Gut microbiome and dietary patterns in different Saudi populations and monkeys
Authors: Marwan A Bakarman
Maha Alawi
Emmanouil Angelakis
Esam I Azhar
Fehmida Bibi
Catherine Robert
Jean-Christophe Lagier
Muhammad Yasir
Didier Raoult
Dipankar Bachar
Asif A Jiman-Fatani
Journal: Scientific Reports (2016)
Discipline: Multidisciplinary
Keywords: Host genetics; environment; lifestyle; gut microbiome; dietary variables
Affiliations: Unit√© de Recherche sur les Maladies Infectieuses et Tropicales Emergentes: URMITE CNRS-IRD 198 UMR 6236, Aix Marseille Universit√©, Facult√© de M√©decine, 27 Bd Jean Moulin, 13385 Marseille, France., Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia., Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia., Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia., Infection Control Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia., Family and Community Medicine Department, Faculty of Medicine, King Abdulaziz University Rabigh, Saudi Arabia.

Abstract:  Host genetics, environment, lifestyle and proximity between hosts strongly influence the composition of the gut microbiome. To investigate the association of dietary variables with the gut microbiota, we used 16S rDNA sequencing to test the fecal microbiome of Bedouins and urban Saudis and we compared it to the gut microbiome of baboons living in close contact with Bedouins and eating their leftovers. We also analyzed fermented dairy products commonly consumed by Bedouins in order to investigate their impact on the gut microbiome of this population. We found that the gut microbiomes of westernized urban Saudis had significantly lower richness and biodiversity than the traditional Bedouin population. The gut microbiomes of baboons were more similar to that of Bedouins compared to urban Saudis, probably due the dietary overlap between baboons and Bedouins. Moreover, we found clusters that were compositionally similar to clusters identified in humans and baboons, characterized by differences in Acinetobacter, Turicibacter and Collinsella. The fermented food presented significantly more bacteria genera common to the gut microbiome of Bedouins compared to urban Saudis. These results support the hypothesis that dietary habits influence the composition of the gut microbiome. 

Retracted: No

PubPeer comments:
 This paper is part of a set of 17 papers relating to the protocol approved by the ethics committee of the King Abdulaziz University (Saudi Arabia) under the **014-CEGMR-2-ETH-P**. We found some of the same authors in the 17 papers. **One protocol approved by the ethic committee under the number 014-CEGMR-2-ETH-P:** Authors mentioned in each paper that the study has been approved by the ethics committee of the King Abdulaziz University (Saudi Arabia) under the number 014-CEGMR-2-ETH-P. Considering an ethics approval number is related to one protocol only, readers could consider the 17 papers are related to the same protocol. **Discrepancies regarding the ethical reason justifying the recruitment of males only** In 6 articles, only one single male participant have been recruited. In one article (see article #5), the authors mention that: * For ethical reasons, all individuals from Saudi Arabia were male *. This mention is really surprising considering the other 10 papers with the same ethical approval number from the same ethical committee describe studies -tOn men and women. -tOr on 1 woman only. Could the authors explain why they have mentioned for article #5 all individuals from Saudi Arabia were male for ethical reason? Especially considering in other papers, the same authors describes that the protocol with the number 014-CEGMR-2-ETH-P have recruited male and women. **Participants and recruitment periods** In the 17 papers, authors mentions that the recruitment has been done on: -tHealthy participants -tAnd or Volunteers with obesity. In 6 papers, the authors mention that the study recruited between 28 and 117 participants depending on the paper. Among these 6 papers, the recruitment period is also different in each paper: -t4 don t provide the recruitment dates. -t1 paper describes a period of recruitment between January 2015 and December 2015 -t1 paper describes a period of recruitment between September 2015 and March 2016 In the other 11 papers, each paper describes a study on only one single participant: -t4 articles describe a study on a 24 year-old male in April 2013 (articles #14, #15, #16, #17) -t1 article describes a study on a 42 years-old women the 24 may 2014 (article #9) -t4 articles describe a study on a 50 years-old women in 2016 (articles #1, #3, #4, #6) -t2 articles describe a study on a 25 years-old male (articles #10 and #13). No data on the recruitment date. Readers could note that the recruitment dates of the studies on a single participant in 2013 and 2014 don t match with the studies on dozens or hundreds of participants recruited in 2015 and 2016. **Monkeys are used in one paper** In one paper, Authors mention that they assessed the gut microbiome and dietary patterns by comparing healthy volunteers and Monkeys population. **Different types of samples** -t1 paper describes a study which collects blood samples only -tThe other papers describe studies which collect stool samples only. **In France, only certified IRB (Comitu00e9 de Protection des Personnes) are qualified to approve prospective study in humans.** 2 papers describes studies performed in two or more countries and including French participants (articles #7 and #8). These papers describes an approval from the IFR48 ethics committee. In accordance with French law, only a certified IRB can approve research in human. Approval from the certified IRB must be obtained before to recruit participants The IFR48 ethics committee is not on the list of the certified IRB in France and don t have the ability to validate a prospective study in human, especially in healthy volunteers. In accordance with Helsinki Declaration and Editors guidances, a clinical research must be approved according to the relevant laws of the countries of the participants. The Editors should clarify this point and ensure that an approval from the Comitu00e9 de Protection des Personnes has been obtained for this protocol, especially considering the recruitment of health volunteers. The date of the approval, the scope of the protocol and the recruitment dates of participants should be clarified for every paper. **Different types of objectives** The 11 papers related to the studies on single participants are intended to describe 1 new bacteria per paper. The 6 other papers describes different types of objectives: -tDiet influence on some blood values -tComparison on the gut microbia in different countries -tComparison of Treponema species between rural and urban population -tImpact of smoking cessation, coffee and bread consumption on the intestinal microbial composition -tGut microbiome and dietary patterns **How the same protocol can cover so many different interventions, different study designs and different types of participants?** Could the authors disclose the protocol of the study 014-CEGMR-2-ETH-P? Or, at least, explain how a unique protocol can cover the diversity of situations described by the 17 papers ? How the same protocol can recruit one single participant in 2013 to describe new bacteria in stools and then start a recruitment of hundreds of participants 2 years later? Or doing another study by adding a population of monkeys in the same protocol ? The Editors should also clarify how the same protocol can cover so many different type of study design, inclusion criteria and exclusion criteria. Could the authors details the ethical approval process and the dates of the ethics approval ? **Salami publication** According to the article  [Salami publication: definitions and examples]  : * Salami publication can be roughly defined as a publication of two or more articles derived from a single study. Articles of such type report on data collected from a single study split into several segments just large enough to gain reasonable results and conclusions, also known as  minimal publishable unit .* (...) * From the publication ethics point of view, it gives undeserved credit to authors, misleads the scientific community and directly influences clinical practice by distorting medical evidence. * **LIST OF THE 17 PAPERS COVERED BY THE SAME ETHICS APPROVAL NUMBER 014-CEGMR-2-ETH-P IN SAUDI ARABIA** 1.t[Current microbiology - Anaerococcus jeddahensis sp. nov., a New Bacterial Species Isolated From Healthy Nomadic Bedouin Woman From Saudi Arabia] 2.t[JPMA - Diet influences levels of plasma lipopolysaccharide [LPS] and its soluble receptor [sCD14] in Saudis] 3.t[New microbes and new infections - Taxono-genomics and description of Gordonibacter massiliensis sp. nov., a new bacterium isolated from stool of healthy patient] 4.t[New microbes and new infections - Description of u2018Arabia massiliensisu2019 gen. nov., sp. nov.,u2018Gordonibacter massiliensisu2019 sp. nov., and u2018Bacilliculturomica massiliensisu2019 gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman] 5.t[New microbes and new infections - Comparison of the gut microbiota of obese individuals from different geographic origins] 6.t[New microbes and new infections - u2018Beduinella massiliensisu2019, gen. nov., sp. nov. a new genus representing a new family in the phylum Firmicutes, and proposal of Beduinellaceae fam. nov.] 7.t[New microbes and new infections - Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals] 8.t[Nutrition diabetes - Comparison of the gut microbiota of people in France and Saudi Arabia] 9.t[Omics: a journal of integrative biology - Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov.] 10.t[Omics: a journal of integrative biology - Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov.] 11.t[PloS one - Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study] 12.t[Scientific reports - Gut microbiome and dietary patterns in different Saudi populations and monkeys] 13.t[Standards in genomic sciences - Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut] 14.t[Standards in genomic sciences - Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov] 15.t[Standards in Genomic Sciences - Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov.] 16.t[Standards in genomic sciences - Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.] 17.t[Standards in genomic sciences - Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov.] ,