the European Union. C.B., M.C.C. and G.P.M. acknowledge the grant AGL2013-47420-R and by the Fun-C-Food CSD2007-00063 project from the Consolider-Ingenio program, both from the Spanish Ministry of Science and Innovation. ; Peer reviewed

Host-microbe interactions at the gastrointestinal interface have emerged as a key component in the governance of human health and disease. Advances in micro-physiological systems are providing researchers with unprecedented access and insights into this complex relationship. These systems combine the benefits of microengineering, microfluidics, and cell culture in a bid to recreate the environmental conditions prevalent in the human gut. Here we present the human-microbial cross talk (HuMiX) platform, one such system that leverages this multidisciplinary approach to provide a representative in vitro model of the human gastrointestinal interface. HuMiX presents a novel and robust means to study the molecular interactions at the host-microbe interface. We summarize our proof-of-concept results obtained using the platform and highlight its potential to greatly enhance our understanding of host-microbe interactions with a potential to greatly impact the pharmaceutical, food, nutrition, and healthcare industries in the future. A number of key questions and challenges facing these technologies are also discussed. (C) 2017 THE AUTHORS. Published by Elsevier LTD on behalf of the Chinese Academy of Engineering and Higher Education Press Limited Company. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). ; CORE [PoC/15/11014639, CORE/14/BM/8066232, CORE/11/BM/1186762]; ATTRACT [ATTRACT/A09/03]; European Union [INTER/JPND/12/01]; Accompany Measures mobility grant - Luxembourg National Research Fund (FNR) [12/AM2c/05]; Luxembourg National Research Fund (FNR) [AFR/PDR 2013-1/BM/5821107]; [PoC15/11014639] ; Open Access Journal ; This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.

B cells possess a predominant role in adaptive immune responses via antibodydependent and -independent functions. The microbiome of the gastrointestinal tract is currently being intensively investigated due to its profound impact on various immune responses, including B cell maturation, activation, and IgA antibody responses. Recent findings have demonstrated the interplay between dietary components, gut microbiome, and autoantibody production. "Western" dietary patterns, such as high fat and high salt diets, can induce alterations in the gut microbiome that in turn affects IgA responses and the production of autoantibodies. This could contribute to multiple pathologies including autoimmune and inflammatory diseases. Here, we summarize current knowledge on the influence of various dietary components on B cell function and (auto)antibody production in relation to the gut microbiota, with a particular focus on the gut–brain axis in the pathogenesis of multiple sclerosis. ; MK was supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (640116), by a SALK-grant from the government of Flanders, Belgium, and by an Odysseus grant of the Research Foundation Flanders, Belgium (FWO). JF is a postdoctoral fellow of the FWO.

BackgroundThe microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, architecture, and external environmental exposures. Here, we present a longitudinal study of United States Air Force Academy cadets (n = 34), which have substantial homogeneity in lifestyle, diet, and age, all factors that influence the human microbiome. We characterized bacterial communities associated with (1) skin and gut samples from roommate pairs, (2) four built environment sample locations inside the pairs' dormitory rooms, (3) four built environment sample locations within shared spaces in the dormitory, and (4) room-matched outdoor samples from the window ledge of their rooms.ResultsWe analyzed 2,170 samples, which generated 21,866 unique amplicon sequence variants. Linear convergence of microbial composition and structure was observed between an occupants' skin and the dormitory surfaces that were only used by that occupant (i.e., desk). Conversely, bacterial community beta diversity (weighted Unifrac) convergence between the skin of both roommates and the shared dormitory floor between the two cadet's beds was not seen across the entire study population. The sampling period included two semester breaks in which the occupants vacated their rooms; upon their return, the beta diversity similarity between their skin and the surfaces had significantly decreased compared to before the break (p < 0.05). There was no apparent convergence between the gut and building microbiota, with the exception of communal bathroom door-handles, which suggests that neither co-occupancy, diet, or lifestyle homogenization had a significant impact on gut microbiome similarity between these cadets over the observed time frame. As a result, predictive classifier models were able to identify an individual more accurately based on the gut microbiota (74%) compared to skin (51%).ConclusionsTo the best of our ...

Microbioma gastrointestinal; Ferro; Obesitat ; Microbioma gastrointestinal; Hierro; Obesidad ; Gastrointestinal microbiome; Iron; Obesity ; Background: The gut microbiome and iron status are known to play a role in the pathophysiology of non-alcoholic fatty liver disease (NAFLD), although their complex interaction remains unclear. Results: Here, we applied an integrative systems medicine approach (faecal metagenomics, plasma and urine metabolomics, hepatic transcriptomics) in 2 well-characterised human cohorts of subjects with obesity (discovery n = 49 and validation n = 628) and an independent cohort formed by both individuals with and without obesity (n = 130), combined with in vitro and animal models. Serum ferritin levels, as a markers of liver iron stores, were positively associated with liver fat accumulation in parallel with lower gut microbial gene richness, composition and functionality. Specifically, ferritin had strong negative associations with the Pasteurellaceae, Leuconostocaceae and Micrococcaea families. It also had consistent negative associations with several Veillonella, Bifidobacterium and Lactobacillus species, but positive associations with Bacteroides and Prevotella spp. Notably, the ferritin-associated bacterial families had a strong correlation with iron-related liver genes. In addition, several bacterial functions related to iron metabolism (transport, chelation, heme and siderophore biosynthesis) and NAFLD (fatty acid and glutathione biosynthesis) were also associated with the host serum ferritin levels. This iron-related microbiome signature was linked to a transcriptomic and metabolomic signature associated to the degree of liver fat accumulation through hepatic glucose metabolism. In particular, we found a consistent association among serum ferritin, Pasteurellaceae and Micrococcacea families, bacterial functions involved in histidine transport, the host circulating histidine levels and the liver expression of GYS2 and SEC24B. Serum ferritin was also related to bacterial glycine transporters, the host glycine serum levels and the liver expression of glycine transporters. The transcriptomic findings were replicated in human primary hepatocytes, where iron supplementation also led to triglycerides accumulation and induced the expression of lipid and iron metabolism genes in synergy with palmitic acid. We further explored the direct impact of the microbiome on iron metabolism and liver fact accumulation through transplantation of faecal microbiota into recipient's mice. In line with the results in humans, transplantation from 'high ferritin donors' resulted in alterations in several genes related to iron metabolism and fatty acid accumulation in recipient's mice. Conclusions: Altogether, a significant interplay among the gut microbiome, iron status and liver fat accumulation is revealed, with potential significance for target therapies. ; This work was supported by EU-FP7 FLORINASH (Health-F2-2009-241913) to R.B., M.F., J.M.F.R., E.H. and J.K.N. Infrastructure support was provided by the National Institute for Health Research (NIHR) Imperial Biomedical Research Centre (BRC). L.H. was in receipt of an MRC Intermediate Research Fellowship in Data Science (grant number MR/L01632X/1, UK Med-Bio). This work was also partly supported by funding to M.-E.D. (EU METACARDIS under agreement HEALTH-F4-2012-305312, Neuron II under agreement 291840 and the MRC MR/M501797/1) and by grants from the French National Research Agency (ANR-10-LABX-46 [European Genomics Institute for Diabetes]), from the National Center for Precision Diabetic Medicine – PreciDIAB, which is jointly supported by the French National Agency for Research (ANR-18-IBHU- 0001), by the European Union (FEDER), by the Hauts-de-France Regional Council (Agreement 20001891/NP0025517) and by the European Metropolis of Lille (MEL, Agreement 2019_ESR_11) and by Isite ULNE (R-002-20-TALENTDUMAS), also jointly funded by ANR (ANR-16-IDEX-0004-ULNE) the Hauts-de- France Regional Council (Agreement 20002045) and by the European Metropolis of Lille (MEL). J.M.-P. is funded by the Miguel Servet Program from the Instituto de Salud Carlos III (ISCIII CP18/00009), co-funded by the European Social Fund 'Investing in your future'. María Arnoriaga Rodríguez is funded by a predoctoral Río Hortega contract (CM19/00190, co-funded by European Social Fund 'Investing in your future') from the Instituto de Salud Carlos III, Spain. This work was supported by grants to AM from the Spanish Ministry of Science and Innovation (PID2019-105969GB-I00) and Generalitat Valenciana (project Prometeo/2018/133)

BackgroundThe microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, architecture, and external environmental exposures. Here, we present a longitudinal study of United States Air Force Academy cadets (n = 34), which have substantial homogeneity in lifestyle, diet, and age, all factors that influence the human microbiome. We characterized bacterial communities associated with (1) skin and gut samples from roommate pairs, (2) four built environment sample locations inside the pairs' dormitory rooms, (3) four built environment sample locations within shared spaces in the dormitory, and (4) room-matched outdoor samples from the window ledge of their rooms.ResultsWe analyzed 2,170 samples, which generated 21,866 unique amplicon sequence variants. Linear convergence of microbial composition and structure was observed between an occupants' skin and the dormitory surfaces that were only used by that occupant (i.e., desk). Conversely, bacterial community beta diversity (weighted Unifrac) convergence between the skin of both roommates and the shared dormitory floor between the two cadet's beds was not seen across the entire study population. The sampling period included two semester breaks in which the occupants vacated their rooms; upon their return, the beta diversity similarity between their skin and the surfaces had significantly decreased compared to before the break (p < 0.05). There was no apparent convergence between the gut and building microbiota, with the exception of communal bathroom door-handles, which suggests that neither co-occupancy, diet, or lifestyle homogenization had a significant impact on gut microbiome similarity between these cadets over the observed time frame. As a result, predictive classifier models were able to identify an individual more accurately based on the gut microbiota (74%) compared to skin (51%).ConclusionsTo the best of our knowledge, this is the first study to show an increase in skin microbial similarity of two individuals who start living together for the first time and who are not genetically related or romantically involved. Cohabitation was significantly associated with increased skin microbiota similarity but did not significantly influence the gut microbiota. Following a departure from the occupied space of several weeks, the skin microbiota, but not the gut microbiota, showed a significant reduction in similarity relative to the building. Overall, longitudinal observation of these dynamics enables us to dissect the influence of occupation, diet, and lifestyle factors on occupant and built environment microbial ecology.

Relación dieta-microbioma; Validación relativa; Desarrollo de sFFQ ; Relació dieta-microbioma; Validació relativa; Desenvolupament sFFQ ; Diet–microbiome relationship; Relative validation; sFFQ development ; Diet is recognised as the main driver of changes in gut microbiota. However, linking habitual dietary intake to microbiome composition and activity remains a challenge, leaving most microbiome studies with little or no dietary information. To fill this knowledge gap, we conducted two consecutive studies (n = 84: a first pilot study (n = 40) to build a web-based, semi-quantitative simplified FFQ (sFFQ) based on three 24-h dietary recalls (24HRs); a second study (n = 44) served to validate the newly developed sFFQ using three 24HRs as reference method and to relate gut microbiome profiling (16S rRNA gene) with the extracted dietary and lifestyle data. Relative validation analysis provided acceptable classification and agreement for 13 out of 24 (54%) food groups and 20 out of 29 nutrients (69%) based on intraclass correlation coefficient, cross-classification, Spearman's correlation, Wilcoxon test, and Bland–Altman. Microbiome analysis showed that higher diversity was positively associated with age, vaginal birth, and intake of fruit. In contrast, microbial diversity was negatively associated with BMI, processed meats, ready-to-eat meals, sodium, and saturated fat. Our analysis also revealed a correlation between food groups or nutrients and microbial composition. Overall, we provide the first dietary assessment tool to be validated and correlated with microbiome data for population studies. ; This study was supported by grants from by the Instituto de Salud Carlos III/FEDER (PI17/00614; PI20/00130), a government agency. Francisca Yáñez was supported by a fellowship from ANID, BECAS Chile, No. 72190278. Zixuan Xie received a fellowship from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Action, Innovative Training Network: FunHoMic; grant number 812969.

The gastrointestinal tract harbors most of the microbiota associated with humans. In recent years, there has been a surge of interest in assessing the relationships between the gut microbiota and several gut alterations, including colorectal cancer. Changes in the gut microbiota in patients suffering colorectal cancer suggest a possible role of host-microbe interactions in the origin and development of this malignancy and, at the same time, open the door for novel ways of preventing, diagnosing, or treating this disease. In this review we survey current knowledge on the healthy microbiome of the gut and how it is altered in colorectal cancer and other related disease conditions. In describing past studies we will critically assess technical limitations of different approaches and point to existing challenges in microbiome research. We will have a special focus on host-microbiome interaction mechanisms that may be important to explain how dysbiosis can lead to chronic inflammation and drive processes that influence carcinogenesis and tumor progression in colon cancer. Finally, we will discuss the potential of recent developments of novel microbiota-based therapeutics and diagnostic tools for colorectal cancer. ; This work was supported by grants from COST (European Cooperation in Science and Technology), COST Action CA17118; from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and grants 'Centro de Excelencia Severo Ochoa' SEV-2012-0208, and BFU2015-67107 cofounded by European Regional Development Fund; from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation programme under the grant agreement ERC-2016-724173, and the Marie Sklodowska-Curie grant agreement No H2020-MSCA-ITN-2014-642095; and from Instituto Nacional de Bioinformatica (INB, grant PT17/0009/0023 - ISCIII-SGEFI/ERDF).

peer-reviewed ; Autism spectrum disorder (ASD) is one of the most prevalent neurodevelopmental conditions worldwide. There is growing awareness that ASD is highly comorbid with gastrointestinal distress and altered intestinal microbiome, and that host-microbiome interactions may contribute to the disease symptoms. However, the paucity of knowledge on gut-brain axis signaling in autism constitutes an obstacle to the development of precision microbiota-based therapeutics in ASD. To this end, we explored the interactions between intestinal microbiota, gut physiology and social behavior in a BTBR T+ Itpr3tf/J mouse model of ASD. Here we show that a reduction in the relative abundance of very particular bacterial taxa in the BTBR gut – namely, bile-metabolizing Bifidobacterium and Blautia species, - is associated with deficient bile acid and tryptophan metabolism in the intestine, marked gastrointestinal dysfunction, as well as impaired social interactions in BTBR mice. Together these data support the concept of targeted manipulation of the gut microbiota for reversing gastrointestinal and behavioral symptomatology in ASD, and offer specific plausible targets in this endeavor. ; The APC Microbiome Institute is a research institute funded by Science Foundation Ireland (SFI) through the Irish Government's National Development Plan. J.F·C, T.G.D, C.S., S.A.J. and C.G.M.G. are supported by SFI (Grant Nos. SFI/12/RC/2273). S.A.J is also funded by SFI-EU 16/ERA-HDHL/3358. J.F·C, C.S. and T.G.D have research support from Mead Johnson, Cremo, 4D Pharma, Suntory Wellness, and Nutricia. J.F.C, C.S., T.G.D and G.C. have spoken at meetings sponsored by food and pharmaceutical companies.

The gut microbiota – the collection of micro-organisms in the gut – can best be viewed as a newly discovered organ, defined as a group of adjacent cells with a function. The gut microbiota, in fact, fulfils a number of important functions: it digests our food, synthesizes amino acids, trains our immune system, and helps resist gastrointestinal infections. The composition and functions of the gut microbiota can therefore have a large impact on our health. In this thesis the role of the gut microbiota in intestinal disorders is systematically analysed using DNA sequencing techniques. The intestinal disease we focus on most is inflammatory bowel disease (IBD), a recurrent remittent inflammatory disease of the gut that comprises Crohn's disease and ulcerative colitis. However, irritable bowel syndrome (IBS), traditionally characterized as a functional disorder consisting of a combination of gut complaints, and bacterial gastroenteritis, a bacterial infection often leading to diarrhoea, were also investigated. One of the most important discoveries of this thesis is the relationship between use of proton pump inhibitors (PPIs), one of most prescribed drugs in Europe and the United States, and the gut microbiota. PPIs work by reducing stomach acid, normally an important barrier to bacteria entering the intestinal tract, and we observed that bacteria normally found in the mouth were now present in the gut of PPI users. PPI users also have a more pro-inflammatory gut microbiota, showing a decrease in favourable butyrate-producing bacteria and an increase in the Enterobacteriaceae that can produce toxin. As a consequence, PPI users are more susceptible to both bacterial gastroenteritis, e.g. that caused by Salmonella spp, and to Clostridium difficile infections. After these results were published in 2016, government officials began to question whether PPIs should remain available as over-the-counter drugs in grocery stores, and this debate was still ongoing as of the writing of this thesis. This discovery received a lot of media attention in the written press: De Telegraaf, Reuters and Scientific American, on the radio: RTV Noord and BNR Nieuwsradio and on the television show Kassa. Another important discovery, the gut metagenomes of IBD and IBS are compared to those of population controls and are described in great detail using the metagenomic sequencing technique. With this technique, we were able to both determine the composition of the gut microbiome and infer its function, strain diversity, the level of virulence and the level of antibiotic resistance, leading to thousands of new results. We also present a computer algorithm that uses gut metagenomes to reliably distinguish IBD from IBS (AUC=0.93), performing much better than faecal calprotectin, which is currently used as a marker to distinguish between the two conditions. In the future, a gut microbiome-based test could reduce the number of painful and costly colonoscopies. This discovery was published in the renowned journal Science Translation Medicine and the Dutch television programme Editie NL on RTL4 discussed its importance for patients with irritable bowel syndrome. The results of this thesis allow us to better understand intestinal disesases and to work towards microbiota-based diagnostics and therapeutics.

International audience ; Feed efficiency (FE) is an important trait in the pig industry, as feed costs are responsible for the major part of production costs. Availability in the market and cost of feed ingredients dictate changes in feed composition. As a result, fibre level and composition can vary between pig diets. Microbiota in the gastrointestinal tract play an important role in fibre digestion, because they produce enzymes that break down fibre structures and deliver volatile fatty acids (VFA) to the pig. These VFA can be used as metabolic energy sources. As such, microbial fermentation could influence FE in pigs. The aim of this study was to investigate the association between FE and faecal microbiome in commercial grower-finisher pigs. Three-way crossbreed grower-finisher pigs (154) were either fed a diet based on corn/soybean meal (CS) or a diet based on wheat/barley/by-products (WB). Faecal samples were collected on the day before slaughter (mean body weight 122 kg), and sequenced for the V3-V4 16S ribosomal DNA regions. Sequences we clustered according to operational taxonomic units (OTU) for each individual. A partial least square regression was applied to the dataset, together with a discriminant analysis using principal components of FE extreme groups (10 high and 10 low FE animals for each diet by sex-combination). Pigs on different diets and males vs females had a very distinct microbiome, needing only two OTUs for diet (P=0.018) and 18 OTUs for sex (P=0.002) to separate the groups. Faecal microbiome was not related to FE groups fed the CS diet, but there were sex specific OTUs related to FE in male and female pigs in the groups fed the WB diet. In conclusion, our results show a diet and sex dependent relationship between the faecal microbial composition and FE in grower-finisher pigs at slaughter weight. This study is part of the Feed-a-Gene project and received funding from the European Union's H2020 program under grant agreement no. 633531.