Optimizing methods and dodging pitfalls in microbiome research

Kim, Dorothy; Hofstaedter, Casey E.; Zhao, Chunyu; Mattei, Lisa M.; Tanes, Ceylan; Clarke, Erik L.; Lauder, Abigail; Sherrill-Mix, Scott; Chehoud, Christel; Kelsen, Judith R.; Conrad, Máire A.; Collman, Ronald G.; Baldassano, Robert N.; Bushman, Frederic D.; Bittinger, Kyle

doi:10.1186/s40168-017-0267-5

Cited by 441 publications

(420 citation statements)

References 129 publications

(116 reference statements)

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“…Specifically, whether changes in bacteria, such as C acnes and Pseudomonas species, on superficial skin layers contribute to or reflect changes in follicular microbiota may be investigated. Future iterations of our study may also use mock community controls, 45 which we did not use, to account for foreign DNA that may have been introduced into 16S rRNA gene analysis through use of cotton swabs.…”

Section: Discussionmentioning

confidence: 99%

Association of Systemic Antibiotic Treatment of Acne With Skin Microbiota Characteristics

Chien¹,

Tsai²,

Leung³

et al. 2019

JAMA Dermatol

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IMPORTANCE Given the widespread use of systemic antibiotics for treatment of moderate to severe acne, it is important to understand the associations of such antibiotic use with changes not only in Cutibacterium acnes (formerly Propionibacterium acnes) but also in the complete bacterial community of the skin. OBJECTIVE To examine the composition, diversity, and resilience of skin microbiota associated with systemic antibiotic perturbation in individuals with acne. DESIGN, SETTING, AND PARTICIPANTS This longitudinal cohort study conducted at an academic referral center in Maryland from February 11 to September 23, 2014, included 4 female participants who had received a recent diagnosis of acne vulgaris, showed comedonal and inflammatory acne on the face, were at least 18 years old, and had no recent use of systemic or topical treatments for acne, including antibiotics and retinoids. Data analysis was performed between July 5, 2017, and November 7, 2018. INTERVENTIONS Participants were prescribed oral minocycline, 100 mg, twice daily for 4 weeks. Skin areas on the forehead, cheek, and chin were sampled for 16S ribosomal RNA gene sequencing at baseline, 4 weeks after starting minocycline treatment, and then 1 week and 8 weeks after discontinuation of treatment. MAIN OUTCOMES AND MEASURES Skin microbiota examined with respect to relative abundance of bacterial taxa, a diversity (represents within-sample microbial diversity), and β diversity (represents between-sample microbial diversity). Acne status evaluated with photography and lesion count. RESULTS Of the 4 patients included in this study, 2 were 25 years old, 1 was 29 years old, and 1 was 35 years old; 2 were white women, 1 was an African American woman, and 1 was an Asian woman. Across all 4patients, antibiotic treatment was associated with a 1.4-fold reduction in the level of Cacnes (difference, −10.3%; 95% CI, −19.9% to −0.7%; P = .04) with recovery following cessation of treatment. Distinct patterns of change were identified in multiple bacterial genera, including a transient 5.6-fold increase in the relative abundance of Pseudomonas species (difference, 2.2%; 95% CI, 0.9%−3.4%; P < .001) immediately following antibiotic treatment, as well asa persistent 1.7-fold increase in the relative abundance of Streptococcus species (difference, 5.4%; 95% CI, 0.3%−10.6%; P = .04) and a 4.7-fold decrease in the relative abundance of Lactobacillus species (difference, −0.8%; 95% CI, −1.4% to −0.2%; P = .02) 8 weeks following antibiotic treatment withdrawal. In general, antibiotic administration was associated with an initial decrease from baseline of bacterial diversity followed by recovery. Principal coordinates analysis results showed moderate clustering of samples by patient (analysis of similarity, R = 0.424; P = .001) and significant clustering of samples by time in one participant (analysis of similarity, R = 0.733; P = .001). CONCLUSIONS AND RELEVANCE In this study, systemic antibiotic treatment of acne was associated with changes in the composition an...

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Section: Discussionmentioning

confidence: 99%

Association of Systemic Antibiotic Treatment of Acne With Skin Microbiota Characteristics

Chien¹,

Tsai²,

Leung³

et al. 2019

JAMA Dermatol

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“…16S sequencing was performed; primers annealing to the V1–V2 region of the 16S bacterial gene were used for amplification as described previously (McKenna et al, 2008). Purified products from the samples were pooled in equal amounts and sequenced using Illumina MiSeq; positive and negative controls were used (Kim et al, 2017). Sequence data was processed using Quantitative Insights Into Microbial Ecology (QIIME) version 1.9 (Caporaso et al, 2010).…”

Section: Methodsmentioning

confidence: 99%

Childhood adversity impact on gut microbiota and inflammatory response to stress during pregnancy

Hantsoo

Jašarević

Criniti

et al. 2019

Brain, Behavior, and Immunity

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120

105

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Background: Adverse childhood experiences (ACEs), such as abuse or chronic stress, program an exaggerated adult inflammatory response to stress. Emerging rodent research suggests that the gut microbiome may be a key mediator in the association between early life stress and dysregulated glucocorticoid-immune response. However, ACE impact on inflammatory response to stress, or on the gut microbiome, have not been studied in human pregnancy, when inflammation increases risk of poor outcomes. The aim of this study was to assess the relationships among ACE, the gut microbiome, and cytokine response to stress in pregnant women. Methods: Physically and psychiatrically healthy adult pregnant women completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and gave a single stool sample between 20 and 26 weeks gestation. Stool DNA was isolated and 16S sequencing was performed. Three 24-hour food recalls were administered to assess dietary nutrient intake. A subset of women completed the Trier Social Stress Test (TSST) at 22–34 weeks gestation; plasma interleukin-6 (IL-6), interleukin-1β (IL-1β), high sensitivity C-reactive protein (hsCRP), tumor necrosis factor α (TNF-α), and cortisol were measured at four timepoints pre and post stressor, and area under the curve (AUC) was calculated. Results: Forty-eight women completed the ACE-Q and provided stool; 19 women completed the TSST. Women reporting 2 or more ACEs (high ACE) had greater differential abundance of gut Prevotella than low ACE participants (q=5.7×10^−13). Abundance of several gut taxa were significantly associated with cortisol, IL-6, TNF-α and CRP AUCs regardless of ACE status. IL-6 response to stress was buffered among high ACE women with high intake of docosahexaenoic acid (DHA) (p=0.03) and eicosapentaenoic acid (EPA) (p=0.05). Discussion: Our findings suggest that multiple childhood adversities are associated with changes in gut microbiota composition during pregnancy, and such changes may contribute to altered inflammatory and glucocorticoid response to stress. While preliminary, this is the first study to demonstrate an association between gut microbiota and acute glucocorticoid-immune response to stress in a clinical sample. Finally, exploratory analyses suggested that high ACE women with high dietary intake of ω-3 polyunsaturated fatty acids (PUFAs) had a dampened inflammatory response to acute stress, suggesting potentially protective effects of ω-3s in this high-risk population. Given the adverse effects of inflammation on pregnancy and the developing fetus, mechanisms by which childhood adversity influence the gut-brain axis and potential protective factors such as diet should be further explored.

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“…To account for contaminating environmental and/or artefactual sequences introduced during acquisition, processing, and library preparation of low biomass samples, 23,24,26,27 bronchoscope prewashes, buffer, and sterile water blanks were analyzed using the same workflow. To account for contaminating environmental and/or artefactual sequences introduced during acquisition, processing, and library preparation of low biomass samples, 23,24,26,27 bronchoscope prewashes, buffer, and sterile water blanks were analyzed using the same workflow.…”

Section: Shotgun Metagenomic Sequencing and Bioinformatics Pipelinementioning

confidence: 99%

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

Abbas

Young

Clarke

et al. 2019

American Journal of Transplantation

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Solid organ transplantation disrupts virus-host relationships, potentially resulting in viral transfer from donor to recipient, reactivation of latent viruses, and new viral infections. Viral transfer, colonization, and reactivation are typically monitored using assays for specific viruses, leaving the behavior of full viral populations (the "virome") understudied. Here we sought to investigate the temporal behavior of viruses from donor lungs and transplant recipients comprehensively. We interrogated the bronchoalveolar lavage and blood viromes during the peritransplant period and 6-16 months posttransplant in 13 donor-recipient pairs using shotgun metagenomic sequencing. Anelloviridae, ubiquitous human commensal viruses, were the most abundant human viruses identified. Herpesviruses, parvoviruses, polyomaviruses, and bacteriophages were also detected. Anelloviridae populations were complex, with some donor organs and hosts harboring multiple contemporaneous lineages. We identified transfer of Anelloviridae lineages from donor organ to recipient serum in 4 of 7 cases that could be queried, and immigration of lineages from recipient serum into the allograft in 6 of 10 such cases. Thus, metagenomic analyses revealed that viral populations move between graft and host in both directions, showing that organ transplantation involves implantation of both the allograft and commensal viral communities.

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Optimizing methods and dodging pitfalls in microbiome research

Cited by 441 publications

References 129 publications

Association of Systemic Antibiotic Treatment of Acne With Skin Microbiota Characteristics

Association of Systemic Antibiotic Treatment of Acne With Skin Microbiota Characteristics

Childhood adversity impact on gut microbiota and inflammatory response to stress during pregnancy

Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

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