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1.
Female genital tract microbiota affecting the risk of preterm birth: What do we know so far? A review.
Tsonis, O, Gkrozou, F, Harrison, E, Stefanidis, K, Vrachnis, N, Paschopoulos, M
European journal of obstetrics, gynecology, and reproductive biology. 2020;:168-173
Abstract
Spontaneous Preterm birth (SPTB) is a common obstetric complication affecting 12.9 million births worldwide and is the leading cause of neonatal morbidity and mortality. Disruption in the vaginal microbiota has an impact on the maternal immunological profile leading to SPTBs. Scientists have struggled to link maternal infectious agents with the dysregulation of the maternal immune response in cases of SPTBs. Throughout the last decade, important findings regarding the role of microbiota and its genome, the so-called microbiome, have linked alterations within the population of the microorganisms in our bodies with changes in nutrition, immunity, behaviour and diseases. In this review, evidence regarding the female genital tract microbiota and microbiome has been examined to help further our understanding of its role in disrupting the maternal immune system resulting in spontaneous preterm birth.
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2.
Understanding the impact of antibiotic perturbation on the human microbiome.
Schwartz, DJ, Langdon, AE, Dantas, G
Genome medicine. 2020;(1):82
Abstract
The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome's ecological balance, commonly by antibiotics, can cause and exacerbate diseases. To predict and successfully rescue such perturbations, first, we must understand the underlying taxonomic and functional dynamics of the microbiome as it changes throughout infancy, childhood, and adulthood. We offer an overview of the healthy gut bacterial architecture over these life stages and comment on vulnerability to short and long courses of antibiotics. Second, the resilience of the microbiome after antibiotic perturbation depends on key characteristics, such as the nature, timing, duration, and spectrum of a course of antibiotics, as well as microbiome modulatory factors such as age, travel, underlying illness, antibiotic resistance pattern, and diet. In this review, we discuss acute and chronic antibiotic perturbations to the microbiome and resistome in the context of microbiome stability and dynamics. We specifically discuss key taxonomic and resistance gene changes that accompany antibiotic treatment of neonates, children, and adults. Restoration of a healthy gut microbial ecosystem after routine antibiotics will require rationally managed exposure to specific antibiotics and microbes. To that end, we review the use of fecal microbiota transplantation and probiotics to direct recolonization of the gut ecosystem. We conclude with our perspectives on how best to assess, predict, and aid recovery of the microbiome after antibiotic perturbation.
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3.
A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species.
Bruns, TD, Chung, JA, Carver, AA, Glassman, SI
PloS one. 2020;(3):e0222691
Abstract
We have designed a pyrocosm to enable fine-scale dissection of post-fire soil microbial communities. Using it we show that the peak soil temperature achieved at a given depth occurs hours after the fire is out, lingers near this peak for a significant time, and is accurately predicted by soil depth and the mass of charcoal burned. Flash fuels that produce no large coals were found to have a negligible soil heating effect. Coupling this system with Illumina MiSeq sequencing of the control and post-fire soil we show that we can stimulate a rapid, massive response by Pyronema, a well-known genus of pyrophilous fungus, within two weeks of a test fire. This specific stimulation occurs in a background of many other fungal taxa that do not change noticeably with the fire, although there is an overall reduction in richness and evenness. We introduce a thermo-chemical gradient model to summarize the way that heat, soil depth and altered soil chemistry interact to create a predictable, depth-structured habitat for microbes in post-fire soils. Coupling this model with the temperature relationships found in the pyrocosms, we predict that the width of a survivable "goldilocks zone", which achieves temperatures that select for postfire-adapted microbes, will stay relatively constant across a range of fuel loads. In addition we predict that a larger necromass zone, containing labile carbon and nutrients from recently heat-killed organisms, will increase in size rapidly with addition of fuel and then remain nearly constant in size over a broad range of fuel loads. The simplicity of this experimental system, coupled with the availability of a set of sequenced, assembled and annotated genomes of pyrophilous fungi, offers a powerful tool for dissecting the ecology of post-fire microbial communities.
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4.
Microbiome Composition in Pediatric Populations from Birth to Adolescence: Impact of Diet and Prebiotic and Probiotic Interventions.
Davis, EC, Dinsmoor, AM, Wang, M, Donovan, SM
Digestive diseases and sciences. 2020;(3):706-722
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Abstract
Diet is a key regulator of microbiome structure and function across the lifespan. Microbial colonization in the first year of life has been actively researched; however, studies during childhood are sparse. Herein, the impact of dietary intake and pre- and probiotic interventions on microbiome composition of healthy infants and children from birth to adolescence is discussed. The microbiome of breastfed infants has lower microbial diversity and richness, higher Proteobacteria, and lower Bacteroidetes and Firmicutes than those formula-fed. As children consume more complex diets, associations between dietary patterns and the microbiota emerge. Like adults, the microbiota of children consuming a Western-style diet is associated with greater Bacteroidaceae and Ruminococcaceae and lower Prevotellaceae. Dietary fibers and pre- or/and probiotics have been tested to modulate the gut microbiota in early life. Human milk oligosaccharides and prebiotics added to infant formula are bifidogenic and decrease pathogens. In children, prebiotics, such as inulin, increase Bifidobacterium abundance and dietary fibers reduce fecal pH and increase alpha diversity and calcium absorption. Probiotics have been administered to the mother during pregnancy and breastfeeding or directly to the infant/child. Findings on maternal probiotic administration on bacterial taxa are inconsistent. When given directly to the infant/child, some changes in individual taxa are observed, but rarely is overall alpha or beta diversity affected. Cesarean-delivered infants appear to benefit to a greater degree than those born vaginally. Infancy and childhood represent an opportunity to beneficially manipulate the microbiome through dietary or prebiotic interventions, which has the potential to affect both short- and long-term health outcomes.
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A Revolutionizing Approach to Autism Spectrum Disorder Using the Microbiome.
Johnson, D, Letchumanan, V, Thurairajasingam, S, Lee, LH
Nutrients. 2020;(7)
Abstract
The study of human microbiota and health has emerged as one of the ubiquitous research pursuits in recent decades which certainly warrants the attention of both researchers and clinicians. Many health conditions have been linked to the gut microbiota which is the largest reservoir of microbes in the human body. Autism spectrum disorder (ASD) is one of the neurodevelopmental disorders which has been extensively explored in relation to gut microbiome. The utilization of microbial knowledge promises a more integrative perspective in understanding this disorder, albeit being an emerging field in research. More interestingly, oral and vaginal microbiomes, indicating possible maternal influence, have equally drawn the attention of researchers to study their potential roles in the etiopathology of ASD. Therefore, this review attempts to integrate the knowledge of microbiome and its significance in relation to ASD including the hypothetical aetiology of ASD and its commonly associated comorbidities. The microbiota-based interventions including diet, prebiotics, probiotics, antibiotics, and faecal microbial transplant (FMT) have also been explored in relation to ASD. Of these, diet and probiotics are seemingly promising breakthrough interventions in the context of ASD for lesser known side effects, feasibility and easier administration, although more studies are needed to ascertain the actual clinical efficacy of these interventions. The existing knowledge and research gaps call for a more expanded and resolute research efforts in establishing the relationship between autism and microbiomes.
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Population Genetics in the Human Microbiome.
Garud, NR, Pollard, KS
Trends in genetics : TIG. 2020;(1):53-67
Abstract
While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population genetic models, facilitate quantification of microbiome genetic variation and inferences about how this diversity arises, evolves, and correlates with traits of both microbes and hosts. In this review, we explore the population genetic forces (mutation, recombination, drift, and selection) that shape microbiome genetic diversity within and between hosts, as well as efforts towards predictive models that leverage microbiome genetics.
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Nutrients and Microbiota in Lung Diseases of Prematurity: The Placenta-Gut-Lung Triangle.
Piersigilli, F, Van Grambezen, B, Hocq, C, Danhaive, O
Nutrients. 2020;(2)
Abstract
Cardiorespiratory function is not only the foremost determinant of life after premature birth, but also a major factor of long-term outcomes. However, the path from placental disconnection to nutritional autonomy is enduring and challenging for the preterm infant and, at each step, will have profound influences on respiratory physiology and disease. Fluid and energy intake, specific nutrients such as amino-acids, lipids and vitamins, and their ways of administration -parenteral or enteral-have direct implications on lung tissue composition and cellular functions, thus affect lung development and homeostasis and contributing to acute and chronic respiratory disorders. In addition, metabolomic signatures have recently emerged as biomarkers of bronchopulmonary dysplasia and other neonatal diseases, suggesting a profound implication of specific metabolites such as amino-acids, acylcarnitine and fatty acids in lung injury and repair, inflammation and immune modulation. Recent advances have highlighted the profound influence of the microbiome on many short- and long-term outcomes in the preterm infant. Lung and intestinal microbiomes are deeply intricated, and nutrition plays a prominent role in their establishment and regulation. There is an emerging evidence that human milk prevents bronchopulmonary dysplasia in premature infants, potentially through microbiome composition and/or inflammation modulation. Restoring antibiotic therapy-mediated microbiome disruption is another potentially beneficial action of human milk, which can be in part emulated by pre- and probiotics and supplements. This review will explore the many facets of the gut-lung axis and its pathophysiology in acute and chronic respiratory disorders of the prematurely born infant, and explore established and innovative nutritional approaches for prevention and treatment.
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Acne treatments: future trajectories.
Dessinioti, C, Dreno, B
Clinical and experimental dermatology. 2020;(8):955-961
Abstract
Current acne treatments present several limitations, posing the need for new effective therapies for long-term administration for recalcitrant or relapsing acne. Key players in acne that may emerge as targets for future acne treatments include the cutaneous loss of diversity of Cutibacterium (formerly Propionibacterium) acnes phylotypes and the insulin-like growth factor-1 signalling pathway. New data about the loss of diversity of microbiota in acne provides the rationale for the potential use of oral or topical probiotics. Another therapeutic approach to modulate the microbiota could be topical formulation of C. acnes bacteriophages to target specifically the pathogenic 'acnegenic' C. acnes phylotypes. Insulin-sensitizing agents such as metformin, myo-inositol and d-chiro-inositol represent promising agents, but to date there have been only limited studies and much heterogeneity in the methods of assessing acne efficacy outcomes. Moving towards a holistic approach for patients with acne is the future, by taking into account both internal and external factors, such as pollution, stress, acne family history, age, smoking habits and diet, and addressing quality of life and the psychological impact of acne.
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Influence of Microbiota on NSAID Enteropathy: A Systematic Review of Current Knowledge and the Role of Probiotics.
Rekatsina, M, Paladini, A, Cifone, MG, Lombardi, F, Pergolizzi, JV, Varrassi, G
Advances in therapy. 2020;(5):1933-1945
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Abstract
Microbiota are increasingly studied, providing more precise information on their important role in physiologic processes. They also influence some pathologic processes, such as NSAID-induced enteropathy. This side effect is much more diffuse than it has been described in the past. It derives mainly from the local action of the medicines and is caused by the local binding of gram-negative bacterial lipopolysaccharides and infiltration of neutrophils into the intestinal mucosa. The initial interest in the interaction between these damages and microbiota is very old, but new and interesting data are available. This review aims to focus on recent studies on NSAID-induced enteropathy, an often-underestimated medical condition, and on the influence of microbiota on this condition. Apart from the broadly investigated use of antibiotics and other mucosal protective solutions, this systematic review focuses mostly on the use of probiotics, which directly influence intestinal microflora. Other important factors influencing NSAID-induced enteropathy, such as sex, advanced age, infection and use of proton pump inhibitors, are also discussed.
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Effects of Colloidal Oatmeal Topical Atopic Dermatitis Cream on Skin Microbiome and Skin Barrier Properties.
Capone, K, Kirchner, F, Klein, SL, Tierney, NK
Journal of drugs in dermatology : JDD. 2020;(5):524-531
Abstract
Atopic dermatitis is characterized by dry, itchy, inflamed skin with a dysbiotic microbiome. In this clinical study (NCT03673059), we compared the effects of an eczema cream containing 1% colloidal oat and a standard moisturizer on the skin microbiome and skin barrier function of patients with mild to moderate eczema. Patients were randomly assigned to treatment with 1% colloidal oat eczema cream or a standard, non-fragranced daily moisturizer. Treatment lasted 14 days, followed by a 7-day regression period. Of 61 patients who completed the study, 30 received the 1% colloidal oat eczema cream and 31 received the standard moisturizer. At 14 days, the 1% colloidal oat eczema cream reduced mean Eczema Area Severity Index and Atopic Dermatitis Severity Index scores by 51% and 54%, respectively. Unlike treatment with the standard moisturizer, treatment with the 1% colloidal oat eczema cream was associated with trends towards lower prevalence of Staphylococcus species and higher microbiome diversity at lesion sites. The 1% colloidal oat eczema cream significantly improved skin pH, skin barrier function, and skin hydration from baseline to day 14, whereas the standard moisturizer improved hydration. Overall, the results demonstrate that topical products can have differing effects on the skin barrier properties and the microbiome. Importantly, we show that the use of a 1% colloidal oat eczema cream improves microbiome composition and significantly repairs skin barrier defects. J Drugs Dermatol. 2020;19(5): doi:10.36849/JDD.2020.4924.