Julien Tap
explore --method=metagenomics gut::microbiota > data
Irritable bowel syndrome (IBS) is a common disorder characterized by abdominal pain, bloating, and changes in bowel habits. The role of the gut microbiota in IBS has been increasingly recognized, and several studies have identified alterations in the gut microbial composition and function in IBS patients.
In a study by Tap et al. (2017), the authors identified an intestinal microbiota signature associated with the severity of IBS using 16S rRNA gene sequencing. They found that IBS patients had a distinct microbiota composition compared to healthy controls, with lower relative abundances of several butyrate-producing bacteria, including Faecalibacterium, Roseburia, and Eubacterium. In a follow-up study, Bennet et al. (2018) found that IBS patients had an altered intestinal antibacterial gene expression response profile, which was linked to bacterial composition and immune activation.
What if we ask an AI to generate a realistic picture about futuristic fermented foods that keep microbiota to stay in an healthy state?
This is what I tried with midjourney. Midjourney is a proprietary artificial intelligence program that creates images from textual descriptions.
here is the result :
it looks scary but still inspiring!
In a recent study1, we combined taxonomic, functional, and network analysis from shotgun metatranscriptomics analysis of fecal samples, which were collected during the ingestion of a habitual diet and two series of a 3-day high-residue challenge diet, before and following 28-days of fermented milk product (FMP) consumption.
FMP consumption was associated with the depletion of gas-producing bacteria and increased hydrogen to methane conversion. It also led to the upregulation of activities such as replication and downregulation of functions related to motility and chemotaxis.
We showed new mecanistic insights about how active FMP may help to improve disgestive confort under high-residue challenge diet.
Oyarzun et al. Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet. 2022. Cell Host Microbe ↩
We published a study entitled “Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome” in Microbiome journal.
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We presented a study entitled “Gut microbiome hysteresis is associated with durable mucosal alterations” during the Keystone Symposia poster session helded at Killarney : “Microbiome: Therapeutic Implications”
(right click to enlarge image)
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.
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.
Ruppe E, Ghozlane A, Tap J et al. Prediction of the intestinal resistome by a three-dimensional structure-based method.2018. Nature microbiology ↩
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.
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.
Tap J, Derrien M et al. Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome.2016. Gastroenterology ↩
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.
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.
Tap J et al. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults.2015. Environmental Microbiology 17: 4954–4964 ↩
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).
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.
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 ↩
