Microbial diversity in individuals and their household contacts following typical antibiotic courses

Abstract

BackgroundAntibiotics are a mainstay of treatment for bacterial infections worldwide, yet the effects of typical antibiotic prescriptions on human indigenous microbiota have not been thoroughly evaluated. We examined the effects of the two most commonly prescribed antibiotics (amoxicillin and azithromycin) in the USA to discern whether short-term antibiotic courses may have prolonged effects on human microbiota.ResultsWe sampled the feces, saliva, and skin specimens from a cohort of unrelated, cohabitating individuals over 6 months. An individual in each household was given an antibiotic, and the other a placebo to discern antibiotic impacts on microbiota, as well as determine whether antibiotic use might reshape the microbiota of each household. We observed household-specific patterns of microbiota on each body surface, which persevered despite antibiotic perturbations. While the gut microbiota within an individual became more dissimilar over time, there was no evidence that the use of antibiotics accelerated this process when compared to household members. There was a significant change in microbiota diversity in the gut and mouth in response to antibiotics, but analogous patterns were not observed on the skin. Those who received 7 days of amoxicillin generally had greater reductions in diversity compared to those who received 3 days, in contrast to those who received azithromycin.ConclusionsAs few as 3 days of treatment with the most commonly prescribed antibiotics can result in sustained reductions in microbiota diversity, which could have implications for the maintenance of human health and resilience to disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0187-9) contains supplementary material, which is available to authorized users.

Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers

“…GERD and BE) in the participants, which could mediate or confound oral microbiome – esophageal cancer associations, and data on medications (e.g. proton-pump inhibitors, antibiotics) which could confound these associations (50,51). Additionally, though our study is the largest of its kind, case sample sizes (n=81 EAC and n=25 ESCC) remained small, limiting statistical power to detect FDR-adjusted significant associations, and our study population was mostly white, limiting generalizability.…”

Host genetics and microbiome associations from the lens of genome wide association studies

“…Recent studies employing these technologies have uncovered evidence for both environmental and host genetic association with the microbiome composition [8,11,20,[22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]. However, to date there is no consensus regarding how and to what extent does host genetics shapes the gut microbiome, as compared to environmental factors.…”

“…First, there is an excessive bacterial similarity among individuals sharing a household, but no such similarity was observed across family members without a history of household sharing [8,20,22,35]. Second, over 20% of gut microbiome β-diversity variance can be inferred via several measured environmental factors, such as answers to food frequency and drug use questionnaires [8,33,34], whereas no statistically significant result was obtained when applying a similar methodology to genetic variants [8].…”

An overview of the effects of antibiotics and medicinal plant extracts on the human microflora

“…In an experiment, a number of volunteers given ampicillin for a short time period showed a significant decrease in the number of gastrointestinal microflora, namely Escherichia coli, enterococci, bifidobacteria, and bacteroids; the worst, two volunteers revealed overgrowth of Candida [2]. As well, in a very recent investigation on the effect of the two most commonly prescribed antibiotics in the USA (Amoxicillin and azithromycin), a sustained reduction of microflora diversity was observed in the oral cavity and gastrointestinal tract as few as 3 days of treatment [11]. In fact, many antibiotics were reported to have a pervasive influence on normal flora such as clindamycin, erythromycin, ciprofloxacin, cefoxitin, cefamandole and trovafloxacin [6].…”