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Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, DenmarkPatrick Munk, Christian Brinch, Frederik Duus Møller, Thomas N. Petersen, Rene S. Hendriksen, Anne Mette Seyfarth, Jette S. Kjeldgaard, Christina Aaby Svendsen & Frank M. AarestrupCentre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UKBram van Bunnik & Mark WoolhouseCentre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, SwedenFanny Berglund & D. G. 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GazeNewcastle University, Newcastle upon Tyne, UKDavid W. Graham & Joshua T. BunceBrightwater Treatment Plant, Woodinville, WA, USABrett LeforDepartment of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USADrew Capone & Joe BrownUniversity of North Carolina, Chapel Hill, USAEmanuele Sozzi & Mark D. SobseyUniversity of Washington, Seattle, WA, USAJohn Scott Meschke, Nicola Koren Beck, Pardi Sukapanpatharam & Phuong TruongBaylor University, Waco, USAMichael DavisColumbia Boulevard WWTP, Portland, USARonald LilienthalEastern Illinois University, Charleston, USASanghoon KangThe Ohio State University, Columbus Ohio, USAThomas E. WittumLaboratorio Tecnolσgico del Uruguay, Montevideo, UruguayNatalia Rigamonti & Patricia BaklayanInstitute of Public Health in Ho Chi Minh City, Ho Chi Minh, VietnamChinh Dang Van, Doan Minh Nguyen Tran & Nguyen Do PhucUniversity of Zambia, Lusaka, ZambiaGeoffrey Kwenda More

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ParticipantsIn total, 80, 63, and 56 participants in the EM, CM, and control groups, respectively, initially agreed to participate in this study. Nevertheless, 28, 12, and 13 individuals in the EM, CM, and control groups, respectively, withdrew their participation and did not bring any fecal samples to the study site. After providing fecal samples, 10 and 6 individuals with EM and CM, respectively, reported intake of probiotics and were excluded from the analysis. No participant in the control group consumed probiotics during the study period. Eventually, 42, 45, and 43 participants in the EM, CM, and control groups, respectively, were enrolled (Fig. 1). The demographic and clinical characteristics of participants are summarized in Table 1. All participants with EM and CM used acute treatments for migraine. Moreover, 25 (59.5%) and 27 (60.0%) participants with EM and CM, respectively, received prophylactic treatment for migraine. Of the 42 participants with EM, 20 used anti-epileptic medications, 11 used beta blockers, 2 used an anti-depressant, and 1 used a calcium-channel blocker for prophylactic treatment. Of the 45 participants with CM, 23 used anti-epileptic medications, 8 used beta blockers, 1 used an anti-depressant, and no participant used calcium-channel blockers for prophylactic treatment. No participant in the EM, CM, and control groups was infected with SARS-CoV-2 before or during participation in the study.Figure 1Flow of participants in a study on the composition of gut microbiota in participants with episodic or chronic migraine.Full size imageTable 1 Demographic and clinical characteristics of participants with episodic and chronic migraine and the control.Full size tableCollection of 16 s RNA sequencing dataWe obtained 7,802,425 read sequences, accounting for 99.8% of the valid sequences from the fecal samples of 130 participants. According to barcode and primer sequence filtering, an average of 59,305 (range, 3716–90,832) observed sequences per sample was recovered for downstream analysis. Thus, 2,242,325 sequences were obtained from the controls for phylogenetic analysis, whereas 2,747,952 and 2,812,148 sequences were obtained from the EM and CM groups, respectively.Microbial diversityAlpha diversity was defined as microbial community richness and evenness. Alpha diversities in the genus richness, as evaluated by Chao1 (Fig. 2A), Shannon (Fig. 2B), and Simpson (Fig. 2C) indices, did not differ significantly among the EM, CM, and control groups. Beta diversity represented the community composition dissimilarity between samples. PCoA with the weighted UniFrac distance (Fig. 3A and Supplementary Fig. S1A, p = 0.176, permutational multivariate analysis of variance [PERMANOVA]), the unweighted UniFrac distance (Fig. 3B and Supplementary Fig. S1B, p = 0.132, PERMANOVA), and the Bray–Curtis dissimilarity index (Fig. 3C and Supplementary Fig. S1C, p = 0.220, PERMANOVA) for beta diversity at the genus level among the EM, CM, and control groups revealed that these three groups could not be separated.Figure 2Alpha diversity at the genus level using Chao1 (A), Shannon (B), and Simpson (C) indices*,†. *Controls (green) and participants with episodic migraine (blue) and chronic migraine (yellow). †In the box plots, the lower boundary of the box indicates the 25th percentile; a blue line within the box marks the median, and the upper boundary of the box indicates the 75th percentile. Whiskers above (red) and below the box (green) indicate the highest and the lowest values, respectively.Full size imageFigure 3Beta diversity of microbiota in principal coordinate analysis plot with the weighted UniFrac distance (A), the unweighted UniFrac distance (B) and the Bray–Curtis dissimilarity index (C)*. *Controls (green) and participants with episodic migraine (blue) and chronic migraine (yellow).Full size imageRelative abundance of fecal microbes between participants with EM and the controlRelative abundance of fecal microbes at the phylum level did not differ significantly among participants in the control, EM, and CM groups (Supplementary Fig. S2). Moreover, Tissierellales (p = 0.001) and Tissierellia (p = 0.001) were more abundant in the EM group than that in the control group at the order and class levels, respectively (Fig. 4A). At the family level, Peptoniphilaceae (p = 0.001) and Eubacteriaceae (p = 0.045) occurred at a significantly higher proportion in the EM group than that in the control group. Furthermore, at the genus level, the abundance of 11 genera differed significantly between the two groups, including one more abundant and 10 less abundant genera in the EM group. Catenibacterium (p = 0.031) and Olsenella (p = 0.038) had the highest relative abundance in the control and EM groups, respectively.Figure 4Taxonomic differences in fecal microbiota among participants. The fold change (log2) denotes the difference in relative abundance between participants with episodic migraine and the control (A), between those with chronic migraine and the control (B), and between those with episodic and chronic migraine (C). CM chronic migraine; EM episodic migraine.Full size imageRelative abundance of fecal microbes between participants with CM and the controlThe analysis results at the class, order, family, genus, and species levels between CM and control groups are illustrated in Fig. 4B. Tissierellia (p = 0.001), Tissierellales (p = 0.001), and Peptoniphilaceae (p = 0.001) were more abundant in the CM group than that in the control group at the class, order, and family levels, respectively; however, at the genus level, the abundances of 18 genera differed significantly, including four more abundant and 14 less abundant genera in the CM group than in the control group.Relative abundance of fecal microbes between participants with EM and CMThe analysis results at the class, order, family, and genus levels between CM and EM groups are summarized in Fig. 4C. At the class level, Bacilli (p = 0.033) were less abundant in the CM group than that in the EM group; however, at the order level, Selenomonadales (p = 0.016) and Lactobacillales (p = 0.034) were less abundant in the CM group than that in the EM group. Moreover, at the class level, Selenomonadaceae (p = 0.016) and Prevotellaceae (p = 0.012) were less abundant in the CM group than that in the EM group. Furthermore, at the genus level, PAC001212_g (p = 0.019) revealed relative positive predominancy in the CM groups, whereas Prevotella (p = 0.019), Holdemanella (p = 0.009), Olsenella (p = 0.033), Adlercreutzia (p = 0.018), and Coprococcus (p = 0.040) revealed relative positive predominancy in the EM group.Association among fecal microbiota and clinical characteristics and comorbidities of migraineAmong the five genera (Roseburia, Eubacterium_g4, Agathobacter, PAC000195_g, and Catenibacterium) depicting predominance or less-predominance both in EM and CM groups, we conducted additional analyses for clinical characteristics and migraine comorbidities.Combining the results of the 42 and 45 participants with EM and CM, respectively, the Poisson regression analysis for relative abundance of microbiota revealed that a higher composition of PAC000195_g (p = 0.040) was significantly associated with lower headache frequency (Table 2). Furthermore, Agathobacter (p = 0.009) had a negative association with severe headache intensity (Table 3). Anxiety was associated with Catenibacterium (p = 0.027); however, depression did not reveal any association with the five genera (Table 3).Table 2 The association between headache frequency and the relative abundance of microbiota.*Full size tableTable 3 The association of severe headache intensity and comorbidities with the relative abundance of microbiota*.Full size tableRelative abundance of fecal microbes in participants with EM based on prophylactic treatmentAlpha and beta diversities in participants with EM did not differ significantly based on their prophylactic treatment (Supplementary Figs S3A–C, S4A–C, and S5A–C). At the genus level, Klebsiella (p = 0.009), Enterobacteriaceae_g (p = 0.006), and Faecalibacterium (p = 0.046) were more abundant in the prophylactic group than the non-prophylactic group (Supplementary Fig. S6A).Relative abundance of fecal microbes in participants with CM based on prophylactic treatmentAlpha and beta diversities in participants with CM did not differ significantly based on prophylactic treatment (Supplementary Figs S7A–C, S8A–C, and S9A–C). Emergencia (p = 0.043), Ruthenibacterium (p = 0.005), Eggerthella (p = 0.003), PAC000743_g (p = 0.034), and Anaerostipes (p = 0.039) were more abundant in the prophylactic group, whereas PAC000196_g (p = 0.049), Fusicatenibacter (p = 0.028), and Faecalibacterium (p = 0.021) were more abundant in the non-prophylactic group at the genus level (Supplementary Fig. S6B). More

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