Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods

Eggers, Shoshannah; Malecki, Kristen; Peppard, Paul E.; Mares, Julie A.; Shirley, Daniel; Shukla, Sanjay Kumar; Poulsen, Keith P.; Gangnon, Ronald E.; Duster, Megan; Kates, Ashley E.; Suen, Garret; Sethi, Ajay K.; Safdar, Nasia

doi:10.1136/bmjopen-2017-019450

Cited by 34 publications

(43 citation statements)

References 34 publications

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“…Dietary fiber appears promising in promoting a diverse, healthy gut microbiota by selecting for fiber-degrading microbes that produce immune-enhancing compounds like butyrate [135]. The Winning the War on Antibiotic Resistance (WARRIOR) project is a study examining associations of dietary fiber consumption with the composition of the gut microbiota and gut colonization by MDROs [136].…”

Section: Prebioticmentioning

confidence: 99%

Gut Microbiota, Antibiotic Therapy and Antimicrobial Resistance: A Narrative Review

2020

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Antimicrobial resistance is a major concern. Epidemiological studies have demonstrated direct relationships between antibiotic consumption and emergence/dissemination of resistant strains. Within the last decade, authors confounded spectrum activity and ecological effects and did not take into account several other factors playing important roles, such as impact on anaerobic flora, biliary elimination and sub-inhibitory concentration. The ecological impact of antibiotics on the gut microbiota by direct or indirect mechanisms reflects the breaking of the resistance barrier to colonization. To limit the impact of antibiotic therapy on gut microbiota, consideration of the spectrum of activity and route of elimination must be integrated into the decision. Various strategies to prevent (antimicrobial stewardship, action on residual antibiotics at colonic level) or cure dysbiosis (prebiotic, probiotic and fecal microbiota transplantation) have been introduced or are currently being developed.

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Section: Prebioticmentioning

confidence: 99%

Gut Microbiota, Antibiotic Therapy and Antimicrobial Resistance: A Narrative Review

2020

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“…We conducted a case-control study on the impact of indoor pet exposure on the human gut microbiota nested within the Survey of the Health of Wisconsin (SHOW) and its ancillary study, the Wisconsin Microbiome Study (WMS) (Eggers et al, 2018). Both SHOW and WMS are ongoing studies assessing the overall health and risk of infection with antibiotic-resistant organisms.…”

Section: Study Design and Populationmentioning

confidence: 99%

“…All participants are over 18 years of age, capable of giving informed consent, able to communicate answers to the interviewers, and are not residents of nursing homes, hospitals, mental health institutions, penal institutions, or fulltime members of the armed forces. The full list of inclusion and exclusion criteria as well as a description of the SHOW and the WMS populations has been published elsewhere (Nieto et al, 2010;Eggers et al, 2018). A description of the SHOW and WMS projects as well as SHOW protocols can be found on the SHOW website (https://www.show.wisc.edu).…”

Section: Study Design and Populationmentioning

confidence: 99%

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Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota

Kates

Jarrett

Skarlupka

et al. 2020

Front. Cell. Infect. Microbiol.

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The human gut microbiome has a great deal of interpersonal variation due to both endogenous and exogenous factors, like household pet exposure. To examine the relationship between having a pet in the home and the composition and diversity of the adult gut microbiome, we conducted a case-control study nested in a larger, statewide study, the Survey of the Health of Wisconsin. Stool samples were collected from 332 participants from unique households and analyzed using 16S rRNA sequencing on the Illumina MiSeq. One hundred and seventy-eight participants had some type of pet in the home with dogs and cats being the most prevalent. We observed no difference in alpha and beta diversity between those with and without pets, though seven OTUs were significantly more abundant in those without pets compared to those with pets, and four were significantly more abundant in those with pets. When stratifying by age, seven of these remained significant. These results suggest that pet ownership is associated with differences in the human gut microbiota. Further research is needed to better characterize the effect of pet ownership on the human gut microbiome.

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“…Genomic DNA extraction. DNA extracted from a single stool pellet or 200 mg of cecal content was subjected PCR amplification and sequencing as described previously (14,45). All sequences were demultiplexed on the Illumina MiSeq and assessed for quality using FastQC v0.11.7 (46).…”

Section: Figmentioning

confidence: 99%

Modified Mouse Model of Clostridioides difficile Infection as a Platform for Probiotic Efficacy Studies

Wolfe

Kates

Barko

et al. 2019

Antimicrob Agents Chemother

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Probiotics may represent a promising approach for reducing Clostridioides (Clostridium) difficile infections (CDIs). A clinical trial conducted by our group demonstrated that CDI patients undergoing adjunctive treatment with Lactobacillus and Bifidobacterium probiotics had a reduction in diarrheal duration and compositional changes in their stool microbiomes. Here, we modified a CDI mouse model to represent clinical outcomes observed in patients and employed this model to identify evidence for the prevention of primary CDI and relapse with the same probiotic. Mice (n = 80) were administered 0.25 mg/ml cefoperazone over 5 days and subsequently challenged with 102 C. difficile VPI 10463 spores. A subset of mice (n = 40) were administered 108 CFU of probiotics daily alongside cefoperazone pretreatment and until experimental endpoints were reached. Clinical scoring was performed daily on mice and used to evaluate CDI onset and severity. Moderate CDI in mice was defined by survival beyond day 3 postinfection, while mice with severe CDI were those who succumbed to infection prior to day 3 postinfection. Sequencing and analysis of 16S rRNA from stool content were performed to determine compositional alterations to the microbiota. Using total clinical scores, we identified an association between probiotic treatment and delayed onset of primary CDI and relapse by approximately 12 to 24 h (P < 0.001). The stool microbiome of mice with moderate CDI receiving probiotic treatment was significantly enriched with Lachnospiraceae during primary CDI (P < 0.05). The outcomes observed present an opportunity to use this modified CDI mouse model to examine the efficacy of nonantibiotic options for CDI management.

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Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods

Cited by 34 publications

References 34 publications

Gut Microbiota, Antibiotic Therapy and Antimicrobial Resistance: A Narrative Review

Gut Microbiota, Antibiotic Therapy and Antimicrobial Resistance: A Narrative Review

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota

Modified Mouse Model of Clostridioides difficile Infection as a Platform for Probiotic Efficacy Studies

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