Predict the gut microbiota resistome

The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. A collaboration between several research institute including INRA, AP-HP and Institut Pasteur succeed to predict more than 6,000 ARDs from the gut microbiota using protein structural model.

Seing metagenomic data in 3D

A study1 published in Nature Microbiology in November 2018 showed that a new developped method based on 3D structural modeling was able to predict 10-fold more ARDS genes than previous studies. To confirm those prediction, several distant hit were tested using gene synthesis confirming their ability to confer antibiotic resistance. In addition, authors were able to cluster individuals into six resistotypes very closely related to previous enterotypes.

  1. Ruppe E, Ghozlane A, Tap J et al. Prediction of the intestinal resistome by a three-dimensional structure-based method.2018. Nature microbiology 

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Symptoms severity of irritable bowel syndrome associated with gut microbiota

Irritable bowel syndrome (IBS) is the most prevalent functional gastrointestinal disorder in western societies, characterized by chronic abdominal pain and discomfort. It affects about 11% of the adult population and strongly impairs quality of life, social function, work productivity and brings substantial costs to health-care services. The etiology of IBS remains poorly understood and the search for biomarkers is ongoing. It is now well accepted that IBS is a disorder involving multiple pathophysiological mechanisms where composition of gut microbiota has been proposed as one of the potentially important factors.

IBS Microbiota Gastroenterology

A study1 published in Gastroenterology in Octobre 2016 showed how some gut microbiota species were associated with IBS symptoms severity. Information on the fecal and mucosa-associated microbiota of patients with IBS were collected. The study evaluated whether these were associated with symptoms of gastrointestinal discomfort with a focus on the severity of symptoms.

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Gut microbiota richness promotes its stability upon increased dietary fibre intake

A study1 published in Environmental Microbiology in September 2015 showed how gut microbiota stability depend of its richness when individuals took high fiber diet. Using various methods to study the gut microbiome, we observed that higher microbiota richness was associated with higher microbiota stability upon increased dietary fibre intake. Metatranscriptomics analysis showed that numerous glycan metabolism were also modulated including carbohydrate active enzymes. Individual with higher richness and higher stability had higher diversity of short chain fatty acid comprising acetate, propionate and butyrate but also caproate and valerate compared to the lower richness microbiota.

AlimIntest INRA press

In addition, this study showed that a simple food vegetable questionaire summarized into a vegetable diversity index could be predictive of gut microbiota richness. Gut microbiota richness should definitly be taken into account before any nutritional intervention.

Using gut microbiota to detect colon cancer

A study1 published in Molecular System Biology showed how gut microbiota could be used to detect colon cancer in combination with standard fecal occult blood test (FOBT). The potential is huge as the detection could be increased notably for early stage cancer (where curation have a better prognostic notably).

crc msb snapshot

As a co-authors, I would like to give some additional insight regarding this paper like a “making of”, we could say. First of all, this study is the consequence of a fruitful collaboration between important institution between France (AP-HP) and Germany (EMBL, DKFZ). The most challenging part was to get samples in a right way directly from hospital, to improve current machine learning method to adapt them to metagenomics data and to devellop protocol to study the tumor environment.

  1. Zeller G, Tap J, Voigt AY et al. Potential of fecal microbiota for early‐stage detection of colorectal cancer. 2014. Molecular Systems Biology 10:766 

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Human gut metagenomics, five years of exciting exploration

IHMC logo

I defended my PhD in December 2009 and I knew that gut metagenomics will become more and more exiting with such big consortia such as MetaHIT and HMP. Combining with other gut microbiome initiatives within the international human microbiome consortium, they contributed to establish new resources, methods and clinical potential applications using metagenomics datasets.

I made a very rapid review here of huge step articles published during the last five years (I probably forget some of them).

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Gut Microbiota for Health summit 2014

The Gut Microbiota for Health summit organized by AGA with ENSM took place in Miami, 8-9 March 2014.

GMFH 2014 Miami

Scientific exchanges were around the role of gut microbiota in various disease like IBS, IBD and metabolic syndrome like obesity. Six workshop were organized related for instance to issues surrounding fecal microbiota transplant. Gut brain axis was also a hot topics. The summit was broadcasted live (see the webcast) and associated with tweets under the hastag #GMFH2014

Miami GMFH2014

More about the gut microbiota for health 2014 summit with the digital press folder and the GMFH2014 storify. Generally, you can find more informations about this event and gut microbiota events at http://www.gutmicrobiotaforhealth.com. The official summit report is now available as a PDF by following this link.

The 4th Gut Microbiota for Health Summit will be held in Barcelona in March 2015.

What is MetaGenoPolis ?

I’m working since 1 year at Metagenopolis unit at INRA institute. Here is below the presentation video.

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MetaGenoPolis (MGP) has as strategic goal to demonstrate the impact of the human gut microbiota on health and disease, by making available quantitative and functional Metagenomics technology to the medical, academic and industrial communities.

More about MGP (tools and numbers), download pdf slides

A new metagenomic marker genes method to study microbiota

Numerical ecology analysis of microbiota by metagenomic sequencing, currently depend on the availability of DNA sequences of microbial genomes in the public databases. Often this approach leads to biased interpretation because the majority of the microbial community has no reference genome. To overcome this methodological obstacle, the [MetaHIT](http://www.metahit.eu) consortium presented a new method...

Gastric bypass help the crosstalk between microbiota and host adipocytes

ICAN

Following their story about gastric bypass and its impact gut microbiota and metabolic parameters, AP-HP, ICAN and INRA scientists continued to bring new discovers about the crosstalk between the gut microbiota and the host adipocytes. Variations of gut microbiota after gastric bypass were associated with changes in white adipose tissue gene expression. Those results may stimulate deeper investigation about relation between gut microbiota and adipocytes during weight loss.

Mycobacterium tuberculosis origins

mycobacterium tuberculosis

In 2006, I worked at Pasteur Institute (Sylvain Brisse groups) on characterization of special smooth strains isolated in Africa1 which seems to be related to M.tuberculosis (known to have a rough phenotype). Using 16 housekeeping genes, we showed that those strains belong to the same species of M. tuberculosis showing an higher diversity than previously observed.

Following this work, in 2013, the Pasteur institute finally published2 a set of genome of those smooth strains concluding that M. tuberculosis emerged from an ancestral pool of mycobacteria by gain of persistence and virulence mechanisms.