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Investigation of interaction of smoked dietary products with gut microbiome

 

 

Funding: European Regional Development Fund (ERDF) “On Implementation of Activity 1.1.1.2 “Post-doctoral Research Aid” of the Specific Aid Objective 1.1.1 “To increase the research and innovative capacity of scientific institutions of Latvia and the ability to attract external financing, investing in human resources and infrastructure” of the Operational Programme “Growth and Employment”

Project Title:Investigation of interaction of smoked dietary products with gut microbiome

Project Nr.: 1.1.1.2/VIAA/1/16/128

Period: 36 month (1st January 2018 – 31 st December 2020)

Project costs: 133 806,00 EUR

Project implementer: Dr.biol. I. Kalniņa

Considering the immense choice of harboured enzymes the gut microbiome is a serious contributor to biotransformation of incoming compounds with a prominent role in health and disease. Wood smoke used in processing of food products for flavouring and preservation contains a great variety of compounds with potential to interact with the microbiome. The main objective of the project will be multidimensional investigation of the impact smoked food especially fish consumption exerts on human gut microbiome to gain insight in the responding functional pathways and metabolic consequences. The study will be designed as the crossover dietary intervention including following experimental steps: evaluation of taxonomic and functional composition of the microbiome in humans, detailed characterisation of distinct target communities using gnotobiotic mice, investigation of impact of smoke compounds on microbial communities residing in distinct sections of the gut. Implementation of the proposed project will give insight in the mutual interaction of bacterial taxa and the role individual members play in the community, as well as add mechanistic understanding on "microbiome to host" metabolic crosstalk. Answering these questions will contribute to the data pool necessary for designing microbiome based tools and consultation on dietary choice to improve healthcare.

Information published 02.01.2018.

 

Progress of the project

1 January 2018 - 31 March 2018

 The project is aimed at investigation of the impact of smoked food consumption on the human gut microbiome. It is expected that the crossover dietary intervention study will provide novel information not only on the response of gut microbiome to the smoked foods, but also wide spectrum of other food items commonly included in daily diet. During the first quarter of the project implementation study specific informed consent forms and questionnaires for diet and lifestyle related information collection have been elaborated. The project protocol has been submitted for consideration to the Central Medical Ethics Committee. Currently planning of the dietary intervention stage and survey of potential participants is in progress.

Information published 29.03.2018.

 

Progress of the project

1 April 2018 – 30 June 2018

For evaluation of impact increased smoked food consumption has on the human gut microbiome 26 participants have been recruited to dietary intervention study. Two participants have withdrawn from the study during the second week due to the factors incompatible with requirements of the study. The study is designed to contain three week-long intervention periods concurrently covering all types of target diet (fish, smoked fish and smoked ham) intervened by washout periods two weeks each. Dietary intervention phase of the project will be completed by the end of the august. General phenotypic information from the participants who continue the intervention has been collected using LGDB and project specific questionnaires comprising questions on medication, diet as well as other lifestyle factors. Background lifestyle factors during the intervention are controlled using standardized inquiry forms filled up throughout the study. The study protocol has been approved by Central Medical Ethics Committee of Latvia (Nr. 1/18-06-07).

Information published 29.06.2018.

 

Progress of the project

1 July 2018 – 30 September 2018

Recently dietary intervention stage of the project has been completed. In total 24 participants aged 19 - 62 years (average age 39,5 years) were involved in 11 weeks long study comprising three week-long intervention periods concurrently covering three types of target diet.  The target diet included fish (salmon provided raw and cooked at home), smoked salmon and smoked pork (in both cases smoked with hardwood smoke). During the study participants monitored their daily diet as well as reported used food supplements and medicaments. Blood samples were collected before and after each intervention period for biochemical analysis (complete blood count, lipids and inflammatory markers) and participants donated stool samples for the gut microbiome analysis. Currently samples are under processing for the gut microbiome profiling including high throughput sequencing analysis.

Information published 28.09.2018.

 

Progress of the project

1 October 2018 – 31 December 2018

During the concluding phase of the first part of the project we have finished sample processing for the gut microbiome analyses. The study participants were asked to donate blood samples for biochemical measurements and samples for gut microbiome according to the eight visit schedule. From 24 participants included in the dietary intervention study the full set of samples was donated by 21 participants. No microbial DNA was obtained from two samples leaving 180 samples for the gut microbiome profiling with high throughput sequencing approach. Concurrently the follow-up data on habitual diets, physical activity and medication on the daily bases were collected using questionnaires to add information on factors interacting with the gut microbiome. Thus the first stage of the project has been completed.

Information published 28.12.2018.

 

Progress of the project

1 January 2019 – 31 March 2019

Whole-metagenome shotgun sequencing has been selected as the method of choice for assessment of variation in the composition of the gut microbiome induced by dietary changes. Current approach provides information on both taxonomic content as well as functional characteristics of microbial communities residing in the gut covering not only bacteria but also eukaryotes. During the first quarter of the second project phase optimization of the protocols for the specific needs of the study has been performed. For the metagenomic profiling library preparation of collected microbial DNA samples is in progress. It is expected that metagenomic profiling in combination with longitudinal data on habitual diet will not only give insight on the influence of smoked product consumption on processes occurring in gastrointestinal microbial communities, but also will reveal additional information on functional dietary factors essential for our understanding of the gut ecosystem.

Information published 29.03.2019.

 

Progress of the project

1 April 2019 – 30 June 2019

During the last quarter of the project implementation characterisation the gut microbiome composition has been completed. The gut microbiome profiling in 180 samples donated by 23 volunteers participating in the dietary intervention study was performed with whole-metagenome sequencing using MGISeq-2000 sequencer. Obtained sequencing coverage was at least 22 million raw reads per sample. Quality filtering of reads with trimmomatic tool removed up to 15% of reads. HUMAnN2 pipeline including MetaPhlAn2 tool and Kraken2 software were used for functional and taxonomic profiling of gut microbiome communities. Statistical analysis was performed with R program packages and Galaxy module LEfSe. First data show that limited consumption of smoked products has no obvious impact on the gut microbiome. However several suggestive associations with habitual dietary variables have been observed and are currently under investigation.

Information published 28.06.2019.

 

Progress of the project

1 July 2019 – 30 September 2019

Currently investigation of interactions between dietary factors, in particular smoked products, and human gut microbiota is continued with in-depth analysis of diverse metadata collected during the intervention study. This includes targeted analysis of specific taxa selected on the basis of their functional characteristics and/or role in the host physiology (e.g. A. muciniphila). A set of metabolites for further analysis will be adjusted to complement analysis of specific bacterial taxa. At the same time the sequencing step including analysis of additional samples collected from several participants for evaluation of stability of gut bacterial communities has been completed.

Information published 30.09.2019.




Mājas lapas izstrādi finansēja ERAF 2.1.1.2. aktivitātes projekts Nr. 2010/0196/2DP/2.1.1.2.0/10/APIA/VIAA/004 "Latvijas biomedicīnas pētījumu integrācija Eiropas zinātnes telpā".