Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains

Abstract

Probiotics have been used for decades to alleviate the negative side-effects of oral antibiotics, but our mechanistic understanding on how they work is so far incomplete. Here, we performed a metagenomic analysis of the fecal microbiota in participants who underwent a 14-d Helicobacter pylori eradication therapy with or without consumption of a multi-strain probiotic intervention ( L. paracasei CNCM I-1518, L. paracasei CNCM I-3689, L. rhamnosus CNCM I-3690, and four yogurt strains) in a randomized, double-blinded, controlled clinical trial. Using a strain-level analysis for detection and metagenomic determination of replication rate, ingested strains were detected and replicated transiently in fecal samples and in the gut during and following antibiotic administration. Consumption of the fermented milk product led to a significant, although modest, improvement in the recovery of microbiota composition. Stratification of participants into two groups based on the degree to which their microbiome recovered showed i) a higher fecal abundance of the probiotic L. paracasei and L. rhamnosus strains and ii) an elevated replication rate of one strain ( L. paracasei CNCMI-1518) in the recovery group. Collectively, our findings show a small but measurable benefit of a fermented milk product on microbiome recovery after antibiotics, which was linked to the detection and replication of specific probiotic strains. Such functional insight can form the basis for the development of probiotic-based intervention aimed to protect gut microbiome from drug treatments.

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy

“…Finally, the relative abundance of Bifidobacterium was lower in subjects with recent antibiotic intake (Mann-Whitney, P < 0.001) [Supplementary Figure 2]. Despite the considerable analytical differences between studies, this dataset reproduced the major associations previously reported between Bifidobacterium and age [27] , lifestyle [28] , health status [1,29,30] , and antibiotic use [31][32][33] in individual cohorts.…”

“…Here, we studied the variability of the gut microbiome as a function of the resident Bifidobacterium community, using a public database compiling curated metagenomics-based studies, mostly performed in adults from Western countries. We first checked that we could reproduce the previously reported findings of a lower abundance of Bifidobacterium species in antibiotic users [31][32][33] and individuals with diseases [1] or adopting a nonwesternized lifestyle [28] , the differential prevalence of most Bifidobacterium species depending on age [10] , the high prevalence of B. longum throughout the human lifespan [27] , and the higher prevalence of B. adolescentis in healthy subjects than in those with diseases [29,30] .…”

“…We filtered the 9.515 datasets as follows to obtain a final dataset relating to 5.329 subjects for DMM: (1) We retained individuals who had not had antibiotic treatment as declared in the cMD (antibiotic use = no) (N = 216) or without information (N = 3.571) to prevent bias in the diversity calculation; (2) We excluded subjects with a total count < 500, to overcome Bifidobacterium underdetection issues (N = 19); (3) We excluded subjects with no Bifidobacterium species total reads count as a DMM standard (N = 380). DMM models were calculated for different numbers (k) of clusters, k ∈ [1,30], and evaluated with the Bayesian information criterion (BIC) and five different seeds. These methods are based on minimizing a penalized criterion, taking into account model fit and complexity.…”

Strategies for applying probiotics in the antibiotic management ofClostridioides difficileinfection

“…Interestingly, previous studies showed significant improvements in the gut ecology of patients who received probiotic interventions at the end of antibiotic therapy compared to patients who did not receive interventions. 30 Probiotic intervention in the first hours after antibiotic intake can provide good prevention of pCDI, as demonstrated in several clinical…”

Why Give My Surgical Patients Probiotics

“…Probiotics, even as milk-fermented products, have been used empirically for decades to alleviate the negative side effects of oral antibiotics, but understanding of the way they work is so far incomplete. A metagenomic analysis of the fecal microbiota of 135 subjects, who received a 14 d scheme of antibiotics revealed a rapid alteration of gut microbiota, a decrease in richness and diversity, a bloom of pathobionts of the family Enterobacteriaceae , and the depletion of several taxa including Bifidobacterium and butyrate producers [ 54 ]. The co-administration of probiotics showed a small, but measurable, benefit on microbiome recovery after antibiotics, which was linked to the detection and replication of specific probiotic strains.…”