Associations Between Dysmenorrhea Symptom-Based Phenotypes and Vaginal Microbiome: A Pilot Study

Human microbiome research provides rich opportunities to elucidate factors influencing health, uncover novel biomarkers, and expand disease treatment options. A well-conducted microbiome study depends not only on a rigorous design but also on successfully engaging participants in collecting quality samples. In this paper, we aim to describe (1) strategies our team used to engage adolescents and young adults in vaginal and gut microbiome sample self-collection and (2) their effectiveness. In our prospective, longitudinal, feasibility study of 20 female adolescents and young adults, research participants self-collected vaginal and gut microbiome samples at home. Using a participatory and iterative process, we developed strategies to engage participants in sample self-collection, including (1) providing clear instructions to ensure comprehension and buy-in, (2) providing a user-friendly take-home package, (3) minimizing disgust/embarrassment associated with sample collection, and (4) follow-up communications to facilitate sample collections and return. With these strategies, we achieved 100% participant retention and 100% sample return rates. All samples ( n = 80, 100%) were usable for downstream 16s rRNA gene sequencing and analysis. All participants rated the study procedures as acceptable, and qualitative data showed that strategies were well received by participants. This study suggests that carefully planning and implementing strategies to engage participants in sample self-collection can result in high degrees of participant compliance, sample quality, and participant satisfaction in microbiome research.

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Captivity humanizes the primate microbiome

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1521835113 ◽

2016 ◽

Vol 113 (37) ◽

pp. 10376-10381 ◽

Cited By ~ 168

Author(s):

Jonathan B. Clayton ◽

Pajau Vangay ◽

Hu Huang ◽

Tonya Ward ◽

Benjamin M. Hillmann ◽

...

Keyword(s):

Gut Microbiome ◽

Meta Analysis ◽

Human Microbiome ◽

16S Rrna Gene Sequencing ◽

Modern Human ◽

Primate Species ◽

Rrna Gene ◽

Human Gut ◽

Dietary Analysis ◽

Human Gut Microbiome

The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, autoimmune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequencing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.

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A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing

10.1101/286526 ◽

2018 ◽

Cited By ~ 7

Author(s):

LW Hugerth ◽

M Seifert ◽

AAL Pennhag ◽

J Du ◽

MC Hamsten ◽

...

Keyword(s):

Dna Extraction ◽

Large Scale ◽

Human Microbiome ◽

Population Level ◽

16S Rrna Gene Sequencing ◽

Extraction Methods ◽

Storage Conditions ◽

Rrna Gene ◽

Sample Collection ◽

Dna Extraction Methods

ABSTRACTThe advent of affordable high-throughput DNA sequencing has opened up a golden age of studies in the human microbiome. In order to understand the role of the human microbiota, standardized methods for large-scale, population-level studies are needed to avoid underpowered or poorly designed studies. The biggest bottlenecks to population-level microbiomics are sample collection, storage and DNA extraction. Here, we describe a flexible automated approach to process intestinal biopsies, fecal samples and vaginal swabs from sample collection to OTU table. We have evaluated storage conditions, DNA extraction methods, PCR strategies and bioinformatic pipelines for these three sample types, and present here a set of guidelines and best practices for each of these steps.

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Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

Scientific Reports ◽

10.1038/s41598-020-80557-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Esteban Góngora ◽

Kyle H. Elliott ◽

Lyle Whyte

Keyword(s):

Gut Microbiome ◽

Sulfur Isotopes ◽

Trophic Position ◽

Isotope Analysis ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Uria Lomvia ◽

Fecal Microbiome ◽

Prey Specialization ◽

Rrna Gene Sequencing

AbstractThe role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

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Gut Feeling

European Psychiatry ◽

10.1016/j.eurpsy.2016.01.1860 ◽

2016 ◽

Vol 33 (S1) ◽

pp. S504-S505

Author(s):

C. Cotta ◽

G. Jesus ◽

V. Vila Nova ◽

C. Moreira

Keyword(s):

Mental Disorders ◽

Gut Microbiota ◽

Gut Microbiome ◽

Bacterial Infections ◽

Human Microbiome ◽

Dietary Interventions ◽

Scientific Databases ◽

Antibiotic Drugs ◽

Microbiome Research ◽

Competing Interest

IntroductionThere is growing evidence of the importance of nutrition in mental disorders. Gut microbiota, influenced by environmental factors such as diet and stress, has been proposed as one of the players on a dynamic called gut-brain axis, which is thought to have an influence on behaviour and mental health.Objectives and aimsTo summarize recent evidence on the topic, and its potential role in psychiatric interventions.MethodsThe authors review updated literature collected from online scientific databases.ResultsThe development of the brain itself has been shown to be influenced by the gut microbiome. Research demonstrates that the composition of the microbiota has influence on behaviour through neuroendocrine and other neuroactive messengers production by the bacteria within the gut lumen. Studies in germ-free animals, animals exposed to bacterial infections, probiotic suplements or antibiotic drugs suggest a role for the gut microbiota in the regulation of anxiety, mood, cognition and pain. The gut microbiome has been implicated in brain disorders including anxiety and depression, multiple sclerosis, Alzheimer's disease, Parkinson's disease, and autism.ConclusionsThe treatment of mental disorders is usually based on pharmacological and psychotherapeutic interventions, and little attention is given to dietary interventions. The emerging field of research focused on the human microbiome suggests an important role for the gut microbiota in influencing brain development, behaviour and mood in humans, and points new strategies for developing novel therapeutics for mental disorders.Disclosure of interestThe authors have not supplied their declaration of competing interest.

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The natural course of DSM-IV somatoform disorders and syndromes among adolescents and young adults: a prospective-longitudinal community study

European Psychiatry ◽

10.1016/s0924-9338(02)00686-7 ◽

2002 ◽

Vol 17 (6) ◽

pp. 321-331 ◽

Cited By ~ 81

Author(s):

Roselind Lieb ◽

Petra Zimmermann ◽

Robert H Friis ◽

Michael Höfler ◽

Sven Tholen ◽

...

Keyword(s):

Risk Factors ◽

Substance Use ◽

Young Adults ◽

Somatoform Disorders ◽

Epidemiologic Study ◽

Natural Course ◽

Adolescents And Young Adults ◽

Prospective Longitudinal ◽

Over Time

SummaryObjective.Although somatoform disorders are assumed to be chronic clinical conditions, epidemiological knowledge on their natural course based on representative samples is not available.Method.Data come from a prospective epidemiologic study of adolescents and young adults in Munich, Germany. Respondents’ diagnoses (N = 2548) at baseline and follow-up on average 42 months later are considered. The follow-up incidence, stability as well as selected baseline risk factors (sociodemographics, psychopathology, trauma exposure) for the incidence and stability of somatoform disorders and syndromes are prospectively examined. Diagnostic information was assessed by using the standardized Munich-Composite International Diagnostic Interview (M-CIDI).Results.Over the follow-up period, incidence rate for any of the covered somatoform diagnoses was 25.7%. Stability for the overall group of any somatoform disorder/syndrome was 48%. Female gender, lower social class, the experience of any substance use, anxiety and affective disorder as well as the experience of traumatic sexual and physical threat events predicted new onsets of somatoform conditions, while stability was predicted by being female, prior existing substance use, affective and eating disorders as well as the experience of a serious accident.Conclusions.At least for a substantial proportion of individuals, the overall picture of somatization seems to be relatively stable, but with fluctuation in the symptom picture over time. Being female, the experience of substance use as well as anxiety disorder seem to constitute risk factors for the onset of new somatoform conditions as well as for a stable course over time.

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Alterations of gut microbiota in gestational diabetes patients during the second trimester of pregnancy in the Shanghai Han population

Journal of Translational Medicine ◽

10.1186/s12967-021-03040-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yao Su ◽

Hong-Kun Wang ◽

Xu-Pei Gan ◽

Li Chen ◽

Yan-Nan Cao ◽

...

Keyword(s):

Gestational Diabetes ◽

Gut Microbiota ◽

Gut Microbiome ◽

Sugar Metabolism ◽

16S Rrna Gene Sequencing ◽

Amino Sugar ◽

Fecal Microbiota ◽

Rrna Gene ◽

Second Trimester ◽

Metabolic Hormone

Abstract Background The causes of gestational diabetes mellitus (GDM) are still unclear. Recent studies have found that the imbalance of the gut microbiome could lead to disorders of human metabolism and immune system, resulting in GDM. This study aims to reveal the different gut compositions between GDM and normoglycemic pregnant women and find the relationship between gut microbiota and GDM. Methods Fecal microbiota profiles from women with GDM (n = 21) and normoglycemic women (n = 32) were assessed by 16S rRNA gene sequencing. Fasting metabolic hormone concentrations were measured using multiplex ELISA. Results Metabolic hormone levels, microbiome profiles, and inferred functional characteristics differed between women with GDM and healthy women. Additionally, four phyla and seven genera levels have different correlations with plasma glucose and insulin levels. Corynebacteriales (order), Nocardiaceae (family), Desulfovibrionaceae (family), Rhodococcus (genus), and Bacteroidetes (phylum) may be the taxonomic biomarkers of GDM. Microbial gene functions related to amino sugar and nucleotide sugar metabolism were found to be enriched in patients with GDM. Conclusion Our study indicated that dysbiosis of the gut microbiome exists in patients with GDM in the second trimester of pregnancy, and gut microbiota might be a potential diagnostic biomarker for the diagnosis, prevention, and treatment of GDM.

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Integrative analysis of the gut microbiome and metabolome in a rat model with stress induced irritable bowel syndrome

Scientific Reports ◽

10.1038/s41598-021-97083-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yue Hu ◽

Fang Chen ◽

Haiyong Ye ◽

Bin Lu

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Rat Model ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Metabolic Phenotype ◽

Control Group ◽

Rrna Gene ◽

Microbial Dysbiosis ◽

Irritable Bowel

AbstractStress is one of the major causes of irritable bowel syndrome (IBS), which is well-known for perturbing the microbiome and exacerbating IBS-associated symptoms. However, changes in the gut microbiome and metabolome in response to colorectal distention (CRD), combined with restraint stress (RS) administration, remains unclear. In this study, CRD and RS stress were used to construct an IBS rat model. The 16S rRNA gene sequencing was used to characterize the microbiota in ileocecal contents. UHPLC-QTOF-MS/MS assay was used to characterize the metabolome of gut microbiota. As a result, significant gut microbial dysbiosis was observed in stress-induced IBS rats, with the obvious enrichment of three and depletion of 11 bacterial taxa in IBS rats, when compared with those in the control group (q < 0.05). Meanwhile, distinct changes in the fecal metabolic phenotype of stress-induced IBS rats were also found, including five increased and 19 decreased metabolites. Furthermore, phenylalanine, tyrosine and tryptophan biosynthesis were the main metabolic pathways induced by IBS stress. Moreover, the altered gut microbiota had a strong correlation with the changes in metabolism of stress-induced IBS rats. Prevotella bacteria are correlated with the metabolism of 1-Naphthol and Arg.Thr. In conclusion, the gut microbiome, metabolome and their interaction were altered. This may be critical for the development of stress-induced IBS.

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A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility

10.1101/2020.07.29.226712 ◽

2020 ◽

Author(s):

Blake W. Stamps ◽

Wanda J. Lyon ◽

Adam P. Irvin ◽

Nancy Kelley-Loughnane ◽

Michael S. Goodson

Keyword(s):

Pilot Study ◽

16S Rrna ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Initial Study ◽

Mitigation Strategies ◽

Taxonomic Resolution ◽

Rrna Gene ◽

Traveler’S Diarrhea ◽

Traveler's Diarrhea

AbstractTraveler’s diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers’ diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to traveler’s diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.

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Abstract 18: Gut Microbiome Modifies the Protective Effects of a Mediterranean Dietary Pattern Against Diabetes Mellitus in US Hispanics/ Latinos: The Hispanic Community Health Study/ Study of Latinos (HCHS/SOL)

Circulation ◽

10.1161/circ.141.suppl_1.18 ◽

2020 ◽

Vol 141 (Suppl_1) ◽

Cited By ~ 1

Author(s):

Dong Wang ◽

Qibin Qi ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

...

Keyword(s):

Diabetes Mellitus ◽

Relative Abundance ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Health Study ◽

Rrna Gene ◽

Inverse Association ◽

Protective Effects ◽

Acid Fermentation ◽

Microbiome Composition

Introduction: Little is known about whether the effect of a healthy diet on diabetes mellitus (DM) is modified by the gut microbiome in human. Hypothesis: We hypothesize that the gut microbiome modifies the inverse association between the Mediterranean diet (MedDiet) and risk of DM. Methods: This study included 543 DM cases, 805 with impaired glucose tolerance (IGT) and 394 with normal glucose regulation (NGR) in adults 23-83yrs old from the HCHS/SOL. Fecal samples were profiled using 16s rRNA gene sequencing. We applied QIIME 2 to cluster sequences into OTUs and assign taxonomies, and PICRUSt to predict metagenomic gene functions. Adherence to the MedDiet was evaluated by a MedDiet index using the average of two 24-hr dietary recalls. We applied MaAsLin2 to quantify associations between the MedDiet index and microbial features with adjustment for confounding factors listed in the caption of Fig. 1. Results: MedDiet was associated with phylogenetically diverse, rare, and abundant gut microbes (Fig. 1a). For example, a higher MedDiet index was associated with a higher relative abundance of Faecalibacterium Prausnitzii [FDR-adjusted p (q) =0.002], but a lower relative abundance of Collinsella aerofaciens ( q =0.009). We found that several microbial functions related to plant-derived polysaccharide degradation such as fructuronate reductase ( q =0.02), and short-chain fatty acid fermentation such as butyryl-CoA dehydrogenase ( q =0.002) were enriched in participants with higher MedDiet index. We found that the inverse association between MedDiet and risk of DM was more pronounced in participants with greater abundance of Prevotella copri , but weaker in participants whose gut microbial communities were dominated by Bacteroides ( P interaction =0.02 for IGT/DM vs NGR, Fig. 1b). Conclusions: Adherence to the MedDiet is associated with diverse gut microorganisms and microbial functions. The inverse association between MedDiet and risk of DM might be modified by gut microbiome composition. 1

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Changes in the Intestinal Microbiome during a Multispecies Probiotic Intervention in Compensated Cirrhosis

Nutrients ◽

10.3390/nu12061874 ◽

2020 ◽

Vol 12 (6) ◽

pp. 1874 ◽

Cited By ~ 1

Author(s):

Angela Horvath ◽

Marija Durdevic ◽

Bettina Leber ◽

Katharina di Vora ◽

Florian Rainer ◽

...

Keyword(s):

Gut Microbiome ◽

Controlled Trial ◽

16S Rrna Gene Sequencing ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Microbiome Composition ◽

Beneficial Effects ◽

Compensated Cirrhosis ◽

Gut Barrier Function ◽

Probiotic Treatment

Probiotics have been used in trials to therapeutically modulate the gut microbiome and have shown beneficial effects in cirrhosis. However, their effect on the microbiome of cirrhosis patients is not fully understood yet. Here, we tested the effects of a multispecies probiotic on microbiome composition in compensated cirrhosis. The gut microbiome composition of 58 patients with compensated cirrhosis from a randomized controlled trial who received a daily dose of multispecies probiotics or placebo for six months was analysed by 16S rRNA gene sequencing. Microbiome composition of patients who received probiotics was enriched with probiotic strains and the abundance of Faecalibacterium prausnitzii, Syntrophococcus sucromutans, Bacteroides vulgatus, Alistipes shahii and a Prevotella species was increased in the probiotic group compared to the placebo group. Patients who had microbiome changes in response to probiotic treatment also showed a significant increase in neopterin and a significant decrease in faecal zonulin levels after intervention, which was not observed in placebo-treated patients or patients with unchanged microbiome compositions. In conclusion, multispecies probiotics may enrich the microbiome of compensated cirrhotic patients with probiotic bacteria during a six-month intervention and beneficially change the residential microbiome and gut barrier function.

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