ObjectiveA decade of microbiome studies has linked IBD to an alteration in the gut microbial community of genetically predisposed subjects. However, existing profiles of gut microbiome dysbiosis in adult IBD patients are inconsistent among published studies, and did not allow the identification of microbial signatures for CD and UC. Here, we aimed to compare the faecal microbiome of CD with patients having UC and with non-IBD subjects in a longitudinal study.DesignWe analysed a cohort of 2045 non-IBD and IBD faecal samples from four countries (Spain, Belgium, the UK and Germany), applied a 16S rRNA sequencing approach and analysed a total dataset of 115 million sequences.ResultsIn the Spanish cohort, dysbiosis was found significantly greater in patients with CD than with UC, as shown by a more reduced diversity, a less stable microbial community and eight microbial groups were proposed as a specific microbial signature for CD. Tested against the whole cohort, the signature achieved an overall sensitivity of 80% and a specificity of 94%, 94%, 89% and 91% for the detection of CD versus healthy controls, patients with anorexia, IBS and UC, respectively.ConclusionsAlthough UC and CD share many epidemiologic, immunologic, therapeutic and clinical features, our results showed that they are two distinct subtypes of IBD at the microbiome level. For the first time, we are proposing microbiomarkers to discriminate between CD and non-CD independently of geographical regions.

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To date, meta-omic approaches use high-throughput sequencing technologies, which produce a huge amount of data, thus challenging modern computers. Here we present MetaTrans, an efficient open-source pipeline to analyze the structure and functions of active microbial communities using the power of multi-threading computers. The pipeline is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples. Compared to an existing web application server, MetaTrans shows more efficiency in terms of runtime (around 2 hours per million of transcripts) and presents adapted tools to compare gene expression levels. It has been tested with a human gut microbiome database but also proposes an option to use a general database in order to analyze other ecosystems. For the installation and use of the pipeline, we provide a detailed guide at the following website (www.metatrans.org).

23The gut microbiota synthesize hundreds of molecules, many of which are known to impact 24 host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic 25 acid (DCA) and lithocholic acid (LCA), which accumulate at ~500 µM and are known to block C. 26 difficile growth 1 , promote hepatocellular carcinoma 2 , and modulate host metabolism via the GPCR 27 TGR5 3 . More broadly, DCA, LCA and their derivatives are a major component of the recirculating 28 bile acid pool 4 ; the size and composition of this pool are a target of therapies for primary biliary 29 cholangitis and nonalcoholic steatohepatitis. Despite the clear impact of DCA and LCA on host 30 physiology, incomplete knowledge of their biosynthetic genes and a lack of genetic tools in their 31 native producer limit our ability to modulate secondary bile acid levels in the host. Here, we 32 complete the pathway to DCA/LCA by assigning and characterizing enzymes for each of the steps 33 in its reductive arm, revealing a strategy in which the A-B rings of the steroid core are transiently 34 converted into an electron acceptor for two reductive steps carried out by Fe-S flavoenzymes. 35Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and 36 sufficient for the 8-step conversion of cholic acid to DCA. We then engineer the pathway into 37 Clostridium sporogenes, conferring production of DCA and LCA on a non-producing commensal 38 and demonstrating that a microbiome-derived pathway can be expressed and controlled 39 heterologously. These data establish a complete pathway to two central components of the bile 40 acid pool, and provide a road map for deorphaning and engineering pathways from the microbiome 41 as a critical step toward controlling the metabolic output of the gut microbiota. 42

With long-term exposure to lead, lead accumulates in bone, where it is stored for years. These quiescent lead stores are mobilised when increased bone turnover occurs, and latent lead toxicity may then become symptomatic. Although Graves' disease is a common cause of increased bone turnover, to date hyperthyroidism has been implicated in lead poisoning only twice. We describe herein two cases of hyperthyroidism, one caused by toxic multinodular thyroid enlargement, the second by Graves' disease, leading to lead poisoning. Treatment of hyperthyroidism with radioactive iodine cured both hyperthyroidism and lead poisoning and no chelating agent therapy was necessary. Lead poisoning is an important environmental health problem, and physicians must be aware of the endocrine disorders such as hyperthyroidism and hyperparathyroidism that increase bone turnover, favouring lead mobilisation. Atypical symptoms should draw the physician's attention to the possibility of lead poisoning, particularly in workers with occupational exposure to lead and in areas where lead poisoning is endemic.