a, Total salt intake according to dietary records (n = 12, paired one-tailed t-test). b, c, Metagenome analysis shows loss of Lactobacillus gut populations during human high-salt challenge. All subjects (x axis) for which gut Lactobacilli were detected are shown at baseline and all species detected (y axis) using the mOTU (b) or MetaPhlAn framework (c) for bacterial species identification are shown. Heat map cells show abundance of mOTU (insert counts as fraction of sample total) or average coverage (reads per position) for MetaPhlAn of the Lactobacillus species at baseline (left part of cells, black border) and after high-salt challenge (right part of cells, grey border). Cross markers show complete loss (no detection after high-salt challenge) of each species. In all cases but one (shown), baseline Lactobacillus populations are no longer detected after high salt intake. d, qPCR using Lactobacillus-specific 16S rDNA primers in human faecal samples positive for Lactobacillus at baseline show a loss of the respective species after 14 days of high salt. Lactobacillus 16S rDNA copy number in 4 ng faecal DNA is shown. Symbols indicate study subject, colours indicate respective Lactobacillus species. e, Kaplan–Meier survival curves contrasting the fate of gut Lactobacillus populations (detected using the mOTU framework) following a high-salt challenge (bright red curve) and in healthy control individuals from reference cohorts (n = 121, see Methods) not undergoing any intervention (bright blue curve). This is compared with corresponding survival curves over time for the set of all other detected gut bacterial species following high-salt challenge (high salt others, dark red curve) and without challenge in controls (NSD others, dark blue curve). f, For a clearer view of its time range, only the salt intervention curves from e are shown. Two observations are clear. First, Lactobacillus on average persist for shorter times in the gut than the average of all other species. Second, a high-salt challenge strongly increases gut loss of both Lactobacillus and non-Lactobacillus species. As such, in combination, Lactobacillus loss is highly pronounced after high-salt intervention and significantly (P < 1.62 × 10−8) faster than the average of all species. g–i, Metagenome analysis shows introduction of novel Lactobacillus gut populations during human high-salt challenge. All subjects (x axis) for which gut Lactobacilli were detected following high-salt challenge are shown, and all species detected (y axis) using the SpecI (g), mOTU (h) or MetaPhlAn (i) analysis are shown. Heat map cells show abundance (insert counts as fraction of sample total for SpecI and mOTU) and average coverage (reads per position for MetaPhlAn) of the Lactobacillus species at baseline (left part of cells, black border) and after high-salt challenge (right part of cells, grey border). Cross markers show novel introduction (no detection at baseline) of each species. Source data