Gut microbiota in military international travelers with doxycycline malaria prophylaxis: Towards the risk of a simpson paradox in the human microbiome field

Émilie Javelle (1, 2, 3) , Auŕelie Mayet (4, 5) , Matthieu Million (2, 6) , Anthony Levasseur (2, 4, 6) , Setcheou Rodrigue Allodji (7, 8) , Catherine Marimoutou (4, 5, 9) , Chrystel Lavagna (4) , Jérôme Desplans (4) , Pierre Édouard Fournier (1, 2) , Didier A. Raoult (2, 6) , Gaëtan Texier (1, 4)

1 AMU - Aix Marseille Université
2 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection
3 VITROME - Vecteurs - Infections tropicales et méditerranéennes
4 CESPA - Centre d'épidémiologie et de santé publique des armées [Marseille]
5 SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD - Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale
6 MEPHI - Microbes évolution phylogénie et infections
7 CESP - Centre de recherche en épidémiologie et santé des populations
8 Direction de la recherche [Gustave Roussy]
9 CIC 1410 - Centre d'Investigation Clinique de La Réunion - INSERM

Dysbiosis, developed upon antibiotic administration, results in loss of diversity and shifts in the abundance of gut microbes. Doxycycline is a tetracycline antibiotic widely used for malaria prophylaxis in travelers. We prospectively studied changes in the fecal microbiota of 15 French soldiers after a 4-month mission to Mali with doxycycline malaria prophylaxis, compared to changes in the microbiota of 28 soldiers deployed to Iraq and Lebanon without doxycycline. Stool samples were collected with clinical data before and after missions, and 16S rRNA sequenced on MiSeq targeting the V3-V4 region. Doxycycline exposure resulted in increased alpha-biodiversity and no significant beta-dissimilarities. It led to expansion in Bacteroides, with a reduction in Bifidobacterium and Lactobacillus, as in the group deployed without doxycycline. Doxycycline did not alter the community structure and was specifically associated with a reduction in Escherichia and expression of Rothia. Differences in the microbiota existed at baseline between military units but not within the studied groups. This group-effect highlighted the risk of a Simpson paradox in microbiome studies.

Mots clés: Bacteroides; Deployment; Doxycycline; Group-effect; Gut microbiota; Malaria prophylaxis; Mission; Rothia; Simpson paradox; Soldiers; Tetracycline; Travel

Domaines: Sciences du Vivant [q-bio]

Émilie Javelle, Auŕelie Mayet, Matthieu Million, Anthony Levasseur, Setcheou Rodrigue Allodji, et al.. Gut microbiota in military international travelers with doxycycline malaria prophylaxis: Towards the risk of a simpson paradox in the human microbiome field. Pathogens, 2021, 10 (8), ⟨10.3390/pathogens10081063⟩. ⟨hal-03401828⟩