Rewilding the Human Gut: Reintroduction of the Species Limosilactobacillus Reuteri

Microbial Colonization Clinical Trial

Official title:

Rewilding the Human Gut: Reintroduction of the Species Limosilactobacillus Reuteri

Clinical Trial Details — Status: Completed

Administrative data

• NCT number: NCT03501082
• Other study ID #: Pro00077565
• Status: Completed
• Phase: N/A
• Start date: February 21, 2019
• Est. completion date: January 31, 2020

Study information

• Verified date: May 2020
• Source: University of Alberta
• Contact: n/a
• Is FDA regulated: No
• Study type: Interventional

Clinical Trial Summary

The large intestine is home to trillions of microbes, known as the gut microbiome, which perform essential functions, such as digesting food and fighting disease. The diversity of microbes present in our gut microbiome is influenced by lifestyle factors, such as dietary patterns, medication usage, and sanitation practices. Research shows that the diversity of the human gut microbiome decreases as societies undergo industrialization. For example, fecal samples from rural Papua New Guineans contain an additional 50 microbial species, such as Limosilactobacillus reuteri, not found in people living in the United States.

What has caused the disappearance of L. reuteri in industrialized countries is currently unknown. However, diet is a major factor influencing the composition of the gut microbiome. Microbiota-accessible carbohydrates (MACs) are indigestible carbohydrates that are a primary source of energy for gut microbes. North Americans consume far less of these carbohydrates (which are contained in foods such as beans, yams, and artichokes) than rural Papua New Guineans.

The overall aim of this controlled feeding study is to determine if a strain of L. reuteri isolated from rural Papua New Guinea can be established in the gut of Canadians when taken as a probiotic alongside a non-industrialized-type diet designed to promote its growth. Furthermore, the study will determine:

(i) the physiological and immunological effects of both L. reuteri and the non-industrialized-type diet, and (ii) the effects of both L. reuteri and the non-industrialized-type diet on gut microbiome ecology.

Description:

There is now consistent evidence that industrialization has substantially decreased the bacterial diversity of the gut microbiota (Segata, 2015), likely due to a combination of factors such as use of antibiotics, modern clinical practices, sanitation, and changes in dietary habits. However, the only factor for which empirical evidence exists is the low content of Microbiota-Accessible Carbohydrates (MACs) in Western diets, which are indigestible dietary carbohydrates that become available to the microbes colonizing the intestine (Sonnerburg et al., 2015).

Previous work has confirmed the overall premise of 'microbiome depletion' by demonstrating higher diversity in the fecal microbiota of individuals from rural tribes in Papua New Guinea, which contain an additional of 50 species completely undetectable in North Americans (Martínez et al., 2015). One species detectable in every Papua New Guinean individual by 16S rRNA sequencing but not in a single US control was Limosilactobacillus reuteri (L. reuteri). Interestingly, this species, which is also used as a probiotic, was regularly detected in humans in studies conducted around 1960, but is very rarely found in contemporary humans, suggesting a recent decline of the L. reuteri population in Westerners (Walter et al., 2011). Most importantly, L. reuteri is a member of the gut microbiota in many vertebrate species and exerts benefits towards host immune functions and development, as demonstrated in a number of highly cited publications (Zelante et al. 2013; Buffington et al. 2016; Lamas et al. 2016; He et al. 2017).

It is currently unclear what caused the drop in the L. reuteri population. However, it is likely due to the importance of non-digestible carbohydrates that are present at very low amounts in Western diets, while being abundant in the diet of rural Papua New Guineans, a population that consumes a predominantly plant-based diet.

The goal of this study is to demonstrate that a bacterial species dominant in the non-westernized microbiome can be 'reintroduced' in the gut of Canadians fed a non-industrialized type diet designed to promote the growth of gut bacteria. This study will also determine how this 'reintroduction' and the non-industrialized-type diet influences immune function of the host and host-diet-microbiome metabolic interactions, and explore associations between them. It will further explore the effects of the microbial treatment and the diet on gut microbiome ecology. The central hypothesis is that an isolate of L. reuteri, originating from rural Papua New Guinea, can be established in the gut of Canadians fed a diet containing the carbohydrates known to facilitate the growth of this microbe. It is also hypothesized that this 'reintroduction' and consuming the non-industrialized type diet will be associated with immunological and metabolic benefits to the host. To achieve these goals, the following aims are proposed:

1. To conduct a human trial to determine if a Limosilactobacillus reuteri strain isolated from rural Papua New Guinea (PNG) can be established in the gut of healthy Canadians.

2. To determine if colonization can be improved by feeding a diet specifically designed to provide growth substrates for L. reuteri.

3. To determine how both L. reuteri and the non-industrialized-type diet change the human microbiome, metabolome, cardiometabolic surrogate endpoints, and immune biomarkers of inflammation.

This study will establish if a 'lost species' of bacteria can be reintroduced into the human gut and may provide mechanistic insight to inform how such dietary modulation may be applied to reduce the risk of chronic diseases. Since the L. reuteri strain isolated from rural Papua New Guineans is functionally different from western strains, evidenced by different growth rates on substrates of MACs, this study will further identify potential probiotic strains that were previously uncharacterized due to their overall absence from the industrialized gut microbiome.

Recruitment information / eligibility

• Status: Completed
• Enrollment: 30
• Est. completion date: January 31, 2020
• Est. primary completion date: January 31, 2020
• Accepts healthy volunteers: Accepts Healthy Volunteers
• Gender: All
• Age group: 18 Years to 45 Years

Eligibility

Inclusion Criteria:

• Healthy individuals with a body mass index between 20-29.9 kg/m²

• Have at least one bowel movement per day

• Willing to consume prepared study foods (breakfast, lunch dinner, snacks) for a period of 3 weeks

• Men and pre-menopausal, non-pregnant or non-lactating women

• Non-vegetarian, non-smoking, and alcohol intake =8 drinks/week, and willing to consume 8 drinks per week or less during the course of the study.

• If consuming probiotic containing foods, willing to discontinue eating same, and substitute with non-probiotic containing foods

-=5 h/week of moderate-vigorous exercise.

• Quantity of L. reuteri in screening fecal sample below 10^4 CFU/g

Exclusion Criteria:

• History of diabetes, acute or chronic GI illnesses, conditions, or history of GI surgical intervention

• antibiotic treatment in the last 3 months

• use of dietary supplements (including prebiotics and probiotics, fiber supplements/bars, digestive enzymes/beano)- if consumed, willing to undergo 4 week pre-intervention washout period, and remain free of supplements for duration of study. Exception: multivitamin or vitamin d supplement (1 week washout period)

• use of antihypertensive, lipid-lowering, anti-diabetic, anti-inflammatory (i.e corticosteroids or chronic NSAID use), or laxative medications

• known food allergies or intolerances (including dairy allergic or lactose intolerant)

Related Conditions & MeSH terms

• Communicable Diseases
• Infections
• Microbial Colonization

Intervention

Other:
• L Reuteri PB-W1 Strain
L. Reuteri PB-W1 strain will be prepared in accordance to the standardized operating procedures to prepare Limosilactobacillus reuteri in food grade conditions
• L. Reuteri DSM20016T Strain
L. Reuteri DSM20016T strain will be prepared in accordance to the standardized operating procedures to prepare Limosilactobacillus reuteri in food grade conditions
• Placebo
2 g of maltodextrin will be dissolved in 50 ml water in food grade conditions
• Non-Industrialized-Type Diet
Non-industrialized-type diet will be prepared in a metabolic kitchen, with all meals and snacks provided to participants for three weeks.

Locations

Country	Name	City	State
Canada	University of Alberta	Edmonton	Alberta

Sponsors (1)

Lead Sponsor	Collaborator
University of Alberta

Country where clinical trial is conducted

Canada, 

References & Publications (8)

Buffington SA, Di Prisco GV, Auchtung TA, Ajami NJ, Petrosino JF, Costa-Mattioli M. Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring. Cell. 2016 Jun 16;165(7):1762-1775. doi: 10.1016/j.cell.2016.06.001. — View Citation

He B, Hoang TK, Wang T, Ferris M, Taylor CM, Tian X, Luo M, Tran DQ, Zhou J, Tatevian N, Luo F, Molina JG, Blackburn MR, Gomez TH, Roos S, Rhoads JM, Liu Y. Resetting microbiota by Lactobacillus reuteri inhibits T reg deficiency-induced autoimmunity via adenosine A2A receptors. J Exp Med. 2017 Jan;214(1):107-123. doi: 10.1084/jem.20160961. Epub 2016 Dec 19. — View Citation

Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, Brot L, Taleb S, Couturier-Maillard A, Nion-Larmurier I, Merabtene F, Seksik P, Bourrier A, Cosnes J, Ryffel B, Beaugerie L, Launay JM, Langella P, Xavier RJ, Sokol H. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med. 2016 Jun;22(6):598-605. doi: 10.1038/nm.4102. Epub 2016 May 9. — View Citation

Martínez I, Stegen JC, Maldonado-Gómez MX, Eren AM, Siba PM, Greenhill AR, Walter J. The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes. Cell Rep. 2015 Apr 28;11(4):527-38. doi: 10.1016/j.celrep.2015.03.049. Epub 2015 Apr 16. — View Citation

Segata N. Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity. Curr Biol. 2015 Jul 20;25(14):R611-3. doi: 10.1016/j.cub.2015.05.040. — View Citation

Sonnenburg ED, Sonnenburg JL. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 2014 Nov 4;20(5):779-786. doi: 10.1016/j.cmet.2014.07.003. Epub 2014 Aug 21. — View Citation

Walter J, Britton RA, Roos S. Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4645-52. doi: 10.1073/pnas.1000099107. Epub 2010 Jun 25. Review. — View Citation

Zelante T, Iannitti RG, Cunha C, De Luca A, Giovannini G, Pieraccini G, Zecchi R, D'Angelo C, Massi-Benedetti C, Fallarino F, Carvalho A, Puccetti P, Romani L. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity. 2013 Aug 22;39(2):372-85. doi: 10.1016/j.immuni.2013.08.003. — View Citation

Outcome

Type	Measure	Description	Time frame	Safety issue
Primary	Establishment of L. reuteri (PB-W1 & DSM20016T strains) in the gut of Canadian individuals	The primary outcome of this study is to measure L. reuteri (PB-W1 and DSM20016T strains) establishment in the gut of Canadian individuals. This will be measured by selective bacterial culture from fecal samples and quantified through quantitative PCR using species specific primers.	21 days
Primary	Enhanced persistence of colonization of L. reuteri (PB-W1 & DSM20016T strains) following consumption of non-industrialized-type diet designed to provide growth substrates for L. reuteri	We will measure if the persistence of L. reuteri in the gut of Canadian individuals is enhanced by the consumption of a non-industrialized-type diet specifically designed to provide growth substrates (MACs) for L. reuteri. This will be measured by selective bacterial culture from fecal samples and quantified through quantitative PCR using species specific primers.	21 days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on cardiometabolic surrogate endpoints: fasting glucose and lipid panel.	Plasma from blood samples will be analyzed for changes in glucose, triglycerides, low density lipoprotein (LDL) cholesterol, high density lipoprotein (HDL) cholesterol, non-HDL cholesterol, and total cholesterol (mmol/L).	21 days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on cardiometabolic surrogate endpoints: fasting insulin levels.	Plasma from blood samples will be analyzed for changes in insulin (µIU/L).	21 Days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on cardiometabolic surrogate endpoints: homeostatic model assessment of insulin resistance and quantitative insulin sensitivity check index.	Homeostatic model assessment of insulin resistance and quantitative insulin sensitivity check index will be calculated based on fasting glucose and insulin levels.	21 Days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on cardiometabolic surrogate endpoints: fasting C-reactive protein levels.	Plasma from blood samples will be analyzed for changes in C-reactive protein (mg/L).	21 Days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on cardiometabolic surrogate endpoints: body weight.	Body weight will be measured in kilograms.	21 Days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on inflammatory bowel disease surrogate endpoint: fecal calprotectin levels.	Fecal samples will be analyzed for changes in calprotectin (ng/mg).	21 Days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on biomarkers of gut barrier function: lipopolysaccharide binding protein.	Plasma from blood samples will be analyzed for changes in lipopolysaccharide binding protein (µg/mL).	21 Days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on biomarkers of gut barrier function: fecal zonulin levels.	Fecal samples will be analyzed for changes in zonulin (ng/mg).	21 days
Secondary	Effect of L reuteri strains and the non-industrialized-type diet on the composition of the fecal microbiome.	o Fecal samples will be analyzed using 16S rRNA-sequencing to measure changes in the fecal microbiome at the phylum, class, order, family, genus, and amplicon sequencing variant levels. Fecal microbiome composition will also be analyzed using whole metagenome sequencing to measure changes at the phylum, class, order, family, genus, species, and species-level genome bin levels.	4-21 days
Secondary	Effect of L reuteri strains and the non-industrialized-type diet on the function of the fecal microbiome: enzyme levels.	Fecal samples will be analyzed using whole metagenome sequencing to measure changes in enzymes encoded by gut microbiota.	8 days
Secondary	Effect of L reuteri strains and the non-industrialized-type diet on the function of the fecal microbiome: short-chain fatty acid levels.	Short-chain fatty acids (acetate, propionate, butyrate, valerate) and branched-chain fatty acids (isovalerate, isobutyrate) will be measured in fecal samples using gas chromatography mass spectrometry (µmol/g).	8 & 21 days
Secondary	Effect of L reuteri strains and the non-industrialized-type diet on the function of the fecal microbiome: pH.	Fecal pH will be measured using a pH meter.	8 & 21 days
Secondary	Effect of L. reuteri strains and non-industrialized-type diet on the metabolome.	Plasma metabolome will be assessed to determine changes in molecules with known immunological functions such as indole derivatives of tryptophan and bile acids following the provision of the intervention. This will be measured via high performance chemical isotope labeling liquid chromatography mass spectrometry platform.	8 & 21 days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on host immune response.	Host immune responses will be measured in blood samples by quantifying IgA, selected cytokines, and white blood cell phenotyping using flow cytometry. Mononuclear cells will be isolated from whole blood on ficoll gradients and the ability of cells to respond to challenges (peptidoglycan, phytohemagglutinin, and lipopolysaccharide) will be determined ex vivo.	8 & 21 days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on changes in psychological mood state.	Changes in individual mood state will be measured by the profile of mood states questionnaire (scored between -32 and 200; lower scores indicate more stable mood profiles).	21 days
Secondary	Effect of L. reuteri strains and the non-industrialized-type diet on changes in gastrointestinal symptoms.	Changes in individual gastrointestinal symptoms will be measured by a gastrointestinal symptom questionnaire (scored on a scale of 0-5; higher scores indicating more symptoms).	21 days