title: Microbial diversity in individuals and their household contacts following typical antibiotic courses.
abstract: Antibiotics 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.
  
  
  
  We 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.
  
  
  
  As 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.
authors.affiliation: Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
authors.forename: Shira R
authors.initials: SR
authors.lastname: Abeles
authors.affiliation: Human Longevity, Inc., San Diego, CA, 92121, USA.
authors.forename: Marcus B
authors.initials: MB
authors.lastname: Jones
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
authors.forename: Tasha M
authors.initials: TM
authors.lastname: Santiago-Rodriguez
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Ly
authors.affiliation: Human Longevity, Inc., San Diego, CA, 92121, USA.
authors.forename: Niels
authors.initials: N
authors.lastname: Klitgord
authors.affiliation: Human Longevity, Inc., San Diego, CA, 92121, USA.|Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA.
authors.forename: Shibu
authors.initials: S
authors.lastname: Yooseph
authors.affiliation: Human Longevity, Inc., San Diego, CA, 92121, USA.|Genomic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA.
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.affiliation: Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. dpride@ucsd.edu.|Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. dpride@ucsd.edu.
authors.forename: David T
authors.initials: DT
authors.lastname: Pride
mesh_terms: D000328:Adult; D000658:Amoxicillin / Q000494:pharmacology*; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D017963:Azithromycin / Q000494:pharmacology*; D001419:Bacteria / Q000145:classification / Q000187:drug effects; D044822:Biodiversity; D005190:Family; D005243:Feces / Q000382:microbiology*; D005260:Female; D006801:Humans; D008297:Male; D064307:Microbiota / Q000187:drug effects*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012463:Saliva / Q000382:microbiology*; D012867:Skin / Q000382:microbiology*; D014481:United States; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D012336:RNA, Ribosomal, 16S; D000658:Amoxicillin; D017963:Azithromycin
keywords: 16S rRNA; Antibiotic courses; Antibiotic perturbations; Antibiotics; Gut; Microbiome; Saliva; Skin