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Bibliography on: Microbiome

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ESP: PubMed Auto Bibliography 08 Jul 2020 at 01:46 Created: 


It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2020-07-07

Yang Y, Liu S, Wang Y, et al (2020)

Changes of saliva microbiota in the onset and after the treatment of diabetes in patients with periodontitis.

Aging, 12: pii:103399 [Epub ahead of print].

The relationship between type 2 diabetes mellitus (T2DM) and oral microbiota is still insufficiently recognized. In the present study, we compared the salivary microbiome of nondiabetic individuals, treatment-naïve diabetic patients, and diabetic patients treated with metformin or a combination of insulin and other drugs. The α- and β-diversity demonstrated significant differences in the salivary microbiome between the nondiabetic people and patients with a history of diabetes, while little divergence was found among individuals with a history of diabetes. After characterizing the effects of periodontitis on the microbial composition of each group, the salivary microbiome of the treatment-naïve diabetic patient group was compared with that of nondiabetic people and the metformin/combined treatment groups. The results revealed changes in the contents of certain bacteria after both the onset and the treatment of diabetes; among these differential bacteria, Blautia_wexlerae, Lactobacillus_fermentum, Nocardia_coeliaca and Selenomonas_artemidis varied in all processes. A subsequent correlational analysis of the differential bacteria and clinical characteristics demonstrated that salivary microbes were related to drug treatment and certain pathological changes. Finally, the four common differential bacteria were employed for distinguishing the treatment-naïve diabetic patients from the nondiabetic people and the treated patients, with prediction accuracies of 83.3%, 75% and 75%, respectively.

RevDate: 2020-07-07

Xiaoting L, Shanshan L, Qiuhong W, et al (2020)

Metagenomics approach the intestinal microbiome structure and function in the anti-H1N1 of a traditional chinese medicine acid polysaccharide.

Microbial pathogenesis pii:S0882-4010(20)30717-8 [Epub ahead of print].

Ephedra sinica Stapf polysaccharide is a pure acidic uniform polysaccharide extracted from the traditional Chinese medicine Ephedra sinica Stapf. In our past research, it was found that it has anti-inflammatory response and suppresses immunity. Therefore, in this experiment, mice were infected with FM1 virus, treated with Ephedra sinica Stapf polysaccharide, and metagene sequencing was used to sequence the mouse intestinal contents. As a result, we found that Ephedra sinica Stapf polysaccharide has obvious therapeutic effect on acute lung injury caused by H1N1. In the intestinal flora, the abundance of Lactobacillales and Bifidobacteriaceae increased significantly, and the metabolome increased significantly in the KEGG pathway. The intestinal flora may be an important target of Ephedra sinica Stapf polysaccharides metabolism against H1N1.

RevDate: 2020-07-07

Sanidad KZ, MY Zeng (2020)

Neonatal gut microbiome and immunity.

Current opinion in microbiology, 56:30-37 pii:S1369-5274(20)30070-9 [Epub ahead of print].

Early life is a critical time window for the neonatal gut to be progressively populated with different bacterial species that collectively promote gut maturation. A fully developed and healthy gut microbiome in neonates is an important driver for the development of other aspects of health. Unlike the relatively stable gut microbiome in adults, the developing gut microbiome in neonates exhibits higher plasticity and adaptability. This also underscores the unique window of opportunity for intervention or preventive measures to improve long-term health through modulations of the gut microbiome in early life. Better understanding of the neonatal gut microbiome - how it arises and how it impacts immune cell development - will help us appreciate the underpinnings of immune-related diseases. Here, we examine recent findings on the neonatal gut microbiome and discuss their implications for understanding this important driver of the maturation of the immune system and immunity against infections in early life.

RevDate: 2020-07-07

Lu TX, Zheng Z, Zhang L, et al (2020)

A new model of spontaneous colitis in mice induced by deletion of an RNA m6A methyltransferase component METTL14 in T cells.

Cellular and molecular gastroenterology and hepatology pii:S2352-345X(20)30107-7 [Epub ahead of print].

BACKGROUND AND AIMS: Mouse models of colitis have been used to study the pathogenesis of inflammatory bowel disease (IBD) and for pre-clinical development of therapeutic agents. Various epigenetic pathways have been shown to play important regulatory roles in IBD. Reversible N6-methyladenosine (m6A) methylation represents a new layer of post-transcriptional gene regulation that affects a variety of biological processes. We aim to study how deletion of a critical component of m6A writer complex, METTL14, in T cells affects the development of colitis.

METHODS: Conditional Mettl14 was lineage specifically deleted with CD4-regulated Cre in T cells. Colitis phenotype was determined by H&E staining, colon weight/length ratio and cytokine expression. We additionally utilized T cell transfer model of colitis and adoptive transfer of regulatory T cells. Mice were treated with antibiotics to determine if the colitis could be attenuated.

RESULTS: METTL14 deficiency in T cells induced spontaneous colitis in mice. This was characterized by increased inflammatory cell infiltration, increased colonic weight/length ratio and increased Th1 and Th17 cytokines. The colitis development was due to dysfunctional regulatory T (Treg) cells, as adoptive transfer of wild-type Treg cells attenuated the colitis phenotype. The METTL14 deficient Treg cells have decreased RORγt expression compared to wild-type controls. METTL14 deficiency caused impaired induction of naïve T cells into induced Treg cells. Antibiotic treatment notably attenuated the colitis development.

CONCLUSION: Here we report a new mouse model of spontaneous colitis based on perturbation of RNA methylation in T cells. The colitis is T cell-mediated and dependent on the microbiome. This model represents a new tool for elucidating pathogenic pathways, studying the contribution of intestinal microbiome and preclinical testing of therapeutic agents for inflammatory bowel disease.

RevDate: 2020-07-07

Cau L, Williams MR, Butcher AM, et al (2020)

Staphylococcus epidermidis protease EcpA can be a deleterious component of the skin microbiome in atopic dermatitis.

The Journal of allergy and clinical immunology pii:S0091-6749(20)30953-2 [Epub ahead of print].

BACKGROUND: S. aureus and S. epidermidis are the most abundant bacteria found on the skin of patients with atopic dermatitis (AD). S. aureus is known to exacerbate AD while S. epidermidis was considered as a beneficial commensal organism.

OBJECTIVE: In this study, we hypothesized that S. epidermidis could promote skin damage in AD by the production of a protease that damages the epidermal barrier.

METHODS: Protease activity of S. epidermidis isolates was compared with other staphylococcal species. The capacity of S. epidermidis to degrade the barrier and induce inflammation was examined using human keratinocyte tissue culture and mouse models. Skin swabs from atopic and healthy adult subjects were analyzed for the presence of S. epidermidis genomic DNA and mRNA.

RESULTS: S. epidermidis strains were observed to produce strong cysteine protease activity when grown at high density. The enzyme responsible for this activity was identified to be EcpA, a cysteine protease under quorum sensing control. EcpA was shown to degrade desmoglein-1 and LL-37 in vitro and disrupted the physical barrier and induced skin inflammation in mice. The abundance of S. epidermidis and expression of ecpA mRNA were increased on the skin of some patients with AD and this correlated with disease severity. Another commensal skin bacterial species, S. hominis, can inhibit EcpA production by S. epidermidis.

CONCLUSION: S. epidermidis was commonly regarded as a beneficial skin microbe while S. aureus considered to be deleterious. This study suggests that the overabundance of S. epidermidis found on some atopic patients can act similarly to S. aureus and damage the skin by expression of a cysteine protease.

RevDate: 2020-07-07

Kwong WK (2020)

Microbiome Evolution: Having the Guts to Be Different.

Current biology : CB, 30(13):R766-R768.

Metagenomic sequencing of the gut microbial communities of two closely related bee species, the Western honey bee (Apis mellifera) and the Eastern honey bee (Apis cerana), show that organisms with similar characteristics can harbor unexpected differences in their microbiomes.

RevDate: 2020-07-07

Ogbu D, Xia E, J Sun (2020)

Gut instincts: vitamin D/vitamin D receptor and microbiome in neurodevelopment disorders.

Open biology, 10(7):200063.

The gut microbiome regulates a relationship with the brain known as the gut-microbiota-brain (GMB) axis. This interaction is influenced by immune cells, microbial metabolites and neurotransmitters. Recent findings show gut dysbiosis is prevalent in autism spectrum disorder (ASD) as well as attention deficit hyperactivity disorder (ADHD). There are previously established negative correlations among vitamin D, vitamin D receptor (VDR) levels and severity of ASD as well as ADHD. Both vitamin D and VDR are known to regulate homeostasis in the brain and the intestinal microbiome. This review summarizes the growing relationship between vitamin D/VDR signalling and the GMB axis in ASD and ADHD. We focus on current publications and summarize the progress of GMB in neurodevelopmental disorders, describe effects and mechanisms of vitamin D/VDR in regulating the microbiome and synoptically highlight the potential applications of targeting vitamin D/VDR signalling in neurodevelopment disorders.

RevDate: 2020-07-07

Zhu K, Mao G, Wu D, et al (2020)

Highly Branched RG-I Domain Enrichment are Indispensable for Pectin Mitigating Against High-Fat Diet-Induced Obesity.

Journal of agricultural and food chemistry [Epub ahead of print].

Obesity is associated with gut microbiome dysbiosis. Our previous research has shown that highly branched RG-I enriched pectin (WRP, 531.5 kDa, 70.44% RG-I, Rha:(Gal+Ara)=20) and its oligosaccharide with less branched (DWRP, 12.1 kDa, 50.29% RG-I, Rha:(Gal+Ara)=6) are potential prebiotics. The present study is conducted to uncover the impact by which the content, molecular size and branch degrees of RG-I on the inhibiting effect of high-fat diet (HFD)-induced obesity. The commercial pectin (CP, 496.2 kDa, 35.77% RG-I, Rha:(Gal+Ara)=6), WRP and DWRP were orally administered to HFD-fed C57BL/6J mice (100mg kg-1 d-1) to determine their individual effects on obesity. WRP significantly prevented bodyweight gain, insulin resistance, and inflammatory responses in HFD-fed mice. No obvious anti-obesity effect was observed in either CP or DWRP supplementation. Mechanistic study revealed that CP and DWRP could not enhance the diversity of gut microbiota, while WRP treatment positively modulated the gut microbiota of obese mice by increasing the abundance of Butyrivibrio, Roseburia, Barnesiella, Flavonifractor, Acetivibrio, and Clostridium cluster IV. Furthermore, the WRP significantly promoted browning of white adipose tissue in HFD-fed mice, while CP and DWRP did not.WRP can attenuate the HFD-induced obesity by modulation of gut microbiota and lipid metabolism. Highly branched RG-I domain enrichment are essential for pectin mitigating against the HFD-induced obesity.

RevDate: 2020-07-07

Ouald Chaib A, Levy IE, Ouald Chaib M, et al (2020)

The influence of the gastrointestinal microbiome on infant colic.

Expert review of gastroenterology & hepatology [Epub ahead of print].

INTRODUCTION: Although infantile colic is relatively frequent, its pathophysiology is not yet understood. The aim of this paper is to provide a better understanding of the link between infantile colic and the gastro-intestinal microbiome.

AREAS COVERED: The gastro-intestinal microbiome may already start to develop in the womb and grows exponentially immediately after birth. Factors influencing the microbiome can cause dysbiosis and precipitate symptoms of colic through several mechanisms such as increased gas-production and low grade gut inflammation. Other possible factors are immaturity of the enterohepatic bile acid cycle and administration of antibiotics and other medications during the perinatal period. An effective treatment for all colicky infants has yet to be discovered, but the probiotic Lactobacillus reuteri DSM17938 was shown to be effective in breastfed infants with colic. The scientific databases "Pubmed" and "Google scholar" were searched from inception until 02/2020. Relevant articles were selected based on the abstract.

EXPERT OPINION: Recent literature confirmed that the composition of the gastro-intestinal microbiome is associated with the development of infantile colic. It can be speculated that full sequencing and bioinformatics analysis to identify the microbiome down to the species level may provide answers to the etiology and management of infantile colic.

RevDate: 2020-07-07

Rahmani F, Rayzan E, Rahmani MR, et al (2020)

Clinical and Mutation Description of the First Iranian Cohort of Infantile Inflammatory Bowel Disease: The Iranian Primary Immunodeficiency Registry (IPIDR).

Immunological investigations [Epub ahead of print].

We describe a cohort of 25 Iranian patients with infantile inflammatory bowel disease (IBD), 14 (56%) of whom had monogenic defects. After proper screening, patients were referred for whole exome sequencing (WES). Four patients had missense mutations in the IL10 RA, and one had a large deletion in the IL10 RB. Four patients had mutations in genes implicated in host:microbiome homeostasis, including TTC7A deficiency, and two patients with novel mutations in the TTC37 and NOX1. We found a novel homozygous mutation in the SRP54 in a deceased patient and the heterozygous variant in his sibling with a milder phenotype. Three patients had combined immunodeficiency: one with ZAP-70 deficiency (T+B+NK-), and two with atypical SCID due to mutations in RAG1 and LIG4. One patient had a G6PC3 mutation without neutropenia. Eleven of the 14 patients with monogenic defects were results of consanguinity and only 4 of them were alive to this date.

RevDate: 2020-07-07

Wang Y, Nan MX, Zhao GY, et al (2020)

Coupling 16s rDNA and untargeted mass spectrometry for milk microbial composition and metabolites from dairy cows with clinical and subclinical mastitis.

Journal of agricultural and food chemistry [Epub ahead of print].

The internal environment of the cow's udder directly affects the udder health and milk quality. The 16S rDNA sequencing and liquid chromatography-mass spectrometry (LC-MS) methods were used to investigate the significant differences in milk microbial diversity and metabolites among healthy (H), subclinical mastitis (SM) and clinical mastitis (CM) cows. Results uncovered more than 16 and 192 differently abundant microbiota in phyla and genera level, respectively, and 673 different levels of metabolites enriched in 20 pathways in milk among the 3 groups. This study revealed the positive relevance between Staphylococcus, Streptococcus and ceramide in milk from CM cows. Similarly, Acinetobacter, Corynebacterium were positively associated with testosterone glucuronide, 5-methyl THF in milk from SM cows. Based on the combined analysis of microbiome and metabolome, this study indicated that, apart from the exogenous pathogens, some beneficial symbiotic bacteria, such as Dietzia, Aeromicrobium, Alistipes and Sphingobacterium, etc., rarely reported in milk have been found significantly reduced during mastitis.

RevDate: 2020-07-07

Mu A, Thomas BC, Banfield JF, et al (2020)

Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph.

Environmental microbiology reports [Epub ahead of print].

Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 tons of injected supercritical CO2 (scCO2) in a geosequestration experiment. The observed changes support a key role in the aquifer microbiome for the thermophilic CO-utilising anaerobe Carboxydocella, which decreased in relative abundance post-scCO2 injection. Here, we present results from more detailed metagenomic profiling of this experiment, with genome resolution of the native carboxydotrophic Carboxydocella. We demonstrate a switch in CO-oxidation potential by Carboxydocella through analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the geosequestration experiment. We discuss the potential impacts of scCO2 on subsurface flow of carbon and electrons from oxidation of the metabolic intermediate carbon monoxide (CO). This article is protected by copyright. All rights reserved.

RevDate: 2020-07-07

Meijnikman AS, Aydin O, Prodan A, et al (2020)

Distinct differences in gut microbial composition and functional potential from lean to morbidly obese subjects.

Journal of internal medicine [Epub ahead of print].

INTRODUCTION: The gut microbiome may contribute to the development of obesity. So far, the extent of microbiome variation in people with obesity has not been determined in large cohorts and for a wide range of body mass index (BMI). Here, we aimed to investigate whether the faecal microbial metagenome can explain the variance in several clinical phenotypes associated with morbid obesity.

METHODS: Caucasian subjects were recruited at our hospital. Blood pressure and anthropometric measurements were taken. Dietary intake was determined using questionnaires. Shotgun metagenomic sequencing was performed on faecal samples from 177 subjects.

RESULTS: Subjects without obesity (n = 82, BMI 24.7 ± 2.9 kg m-2) and subjects with obesity (n = 95, BMI 38.6 ± 5.1 kg m-2) could be clearly distinguished based on microbial composition and microbial metabolic pathways. A total number of 52 bacterial species differed significantly in people with and without obesity. Independent of dietary intake, we found that microbial pathways involved in biosynthesis of amino acids were enriched in subjects with obesity, whereas pathways involved in the degradation of amino acids were depleted. Machine learning models showed that more than half of the variance in body fat composition followed by BMI could be explained by the gut microbiome composition and microbial metabolic pathways, compared to 6% of variation explained in triglycerides and 9% in HDL.

CONCLUSION: Based on the faecal microbiota composition, we were able to separate subjects with and without obesity. In addition, we found strong associations between gut microbial amino acid metabolism and specific microbial species in relation to clinical features of obesity.

RevDate: 2020-07-07

Bo TB, Zhang XY, Kohl KD, et al (2020)

Coprophagy prevention alters microbiome, metabolism, neurochemistry, and cognitive behavior in a small mammal.

The ISME journal pii:10.1038/s41396-020-0711-6 [Epub ahead of print].

Many small mammals engage in coprophagy, or the behavior of consuming feces, as a means to meet nutritional requirements when feeding on low-quality foods. In addition to nutritional benefits, coprophagy may also help herbivores retain necessary gut microbial diversity and function, which may have downstream physiological effects, such as maintaining energy balance and cognitive function. Here, we used collars to prevent Brandt's vole (Lasiopodomys brandtii) from engaging in coprophagy and monitored changes in microbial community structure, energy metabolism, and cognitive performance. In this research, we found that coprophagy prevention decreased alpha diversity of the gut microbiota, and altered proportions of microbial taxa such as Bacteroidetes, Firmicutes, and Oscillospira. Preventing coprophagy resulted in a reduced body mass, and increased food intake. Importantly, coprophagy prevention decreased vole cognitive behavior and altered levels of neurotransmitters in brain. Daily acetate administration was able to reverse some of the coprophagy prevention-induced changes in microbiota composition, metabolism, neurochemistry, and cognitive behavior. These findings identify the functional importance of coprophagy behavior and interactions between the gut microbiota, energy metabolism, and neurological function. Our results suggest that coprophagy contributes to stabilizing the gut microbiota, promoting microbial metabolism, maintaining host energy balance and, consequently, altering cognitive performance.

RevDate: 2020-07-07

Chng KR, Ghosh TS, Tan YH, et al (2020)

Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut.

Nature ecology & evolution pii:10.1038/s41559-020-1236-0 [Epub ahead of print].

Loss of diversity in the gut microbiome can persist for extended periods after antibiotic treatment, impacting microbiome function, antimicrobial resistance and probably host health. Despite widespread antibiotic use, our understanding of the species and metabolic functions contributing to gut microbiome recovery is limited. Using data from 4 discovery cohorts in 3 continents comprising >500 microbiome profiles from 117 individuals, we identified 21 bacterial species exhibiting robust association with ecological recovery post antibiotic therapy. Functional and growth-rate analysis showed that recovery is supported by enrichment in specific carbohydrate-degradation and energy-production pathways. Association rule mining on 782 microbiome profiles from the MEDUSA database enabled reconstruction of the gut microbial 'food web', identifying many recovery-associated bacteria as keystone species, with the ability to use host- and diet-derived energy sources, and support repopulation of other gut species. Experiments in a mouse model recapitulated the ability of recovery-associated bacteria (Bacteroides thetaiotaomicron and Bifidobacterium adolescentis) to promote recovery with synergistic effects, providing a boost of two orders of magnitude to microbial abundance in early time points and faster maturation of microbial diversity. The identification of specific species and metabolic functions promoting recovery opens up opportunities for rationally determining pre- and probiotic formulations offering protection from long-term consequences of frequent antibiotic usage.

RevDate: 2020-07-07

Leónidas Cardoso L, Durão P, Amicone M, et al (2020)

Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut.

Nature ecology & evolution pii:10.1038/s41559-020-1235-1 [Epub ahead of print].

In the absence of antibiotics, it is essential that antibiotic resistance has a fitness cost for microorganisms if suspending antibiotics treatment is to be a useful strategy for reducing antibiotic resistance. However, the cost of antibiotic resistance within the complex ecosystem of the mammalian gut is not well understood. Here, using mice, we show that the same antibiotic resistance mutation can reduce fitness in one host, while being neutral or even increasing fitness in other hosts. Such antagonistic pleiotropy is shaped by the microbiota because resistance in germ-free mice is consistently costly across all hosts, and the host-specific effect on antibiotic resistance is reduced in hosts with similar microbiotas. Using an eco-evolutionary model of competition for resources, we identify a general mechanism that underlies between-host variation and predicts that the dynamics of compensatory evolution of resistant bacteria should be host specific, a prediction that was supported by experimental evolution in vivo. The microbiome of each human is close to unique, and our results suggest that the short-term cost of resistances and their long-term within-host evolution are also highly personalized, a finding that may contribute to the observed variable outcome of withdrawing antibiotics to reduce resistance levels.

RevDate: 2020-07-07

Huang WC, Wu MF, Huang CC, et al (2020)

Dynamics of the lung microbiome in intensive care patients with chronic obstructive pulmonary disease and community-acquired pneumonia.

Scientific reports, 10(1):11046 pii:10.1038/s41598-020-68100-4.

Little is known about the composition and clinical implications of lung microbiome in patients with chronic obstructive pulmonary disease (COPD) and community-acquired pneumonia requiring invasive mechanical ventilation and intensive care unit admission. Therefore, this study aimed to explore the longitudinal changes in microbial airway composition and its variations between COPD patients with different weaning outcomes. Fifty-one endotracheal aspirate samples from 21 participants and 5 saline samples were collected as the patient and control group, respectively. Sequence analysis revealed significant increases and upward trends in the relative abundance of the Acinetobacter genus and Acinetobacter baumannii complex species in paired comparisons of sampling points and over time, respectively, in patients with failed weaning (p for trend = 0.012 and 0.012, respectively) but not in those with successful weaning (p for trend = 0.335 and 0.426, respectively). Furthermore, significant changes in the composition of the bacterial community were observed in paired comparisons of sampling points in patients with failed weaning compared with those with successful weaning. The alpha diversity did not differ between the patients with different weaning outcomes. These results further the understanding of longitudinal airway microbiome structure analysis and its clinical implications when managing critically ill patients with and without COPD.

RevDate: 2020-07-07

Keohane DM, Ghosh TS, Jeffery IB, et al (2020)

Microbiome and health implications for ethnic minorities after enforced lifestyle changes.

Nature medicine pii:10.1038/s41591-020-0963-8 [Epub ahead of print].

Modern lifestyles increase the risk of chronic diseases, in part by modifying the microbiome, but the health effects of lifestyles enforced on ethnic minorities are understudied1-3. Lifestyle affects the microbiome early in life, when the microbiome is assembled and the immune system is undergoing maturation4-6. Moreover, the influence of lifestyle has been separated from genetic and geographic factors by studies of genetically similar populations and ethnically distinct groups living in the same geographic location7-11. The lifestyle of Irish Travellers, an ethnically distinct subpopulation, changed with legislation in 2002 that effectively ended nomadism and altered their living conditions. Comparative metagenomics of gut microbiomes shows that Irish Travellers retain a microbiota similar to that of non-industrialized societies. Their microbiota is associated with non-dietary factors and is proportionately linked with risk of microbiome-related metabolic disease. Our findings suggest there are microbiome-related public health implications when ethnic minorities are pressured to change lifestyles.

RevDate: 2020-07-07

Devkota S (2020)

The gut microbiome during acute lifestyle transition.

Nature medicine pii:10.1038/s41591-020-0980-7 [Epub ahead of print].

RevDate: 2020-07-07

Britt A, Bernini M, McSweeney B, et al (2020)

The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica.

Scientific reports, 10(1):11088 pii:10.1038/s41598-020-67851-4.

Long-standing evidence supports the importance of maintaining healthy populations of microbiota for the survival, homeostasis, and complete development of marine mollusks. However, the long-term ecological effects of agricultural runoff on these populations remains largely unknown. Atrazine (6-Chloro-n-ethyl-n'-(1-methylethyl)-triazine-2,4-diamine), a prevalent herbicide in the United States, is often used along tributaries of the Chesapeake Bay where oyster breeding programs are concentrated. To investigate any potential effects atrazine maybe having on mollusk-prokaryote interactions, we used 16S rRNA gene amplicons to evaluate how microbial compositions shift in response to exposure of environmentally relevant concentrations of atrazine previously found within the Chesapeake Bay. The dominant bacterial genera found within all groups included those belonging to Pseudoalteromonas, Burkholderia, Bacteroides, Lactobacillis, Acetobacter, Allobaculum, Ruminococcus, and Nocardia. Our results support previously published findings of a possible core microbial community in Crassostrea virginica. We also report a novel finding: oysters exposed to atrazine concentrations as low as 3 µg/L saw a significant loss of a key mutualistic microbial species and a subsequent colonization of a pathogenic bacteria Nocardia. We conclude that exposure to atrazine in the Chesapeake Bay may be contributing to a significant shift in the microbiomes of juvenile oysters that reduces fitness and impedes natural and artificial repopulation of the oyster species within the Bay.

RevDate: 2020-07-07

Nelson MT, Wolter DJ, Eng A, et al (2020)

Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome.

Thorax pii:thoraxjnl-2019-214187 [Epub ahead of print].

RATIONALE: The most common antibiotic used to treat people with cystic fibrosis (PWCF) is inhaled tobramycin, administered as maintenance therapy for chronic Pseudomonas aeruginosa lung infections. While the effects of inhaled tobramycin on P. aeruginosa abundance and lung function diminish with continued therapy, this maintenance treatment is known to improve long-term outcomes, underscoring how little is known about why antibiotics work in CF infections, what their effects are on complex CF sputum microbiomes and how to improve these treatments.

OBJECTIVES: To rigorously define the effect of maintenance tobramycin on CF sputum microbiome characteristics.

METHODS AND MEASUREMENTS: We collected sputum from 30 PWCF at standardised times before, during and after a single month-long course of maintenance inhaled tobramycin. We used traditional culture, quantitative PCR and metagenomic sequencing to define the dynamic effects of this treatment on sputum microbiomes, including abundance changes in both clinically targeted and untargeted bacteria, as well as functional gene categories.

MAIN RESULTS: CF sputum microbiota changed most markedly by 1 week of antibiotic therapy and plateaued thereafter, and this shift was largely driven by changes in non-dominant taxa. The genetically conferred functional capacities (ie, metagenomes) of subjects' sputum communities changed little with antibiotic perturbation, despite taxonomic shifts, suggesting functional redundancy within the CF sputum microbiome.

CONCLUSIONS: Maintenance treatment with inhaled tobramycin, an antibiotic with demonstrated long-term mortality benefit, primarily impacted clinically untargeted bacteria in CF sputum, highlighting the importance of monitoring the non-canonical effects of antibiotics and other treatments to accurately define and improve their clinical impact.

RevDate: 2020-07-07

Gudjonsson JE, Kabashima K, K Eyerich (2020)

Mechanisms of skin autoimmunity: Cellular and soluble immune components of the skin.

The Journal of allergy and clinical immunology, 146(1):8-16.

Autoimmune diseases are driven by either T cells or antibodies reacting specifically to 1 or more self-antigens. Although a number of self-antigens associated with skin diseases have been identified, the causative antigen(s) remains unknown in the great majority of skin diseases suspected to be autoimmune driven. Model diseases such as pemphigus, dermatitis herpetiformis, and more recently psoriasis have added greatly to our understanding of skin autoimmunity. Depending on the dominant T- or B-cell phenotype, skin autoimmune diseases usually follow 1 of 6 immune response patterns: lichenoid, eczematous, bullous, psoriatic, fibrogenic, or granulomatous. Usually, skin autoimmunity develops as a consequence of several events-an altered microbiome, inherited dysfunctional immunity, antigens activating innate immunity, epigenetic modifications, sex predisposition, and impact of antigens either as neoantigen or through molecular mimicry. This review summarizes currently known antigens of skin autoimmune diseases and discusses mechanisms of skin autoimmunity.

RevDate: 2020-07-07

Alavi S, Mitchell JD, Cho JY, et al (2020)

Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection.

Cell, 181(7):1533-1546.e13.

The gut microbiome is the resident microbial community of the gastrointestinal tract. This community is highly diverse, but how microbial diversity confers resistance or susceptibility to intestinal pathogens is poorly understood. Using transplantation of human microbiomes into several animal models of infection, we show that key microbiome species shape the chemical environment of the gut through the activity of the enzyme bile salt hydrolase. The activity of this enzyme reduced colonization by the major human diarrheal pathogen Vibrio cholerae by degrading the bile salt taurocholate that activates the expression of virulence genes. The absence of these functions and species permits increased infection loads on a personal microbiome-specific basis. These findings suggest new targets for individualized preventative strategies of V. cholerae infection through modulating the structure and function of the gut microbiome.

RevDate: 2020-07-07

Vásquez-Dean J, Maza F, Morel I, et al (2020)

Microbial communities from arid environments on a global scale. A systematic review.

Biological research, 53(1):29 pii:10.1186/s40659-020-00296-1.

Arid environments are defined by the lack of water availability, which is directly related to the mean annual precipitation (MAP), and high values of solar irradiation, which impacts the community composition of animals, plants, and the microbial structure of the soil. Recent advances in NGS technologies have expanded our ability to characterize microbiomes, allowing environmental microbiologists to explore the complete microbial structure. Intending to identify and describe the state-of-the-art of bacterial communities in arid soils at a global scale, and to address the effect that some environmental features may have on them, we performed a systematic review based on the PRISMA guideline. Using a combination of keywords, we identified a collection of 66 studies, including 327 sampled sites, reporting the arid soil bacterial community composition by 16S rDNA gene high-throughput sequencing. To identify factors that can modulate bacterial communities, we extracted the geographical, environmental, and physicochemical data. The results indicate that even though each sampled site was catalogued as arid, they show wide variability in altitude, mean annual temperature (MAT), soil pH and electric conductivity, within and between arid environments. We show that arid soils display a higher abundance of Actinobacteria and lower abundance of Proteobacteria, Cyanobacteria, and Planctomycetes, compared with non-arid soil microbiomes, revealing that microbial structure seems to be strongly modulated by MAP and MAT and not by pH in arid soils. We observed that environmental and physicochemical features were scarcely described among studies, hence, we propose a reporting guideline for further analysis, which will allow deepening the knowledge of the relationship between the microbiome and abiotic factors in arid soil. Finally, to understand the academic collaborations landscape, we developed an analysis of the author's network, corroborating a low degree of connectivity and collaborations in this research topic. Considering that it is crucial to understand how microbial processes develop and change in arid soils, our analysis emphasizes the need to increase collaborations between research groups worldwide.

RevDate: 2020-07-07

Bendová B, Piálek J, Ďureje Ľ, et al (2020)

How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies.

BMC microbiology, 20(1):194 pii:10.1186/s12866-020-01859-8.

BACKGROUND: The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host's health, physiology and phenotype. Once introduced into captivity, however, the gut microbial composition of free-living individuals can change dramatically. At present, little is known about gut microbial changes associated with adaptation to a synanthropic lifestyle in commensal species, compared with their non-commensal counterparts. Here, we compare the taxonomic composition and diversity of bacterial and fungal communities across three gut sections in synanthropic house mouse (Mus musculus) and a closely related non-synanthropic mound-building mouse (Mus spicilegus).

RESULTS: Using Illumina sequencing of bacterial 16S rRNA amplicons, we found higher bacterial diversity in M. spicilegus and detected 11 bacterial operational taxonomic units with significantly different proportions. Notably, abundance of Oscillospira, which is typically higher in lean or outdoor pasturing animals, was more abundant in non-commensal M. spicilegus. ITS2-based barcoding revealed low diversity and high uniformity of gut fungi in both species, with the genus Kazachstania clearly dominant.

CONCLUSIONS: Though differences in gut bacteria observed in the two species can be associated with their close association with humans, changes due to a move from commensalism to captivity would appear to have caused larger shifts in microbiota.

RevDate: 2020-07-07

Kim DH, Kim MH, Kim SB, et al (2020)

Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment.

Animals : an open access journal from MDPI, 10(7): pii:ani10071127.

The microbial community within the rumen can be changed and shaped by heat stress. Accumulating data have suggested that different breeds of dairy cows have differential heat stress resistance; however, the underlying mechanism by which nonanimal factors contribute to heat stress are yet to be understood. This study is designed to determine changes in the rumen microbiome of Holstein and Jersey cows to normal and heat stress conditions. Under heat stress conditions, Holstein cows had a significantly higher respiration rate than Jersey cows. Heat stress increased the rectal temperature of Holstein but not Jersey cows. In the Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, Jersey cows had a significantly higher proportion of genes associated with energy metabolism in the normal condition than that with other treatments. Linear discriminant analysis effect size (LEfSe) results identified six taxa as distinguishing taxa between normal and heat stress conditions in Holstein cows; in Jersey cows, 29 such taxa were identified. Changes in the rumen bacterial taxa were more sensitive to heat stress in Jersey cows than in Holstein cows, suggesting that the rumen mechanism is different in both breeds in adapting to heat stress. Collectively, distinct changes in rumen bacterial taxa and functional gene abundance in Jersey cows may be associated with better adaptation ability to heat stress.

RevDate: 2020-07-07

Redvers N, Yellow Bird M, Quinn D, et al (2020)

Molecular Decolonization: An Indigenous Microcosm Perspective of Planetary Health.

International journal of environmental research and public health, 17(12): pii:ijerph17124586.

Indigenous peoples are resilient peoples with deep traditional knowledge and scientific thought spanning millennia. Global discourse on climate change however has identified Indigenous populations as being a highly vulnerable group due to the habitation in regions undergoing rapid change, and the disproportionate burden of morbidity and mortality already faced by this population. Therefore, the need for Indigenous self-determination and the formal recognition of Indigenous knowledges, including micro-level molecular and microbial knowledges, as a critical foundation for planetary health is in urgent need. Through the process of Indigenous decolonization, even at the smallest molecular scale, we define a method back to our original selves and therefore to our planetary origin story. Our health and well-being is directly reflected at the planetary scale, and we suggest, can be rooted through the concept of molecular decolonization, which through the English language emerged from the 'First 1000 Days Australia' and otherwise collectively synthesized globally. It is through our evolving understanding of decolonization at a molecular level, which many of our Indigenous cultural and healing practices subtly embody, that we are better able to translate the intricacies within the current Indigenous scientific worldview through Western forms of discourse.

RevDate: 2020-07-07

Hoffmann A, Fingerle V, M Noll (2020)

Analysis of Tick Surface Decontamination Methods.

Microorganisms, 8(7): pii:microorganisms8070987.

Various microbial pathogens have been found in ticks such as Ixodes ricinus. However, most studies assessed tick microbiomes without prior decontamination of the tick surface, which may alter the results and mislead conclusions regarding the composition of the tick-borne microbiome. The aim of this study was to test four different decontamination methods, namely (i.) 70% ethanol, (ii.) DNA Away, (iii.) 5% sodium hypochlorite and (iv.) Reactive Skin Decontamination Lotion (RSDL), which have been previously reported for tick surface and animal or human skin decontamination. To test the efficiency of decontamination, we contaminated each tick with a defined mixture of Escherichia coli, Micrococcus luteus, Pseudomonas fluorescens, dog saliva and human sweat. No contamination was used as a negative control, and for a positive control, a no decontamination strategy was carried out. After nucleic acid extraction, the recovery rate of contaminants was determined for RNA and DNA samples by qPCR and tick-borne microbiome analyses by bacterial 16S rRNA and 16S rRNA gene amplicon sequencing. Ticks treated with 5% sodium hypochlorite revealed the lowest number of contaminants followed by DNA Away, RSDL and 70% ethanol. Moreover, tick microbiomes after 5% sodium hypochlorite decontamination clustered with negative controls. Therefore, the efficiency of decontamination was optimal with 5% sodium hypochlorite and is recommended for upcoming studies to address the unbiased detection of tick-borne pathogens.

RevDate: 2020-07-07

Kuźniar A, Włodarczyk K, Grządziel J, et al (2020)

New Insight into the Composition of Wheat Seed Microbiota.

International journal of molecular sciences, 21(13): pii:ijms21134634.

Endophytes are associated with host plants throughout their life history from seed germination to fruit development. One of the most important plant organs colonized by endophytic microbiota is the seed. The aim of this study was to determine the structure of the seed core microbiome inhabiting the endosperms and embryos of eight wheat cultivars with the use of a culture-independent technique. The seeds of Triticum aestivum L. cv. Hondia, Wilejka, STH, Opcja, Tybalt, Euforia and Triticum spelta L. cv. Rokosz and Schwabencorn (producer: Plant Breeding Strzelce Sp. z o.o. Group IHAR) were studied. Rokosz and Hondia were cultured in vitro and in vivo to identify obligatory bacterial endophytes. A restrictive analysis of reads originating from the in vitro plants has demonstrated that the bacterial genera Paenibacillus and Propionibacterium inhabiting Rokosz and Hondia plants have a status of obligatory microorganisms. Greater biodiversity of seed-borne endophytes was found in the seed endosperms than in the embryos. The multiple comparison analysis of the OTU abundance indicated that the seed part significantly influenced the relative abundance. The seed-born microbiome is not statistically significantly dependent on the wheat cultivars; however, it cannot be claimed that every wheat seed is the same.

RevDate: 2020-07-07

EFSA Scientific Committee, Hardy A, Benford D, et al (2018)

Guidance on risk assessment of the application of nanoscience and nanotechnologies in the food and feed chain: Part 1, human and animal health.

EFSA journal. European Food Safety Authority, 16(7):e05327.

The European Food Safety Authority has produced this Guidance on human and animal health aspects (Part 1) of the risk assessment of nanoscience and nanotechnology applications in the food and feed chain. It covers the application areas within EFSA's remit, e.g. novel foods, food contact materials, food/feed additives and pesticides. The Guidance takes account of the new developments that have taken place since publication of the previous Guidance in 2011. Potential future developments are suggested in the scientific literature for nanoencapsulated delivery systems and nanocomposites in applications such as novel foods, food/feed additives, biocides, pesticides and food contact materials. Therefore, the Guidance has taken account of relevant new scientific studies that provide more insights to physicochemical properties, exposure assessment and hazard characterisation of nanomaterials. It specifically elaborates on physicochemical characterisation of nanomaterials in terms of how to establish whether a material is a nanomaterial, the key parameters that should be measured, the methods and techniques that can be used for characterisation of nanomaterials and their determination in complex matrices. It also details the aspects relating to exposure assessment and hazard identification and characterisation. In particular, nanospecific considerations relating to in vivo/in vitro toxicological studies are discussed and a tiered framework for toxicological testing is outlined. It describes in vitro degradation, toxicokinetics, genotoxicity as well as general issues relating to testing of nanomaterials. Depending on the initial tier results, studies may be needed to investigate reproductive and developmental toxicity, immunotoxicity, allergenicity, neurotoxicity, effects on gut microbiome and endocrine activity. The possible use of read-across to fill data gaps as well as the potential use of integrated testing strategies and the knowledge of modes/mechanisms of action are also discussed. The Guidance proposes approaches to risk characterisation and uncertainty analysis, and provides recommendations for further research in this area.

RevDate: 2020-07-07

Nardello LCL, Amado PPP, Franco DC, et al (2020)

Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections.

Journal of endodontics pii:S0099-2399(20)30338-1 [Epub ahead of print].

INTRODUCTION: Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections.

METHODS: Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P < .05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis.

RESULTS: Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P < .05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA ≥ 1%) and active (rRNA/DNA ≥ 1).

CONCLUSIONS: The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections.

RevDate: 2020-07-06

Su CW, Chen CY, Jiao L, et al (2020)

Helminth-induced and Th2-dependent alterations of the gut microbiota attenuate obesity caused by high fat diet.

Cellular and molecular gastroenterology and hepatology pii:S2352-345X(20)30105-3 [Epub ahead of print].

BACKGROUND & AIMS: Epidemiological and animal studies have indicated an inverse correlation between the rising prevalence of obesity and metabolic syndrome and exposure to helminths. Whether helminth-induced immune response contributes to microbiota remodeling in obesity remains unknown. The aim of this study is to explore the immune-regulatory role of helminth in the prevention of HFD-induced obesity through remodeling gut microbiome.

METHODS: C57BL/6J WT and STAT6-/- mice were infected with Heligmosomoides polygyrus and followed by high fat diet (HFD) feeding for 6 weeks. The host immune response, body weight, and fecal microbiota composition were analyzed. We used adoptive transfer of M2 macrophages and microbiota transplantation approaches to determine the impact of these factors on HFD-obesity. We also examined stool microbiota composition and short chain fatty acids (SCFAs) concentration and determined the expression of SCFA-relevant receptors in the recipient mice.

RESULTS: Helminth infection of STAT6-/- (Th2-deficient) mice and adoptive transfer of helminth-induced alternatively activated (M2) macrophages demonstrated that the helminth-associated Th2 immune response plays an important role in the protection against obesity and induces changes in microbiota composition. Microbiota transplantation showed that helminth-induced, Th2-dependent alterations of the gut microbiota are sufficient to confer protection against obesity. Collectively, these results indicate that helminth infection protects against HFD-induced obesity by Th2-dependent, M2 macrophage-mediated alterations of the intestinal microbiota.

CONCLUSION: Our findings provide new mechanistic insights into the complex interplay between helminth infection, the immune system and the gut microbiota in a HFD-induced obesity model and holds promise for gut microbiome-targeted immunotherapy in obesity prevention.

RevDate: 2020-07-06

Zhou R, Llorente C, Cao J, et al (2020)

Deficiency of Intestinal α1-2-fucosylation Exacerbates Ethanol-Induced Liver Disease in Mice.

Alcoholism, clinical and experimental research [Epub ahead of print].

BACKGROUND: Fucosyltransferase 2 (Fut2)-mediated intestinal α1-2-fucosylation is important in maintaining a symbiotic host-microbiota relationship and can protect against several pathogens. Intestinal dysbiosis is an important factor for the progression of experimental ethanol-induced liver disease, but the role of Fut2 in modulating the intestinal glycocalyx during alcohol-associated liver disease is unknown. We investigated the role of Fut2-mediated intestinal α1-2-fucosylation for the development of alcohol-associated liver disease.

METHODS: Immunohistochemistry staining was applied to evaluate α1-2-fucosylation in duodenal biopsies from patients with alcohol use disorder. Wild type (WT) and Fut2 deficient littermate mice were subjected to Lieber DeCarli models of chronic ethanol administration and the chronic-binge ethanol diet (NIAAA model).

RESULTS: Intestinal α1-2-fucosylation was down-regulated in patients with alcohol use disorder. Lack of α1-2-fucosylation in Fut2 deficient mice exacerbates chronic ethanol-induced liver injury, steatosis and inflammation without affecting ethanol metabolism. Dietary supplementation of the α1-2-fucosylated glycan 2'-fucosyllactose ameliorates ethanol-induced liver disease in Fut2 deficient mice in the NIAAA model. Despite no direct effects on growth of Enterococcus faecalis in vitro, intestinal α1-2-fucosylation reduces colonization of cytolysin-positive E. faecalis in the intestine of ethanol-fed mice.

CONCLUSIONS: Intestinal α1-2-fucosylation acts as a host protective mechanism against ethanol-induced liver disease. 2'-FL is an oligosaccharide naturally present in human milk that could be considered as therapeutic agent for alcohol-associated liver disease.

RevDate: 2020-07-06

Ikegami K, Watanabe G, Kumagai J, et al (2020)

The apparition macrophage and Döderlein bacillus is negatively correlated in class I Papanicolaou smear: A morphological examination.

Diagnostic cytopathology [Epub ahead of print].

BACKGROUND: Nonspecific vaginitis, also known as Bacterial vaginosis, unlike genital candidiasis and trichomoniasis, is caused by microbiome breakdown. Döderlein's bacillus are gram-positive bacillus that form a microbiome, reproduce in the female vagina after gaining sexual maturity, secrete lactic acid, and prevent the growth of other vaginitis-causing bacteria. Clue cell are squamous epithelial cells with Gardnerella sp. attached to their cell surface. The presence of clue cell is one of the diagnostic criteria for nonspecific vaginitis. Additionally, although macrophages are reported to protect against candidal vaginitis, there are no reports of studies examining the association between macrophages and clue cell.

MATERIALS AND METHODS: After re-staining 300 class I specimens by cervical cancer screening with Papanicolaou staining, the appearance of Döderlein's bacillus, macrophages, and clue cell was observed.

RESULT: Age group and appearance of Döderlein's bacillus were negatively correlated. The rate of appearance of macrophages was positively correlated with the age group. In people aged 50 years or more, the appearance rate of clue cells was significantly lower in the macrophage appearance group than that in the non-appearance group.

CONCLUSION: This study suggested that macrophages, and not Döderlein's bacillus, may play an important role in defense against nonspecific vaginitis.

RevDate: 2020-07-06

Aguilar P, R Sommaruga (2020)

The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time.

Molecular ecology [Epub ahead of print].

One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and dynamics between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short-term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes of bacterial communities act at different time scales. Overall, our study validates, on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long timescales.

RevDate: 2020-07-06

Tai YK, Ng C, Purnamawati K, et al (2020)

Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc-1α expression: Follow-up to an in vitro magnetic mitohormetic study.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology [Epub ahead of print].

Exercise modulates metabolism and the gut microbiome. Brief exposure to low mT-range pulsing electromagnetic fields (PEMFs) was previously shown to accentuate in vitro myogenesis and mitochondriogenesis by activating a calcium-mitochondrial axis upstream of PGC-1α transcriptional upregulation, recapitulating a genetic response implicated in exercise-induced metabolic adaptations. We compared the effects of analogous PEMF exposure (1.5 mT, 10 min/week), with and without exercise, on systemic metabolism and gut microbiome in four groups of mice: (a) no intervention; (b) PEMF treatment; (c) exercise; (d) exercise and PEMF treatment. The combination of PEMFs and exercise for 6 weeks enhanced running performance and upregulated muscular and adipose Pgc-1α transcript levels, whereas exercise alone was incapable of elevating Pgc-1α levels. The gut microbiome Firmicutes/Bacteroidetes ratio decreased with exercise and PEMF exposure, alone or in combination, which has been associated in published studies with an increase in lean body mass. After 2 months, brief PEMF treatment alone increased Pgc-1α and mitohormetic gene expression and after >4 months PEMF treatment alone enhanced oxidative muscle expression, fatty acid oxidation, and reduced insulin levels. Hence, short-term PEMF treatment was sufficient to instigate PGC-1α-associated transcriptional cascades governing systemic mitohormetic adaptations, whereas longer-term PEMF treatment was capable of inducing related metabolic adaptations independently of exercise.

RevDate: 2020-07-06

Albright MBN, Thompson J, Kroeger ME, et al (2020)

Differences in substrate use linked to divergent carbon flow during litter decomposition.

FEMS microbiology ecology pii:5867763 [Epub ahead of print].

Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing 'high' and 'low' DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features-traits at the organism, pathway, or gene level-linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

RevDate: 2020-07-06

Bhide A, Tailor V, V Khullar (2020)

Interstitial cystitis/bladder pain syndrome and recurrent urinary tract infection and the potential role of the urinary microbiome.

Post reproductive health, 26(2):87-90.

Interstitial cystitis/bladder pain syndrome and recurrent urinary tract infections carry significant burden for those affected. As women enter the menopause, other factors may influence how these conditions manifest. The urinary microbiome has shown that the urine contains extensive numbers of bacteria. There is some evidence to suggest that it is altered depending on the menopausal state of the individual. It is possible that this alteration may go on to influence how the disease course of interstitial cystitis/bladder pain syndrome and recurrent urinary tract infections runs in the post-menopausal group. The review will explore these two conditions and the potential role of the urinary microbiome.

RevDate: 2020-07-06

Carl AG, Harris LD, Feng M, et al (2020)

Narrow-Spectrum Antibiotic Targeting of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis.

Biochemistry [Epub ahead of print].

Antibiotic resistance continues to spread at an alarming rate, outpacing the introduction of new therapeutics and threatening to globally undermine health care. There is a crucial need for new strategies that selectively target specific pathogens while leaving the majority of the microbiome untouched, thus averting the debilitating and sometimes fatal occurrences of opportunistic infections. To address these challenges, we have adopted a unique strategy that focuses on oxygen-sensitive proteins, an untapped set of therapeutic targets. MqnE is a member of the radical S-adenosyl-l-methionine (RS) superfamily, all of which rely on an oxygen-sensitive [4Fe-4S] cluster for catalytic activity. MqnE catalyzes the conversion of didehydrochorismate to aminofutalosine in the essential menaquinone biosynthetic pathway present in a limited set of species, including the gut pathogen Helicobacter pylori (Hp), making it an attractive target for narrow-spectrum antibiotic development. Indeed, we show that MqnE is inhibited by the mechanism-derived 2-fluoro analogue of didehydrochorismate (2F-DHC) due to accumulation of a radical intermediate under turnover conditions. Structures of MqnE in the apo and product-bound states afford insight into its catalytic mechanism, and electron paramagnetic resonance approaches provide direct spectroscopic evidence consistent with the predicted structure of the radical intermediate. In addition, we demonstrate the essentiality of the menaquinone biosynthetic pathway and unambiguously validate 2F-DHC as a selective inhibitor of Hp growth that exclusively targets MqnE. These data provide the foundation for designing effective Hp therapies and demonstrate proof of principle that radical SAM proteins can be effectively leveraged as therapeutic targets.

RevDate: 2020-07-06

Huston WM, G Tachedjian (2020)

Editorial: Interplay of Infection and Microbiome.

Frontiers in cellular and infection microbiology, 10:304.

RevDate: 2020-07-06

Mathers JC (2019)

Paving the way to better population health through personalised nutrition.

EFSA journal. European Food Safety Authority, 17(Suppl 1):e170713 pii:EFS2E170713.

As each individual person differs from the next in multiple ways, it is a beguiling idea that our individual nutritional needs also differ. In support of this idea, findings from nutritional intervention studies provide ample evidence of considerable interindividual variation in response to the same dietary exposure. We have a limited understanding of the mechanisms responsible for this variation but, following sequencing of the human genome, the role of genes in explaining interindividual differences has been centre stage. In addition, evidence of diet-gene interactions that influence phenotype, including health, emphasises the importance of both nature and nurture. Eating patterns are major determinants of health, so public health advice to reduce the risk of common complex diseases focuses on diet. However, most dietary interventions are relatively ineffective and personalised approaches that tailor the intervention to the individual may be more acceptable and more effective. That idea was tested in the Food4Me study in which adults from seven European countries were randomised to one of four treatment groups in an internet-delivered dietary intervention. Compared with the Control (standardised healthy eating advice), those people randomised to a personalised nutrition intervention had bigger, sustained changes, in eating behaviour after 6 months. However, including more complex phenotypic and/or genotypic information in developing the personalised nutrition advice had no added benefit. Research in personalised nutrition is broadening its scope to consider effects mediated by the gut microbiome as well as multiple aspects of genotype and phenotype. Such research has the potential to explain interindividual differences in the response to specific dietary factors and may provide a scientific basis for more refined approaches to personalised nutrition. However, if this research is to make a significant contribution to improving public health, it will need to address the psychological, social, economic and cultural factors that influence eating patterns to ensure that advice is converted into action and that improved dietary habits are sustained in perpetuity.

RevDate: 2020-07-06

Li Q, Wu Y, Wang J, et al (2020)

Linking Short-Chain N-Acyl Homoserine Lactone-Mediated Quorum Sensing and Replant Disease: A Case Study of Rehmannia glutinosa.

Frontiers in plant science, 11:787.

Rehmannia glutinosa, a perennial medicinal plant, suffers from severe replant disease under consecutive monoculture. The rhizosphere microbiome is vital for soil suppressiveness to diseases and for plant health. Moreover, N-acyl homoserine lactone (AHL)-mediated quorum sensing (QS) regulates diverse behavior in rhizosphere-inhabiting and plant pathogenic bacteria. The dynamics of short-chain AHL-mediated QS bacteria driven by consecutive monoculture and its relationships with R. glutinosa replant disease were explored in this study. The screening of QS bacteria showed that 65 out of 200 strains (32.5%) randomly selected from newly planted soil of R. glutinosa were detected as QS bacteria, mainly consisting of Pseudomonas spp. (55.4%). By contrast, 34 out of 200 (17%) strains from the diseased replant soil were detected as QS bacteria, mainly consisting of Enterobacteriaceae (73.5%). Functional analysis showed most of the QS bacteria belonging to the Pseudomonas genus showed strong antagonistic activities against Fusarium oxysporum or Aspergillus flavus, two main causal agents of R. glutinosa root rot disease. However, the QS strains dominant in the replant soil caused severe wilt disease in the tissue culture seedlings of R. glutinosa. Microbial growth assays demonstrated a concentration-dependent inhibitory effect on the growth of beneficial QS bacteria (i.e., Pseudomonas brassicacearum) by a phenolic acid mixture identified in the root exudates of R. glutinosa, but the opposite was true for harmful QS bacteria (i.e., Enterobacter spp.). Furthermore, it was found that the population of quorum quenching (QQ) bacteria that could disrupt the beneficial P. brassicacearum SZ50 QS system was significantly higher in the replant soil than in the newly planted soil. Most of these QQ bacteria in the replant soil were detected as Acinetobacter spp. The growth of specific QQ bacteria could be promoted by a phenolic acid mixture at a ratio similar to that found in the R. glutinosa rhizosphere. Moreover, these quorum-quenching bacteria showed strong pathogenicity toward the tissue culture seedlings of R. glutinosa. In conclusion, consecutive monoculture of R. glutinosa contributed to the imbalance between beneficial and harmful short-chain AHL-mediated QS bacteria in the rhizosphere, which was mediated not only by specific root exudates but also by the QQ bacterial community.

RevDate: 2020-07-06

Ojima MN, Gotoh A, Takada H, et al (2020)

Bifidobacterium bifidum Suppresses Gut Inflammation Caused by Repeated Antibiotic Disturbance Without Recovering Gut Microbiome Diversity in Mice.

Frontiers in microbiology, 11:1349.

The gut microbiome is a dynamic community that significantly affects host health; it is frequently disturbed by medications such as antibiotics. Recently, probiotics have been proposed as a remedy for antibiotic-induced dysbiosis, but the efficacy of such treatments remains uncertain. Thus, the effect of specific antibiotic-probiotic combinations on the gut microbiome and host health warrants further research. We tested the effect vancomycin, amoxicillin, and ciprofloxacin on mice. Antibiotic administration was followed by one of the following recovery treatments: Bifidobacterium bifidum JCM 1254 as a probiotic (PR); fecal transplant (FT); or natural recovery (NR). Each antibiotic administration and recovery treatment was repeated three times over 9 weeks. We used the Shannon Index and Chao1 Index to determine gut microbiome diversity and assessed recovery by quantifying the magnitude of microbial shift using the Bray-Curtis Index of Dissimilarity. We determined the community composition by sequencing the V3-V4 regions of the 16S ribosomal RNA gene. To assess host health, we measured body weight and cecum weight, as well as mRNA expression of inflammation-related genes by reverse-transcription quantitative PCR. Our results show that community response varied by the type of antibiotic used, with vancomycin having the most significant effects. As a result, the effect of probiotics and fecal transplants also varied by antibiotic type. For vancomycin, the first antibiotic disturbance substantially increased the relative abundance of inflammatory species in the phylum Proteobacteria, such as Proteus, but the effect of subsequent disturbances was less pronounced, suggesting that the gut microbiome is affected by past disturbance events. Furthermore, although gut microbiome diversity did not recover, probiotic supplementation was effective in limiting cecum size enlargement and colonic inflammation caused by vancomycin. However, for amoxicillin and ciprofloxacin, the relative abundances of proinflammatory species were not greatly affected, and consequently, the effect of probiotic supplementation on community structure, cecum weight, and expression of inflammation-related genes was comparatively negligible. These results indicate that probiotic supplementation is effective, but only when antibiotics cause proinflammatory species-induced gut inflammation, suggesting that the necessity of probiotic supplementation is strongly influenced by the type of disturbance introduced to the community.

RevDate: 2020-07-06

Zhao L, He K, Luo J, et al (2020)

Co-modulation of Liver Genes and Intestinal Microbiome of Largemouth Bass Larvae (Micropterus salmoides) During Weaning.

Frontiers in microbiology, 11:1332.

In recent years, largemouth bass have become one of the most commonly aquacultured species in China, however, its low survival rate during larval weaning has always been a bottleneck that has restricted industrial development. Understanding the changes in liver metabolism and intestinal microflora during the weaning of largemouth bass larvae can help to design better weaning strategies and improve survival. In this study, liver mRNA and intestinal microflora 16S rRNA genes were analyzed using high-throughput sequencing at the pre, mid, and post weaning stages [15, 30, 45 days post hatching; total length (cm) were 2.21 ± 0.12, 3.45 ± 0.21, 5.29 ± 0.33, respectively]. The transcriptome results revealed that the genes with increased expression were related to amino acid metabolism in the pre-weaning stage, but they were related to fatty acid metabolism in the post-weaning stage. A similar phenomenon was observed in the intestinal microflora where the dominant microbe Proteobacteria (relative abundance 56.32%) in the pre-weaning stage was gradually replaced by Firmicutes (relative abundance 62.81%) by the post-weaning stage. In addition, the three most important digestive enzymes (trypsin, lipase, and amylase) in the intestine were significantly decreased during the mid-weaning stage (P < 0.05), which was also true for some genes crucial to immune pathways in the liver. Overall, these findings showed that weaning in largemouth bass can cause changes in liver metabolism and intestinal microbial communities, which has improved our understanding of fish adaptation to changes in food sources during weaning.

RevDate: 2020-07-06

Lin M, Xiong H, Xiang X, et al (2020)

The Effect of Plant Geographical Location and Developmental Stage on Root-Associated Microbiomes of Gymnadenia conopsea.

Frontiers in microbiology, 11:1257.

Gymnadenia conopsea (L.) R. Br. is an important perennial terrestrial photosynthetic orchid species whose microbiomes are considered to play an important role in helping its germination and growth. However, the assemblage of G. conopsea root-associated microbial communities is poorly understood. The compositions of fungal and bacterial communities from the roots and corresponding soil samples in G. conopsea across distinct biogeographical regions from two significantly different altitudes were characterized at the vegetative and reproductive growth stages. The geographical location, developmental stage and compartment were factors contributing to microbiome variation in G. conopsea. Predominant fungal taxa include Ascomycota, Basidiomycota, Mortierellomycota and Chytridiomycota, whereas Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Verrucomicrobia, Chloroflexi, TM7 and Planctomycetes were predominant bacterial taxa. Using G. conopsea as a model, the structural and functional composition in G. conopsea root-associated microbiomes were comprehensive analyzed. Contrary to previous studies, biogeography was the main factor influencing the microbial community in this study. Besides, compartment and developmental stage should also be considered to analyze the variation of microbiota composition. Although the microbial composition varied greatly by location, the symbiotic microorganisms of G. conopsea still have certain specificity. This study gives an abundant information of G. conopsea root-associated microbiomes and provides new clues to better understanding the factors affecting the composition and diversity of fungal/bacterial communities associated with orchids. Our results also laying a foundation for harnessing the microbiome for sustainable G. conopsea cultivation. Moreover, these results might be generally applicable to other orchidaceae plants.

RevDate: 2020-07-06

Severance EG, Dickerson F, RH Yolken (2020)

Complex Gastrointestinal and Endocrine Sources of Inflammation in Schizophrenia.

Frontiers in psychiatry, 11:549.

A low level, inflammatory phenotype is prevalent in individuals with schizophrenia, but the source of this inflammation is not known. Studies of the gut-brain axis indicate that this inflammation may be related to the translocation of intestinal microbes across a permeabilized gut-vasculature barrier. In addition, studies of the endocrine system support that this inflammation may derive from effects of stress hormones and metabolic imbalances. Gastrointestinal (GI) and endocrine conditions are not mutually exclusive, but rather may have additive effects to produce this inflammatory phenotype in schizophrenia. Here, we examined a series of plasma biomarkers used to measure general inflammation and presumably microbial, gut-derived inflammation in 409 individuals with schizophrenia: c-reactive protein (CRP), lipopolysaccharide-binding protein (LBP), soluble CD14 (sCD14), and IgG antibodies to S. cerevisiae, bovine milk casein, and wheat gluten. Individuals were stratified according to whether or not they had a comorbid GI or endocrine condition, both, or neither. In multivariate regression models, the presence of GI and endocrine conditions was additive for the GI-based marker, LBP, with significant associations only when both conditions were present compared to when both conditions were absent (OR = 2.32, 95th% CI 1.05-5.13, p < 0.03). In contrast, the marker of general inflammation, CRP, was strongly associated with primarily endocrine conditions (OR = 3.64, 95th% CI 1.35-9.84, p < 0.05). Overall associations were largely driven by the GI condition, gastroesophageal reflux disease (GERD), and by the endocrine condition, obesity. In univariate comparisons, S. cerevisiae IgG levels were significantly elevated only in persons with GI conditions (p < 0.02), whereas antibodies to the food antigens were elevated in the presence of either or both conditions (p < 0.005-0.04). More severe psychiatric symptoms were associated only with GI conditions (p < 0.01-0.04). In conclusion, both GI and endocrine abnormalities may contribute to inflammation in schizophrenia, sometimes independently and sometimes as part of interactions which may represent complex integrated pathways. The accumulating evidence for multisystem inflammation in schizophrenia may lead to the development of new strategies to prevent and treat this devastating disorder.

RevDate: 2020-07-06

Harsanyiova J, Buday T, A Kralova Trancikova (2020)

Parkinson's Disease and the Gut: Future Perspectives for Early Diagnosis.

Frontiers in neuroscience, 14:626.

Parkinson's disease (PD) is a neurodegenerative disease characterized by progressive degeneration of dopaminergic neurons, and at the cellular level by the formation of Lewy bodies in the central nervous system (CNS). However, the onset of the disease is believed to be localized to peripheral organs, particularly the gastrointestinal tract (GIT) and the olfactory bulb sooner before neuropathological changes occur in the CNS. Patients already in the pre-motor stage of PD suffer from various digestive problems and/or due to significant changes in the composition of the intestinal microbiome in this early stage of the disease. Detailed analyses of patient biopsies and autopsies as well as animal models of neuropathological changes characteristic of PD provided important information on the pathology or treatment of PD symptoms. However, presently is not clarified (i) the specific tissue in the GIT where the pathological processes associated with PD is initiated; (ii) the mechanism by which these processes are disseminated to the CNS or other tissues within the GIT; and (iii) which neuropathological changes could also serve as a reliable diagnostic marker of the premotor stages of PD, or (iv) which type of GIT tissue would be the most appropriate choice for routine examination of patient biopsies.

RevDate: 2020-07-06

Akimbekov NS, Digel I, Sherelkhan DK, et al (2020)

Vitamin D and the Host-Gut Microbiome: A Brief Overview.

Acta histochemica et cytochemica, 53(3):33-42.

There is a growing body of evidence for the effects of vitamin D on intestinal host-microbiome interactions related to gut dysbiosis and bowel inflammation. This brief review highlights the potential links between vitamin D and gut health, emphasizing the role of vitamin D in microbiological and immunological mechanisms of inflammatory bowel diseases. A comprehensive literature search was carried out in PubMed and Google Scholar using combinations of keywords "vitamin D," "intestines," "gut microflora," "bowel inflammation". Only articles published in English and related to the study topic are included in the review. We discuss how vitamin D (a) modulates intestinal microbiome function, (b) controls antimicrobial peptide expression, and (c) has a protective effect on epithelial barriers in the gut mucosa. Vitamin D and its nuclear receptor (VDR) regulate intestinal barrier integrity, and control innate and adaptive immunity in the gut. Metabolites from the gut microbiota may also regulate expression of VDR, while vitamin D may influence the gut microbiota and exert anti-inflammatory and immune-modulating effects. The underlying mechanism of vitamin D in the pathogenesis of bowel diseases is not fully understood, but maintaining an optimal vitamin D status appears to be beneficial for gut health. Future studies will shed light on the molecular mechanisms through which vitamin D and VDR interactions affect intestinal mucosal immunity, pathogen invasion, symbiont colonization, and antimicrobial peptide expression.

RevDate: 2020-07-06

Rawi MH, Zaman SA, Pa'ee KF, et al (2020)

Prebiotics metabolism by gut-isolated probiotics.

Journal of food science and technology, 57(8):2786-2799.

There are numerous species of bacteria resides in the lumen of human colon. The word 'colon', resembles colony or the colonization of microbiota of which plays an important role in the fermentation of prebiotics. The standpoint of prebiotic nowadays is well reported for attenuating gut dysbiosis in many clinical studies tested on animals and human. However, because of the huge amount of gut microbiome, the attempt to connect the dots between bacterial population and the host are not plainly discernible. Thus, a need to analyse recent research on the pathways of prebiotic metabolism adopted by commonly studied probiotics i.e. Bifidobacteria and Lactobacillus. Several different substrate-dependent gene expressions are induced to break down oligosaccharide molecules shown by those probiotics. The hydrolysis can occur either by membrane bound (extracellular) or cytoplasmic (intracellular) enzyme of the enteric bacteria. Therefore, this review narrates several prebiotic metabolisms occur during gut fermentation, and metabolite production i.e. organic acids conversion.

RevDate: 2020-07-06

Apetoh L (2020)

Anticancer effects of the microbiota: how the microbiome shapes the development of IL-9-producing T cells.

IL-9-producing T cells can harbour potent anti-cancer functions. In this issue of the British Journal of Cancer, Almeida et al. found that the host microbiota enhances in vivo T cell-derived secretion of IL-9, thereby limiting cancer outgrowth.

RevDate: 2020-07-02

Kalantar-Zadeh K, Joshi S, Schlueter R, et al (2020)

Plant-Dominant Low-Protein Diet for Conservative Management of Chronic Kidney Disease.

Nutrients, 12(7): pii:nu12071931.

Keywords: plant-dominant; low-protein; dietary protein intake; glomerular hyperfiltration.

RevDate: 2020-07-05

Kumar J, Rani K, C Datt (2020)

Molecular link between dietary fibre, gut microbiota and health.

Molecular biology reports pii:10.1007/s11033-020-05611-3 [Epub ahead of print].

Natural polysaccharides cellulose, hemicelluloses, inulin etc., galactooligosaccharides (GOS), and fructooligosaccharides (FOS) play a significant role in the improvement of gut microbiota balance and human health. These polysaccharides prevent pathogen adhesion that stimulates the immune system and gut barrier function by servicing as fermentable substrates for the gut microbiota. The gut microbiota plays a key role in the fermentation of non-digestible carbohydrates (NDCs) fibres. Moreover, the gut microbiota is responsible for the production of short-chain fatty acids (SCFAs) like acetate, propionate and butyrate. Acetate is the most abundant and it is used by many gut commensals to produce propionate and butyrate in a growth-promoting cross-feeding process. The dietary fibres affect the gut microbiome and play vital roles in signaling pathways. The SCFAs, acetate, butyrate, and propionate have been reported to affect on metabolic activities at the molecular level. Acetate affects the metabolic pathway through the G protein-coupled receptor (GPCR) and free fatty acid receptor 2 (FFAR2/GPR43) while butyrate and propionate transactivate the peroxisome proliferator-activated receptorsγ (PPARγ/NR1C3) and regulate the PPARγ target gene Angptl4 in colonic cells of the gut. The FFAR2 signaling pathway regulates the insulin-stimulated lipid accumulation in adipocytes and inflammation, however peptide tyrosine-tyrosine (PPY) and glucagon-like peptide 1 regulates appetite. The NDCs via gut microbiota dependent pathway regulate glucose homeostasis, gut integrity and hormone by GPCR, NF-kB, and AMPK-dependent processes.

RevDate: 2020-07-05

Crudo F, Aichinger G, Mihajlovic J, et al (2020)

Gut microbiota and undigested food constituents modify toxin composition and suppress the genotoxicity of a naturally occurring mixture of Alternaria toxins in vitro.

Archives of toxicology pii:10.1007/s00204-020-02831-1 [Epub ahead of print].

Molds of the genus Alternaria produce several mycotoxins, some of which may pose a threat for health due to their genotoxicity. Due to the lack of adequate toxicological and occurrence data, they are currently not regulated. Interactions between mycotoxins, gut microbiota and food constituents might occur after food ingestion, modifying the bioavailability and, therefore, overall toxicity of mycotoxins. The present work aimed to investigate the impact of in vitro short-term fecal incubation on the in vitro DNA-damaging effects exerted by 5 µg/mL of an Alternaria alternata extract, containing, among others, 15 nM alternariol, 12 nM alternariol monomethyl ether, 241 nM altertoxin II and 301 nM stemphyltoxin III, all of which are known as genotoxic. The involvement of microorganisms, undigested food constituents and soluble substances of human fecal samples in modifying the composition and the genotoxicity of the extract was investigated through the application of LC-MS/MS analysis and comet assays in HT-29 cells. Results showed that the potential of the mycotoxins to induce DNA strand breaks was almost completely quenched, even before anaerobic incubation, by contact with the different fractions of the fecal samples, while the potency to induce formamidopyrimidine DNA glycosylase (FPG)-sensitive sites was only slightly reduced. These effects were in line with a reduction of mycotoxin concentrations found in samples analyzed by LC-MS/MS. Although a direct correlation between the metabolic activity of the gut microbiota and modifications in mycotoxin contents was not clearly observed, adsorptive phenomena to bacterial cells and to undigested food constituents might explain the observed modifications.

RevDate: 2020-07-05

Wang TY, Zhang XQ, Chen AL, et al (2020)

A comparative study of microbial community and functions of type 2 diabetes mellitus patients with obesity and healthy people.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10689-7 [Epub ahead of print].

The gut microbiota is crucial in the pathogenesis of type 2 diabetes mellitus (T2DM). However, the metabolism of T2DM patients is not well-understood. We aimed to identify the differences on composition and function of gut microbiota between T2DM patients with obesity and healthy people. In this study, 6 T2DM patients with obesity and 6 healthy volunteers were recruited, and metagenomic approach and bioinformatics analysis methods were used to understand the composition of the gut microbiota and the metabolic network. We found a decrease in the abundance of Firmicutes, Oribacterium, and Paenibacillus; this may be attributed to a possible mechanism and biological basis of T2DM; moreover, we identified three critical bacterial taxa, Bacteroides plebeius, Phascolarctobacterium sp. CAG207, and the order Acidaminococcales that can potentially be used for T2DM treatment. We also revealed the composition of the microbiota through functional annotation based on multiple databases and found that carbohydrate metabolism contributed greatly to the pathogenesis of T2DM. This study helps in elucidating the different metabolic roles of microbes in T2DM patients with obesity.

RevDate: 2020-07-05

Lee JA, Yoo SY, Oh HJ, et al (2020)

Differential immune microenvironmental features of microsatellite-unstable colorectal cancers according to Fusobacterium nucleatum status.

Cancer immunology, immunotherapy : CII pii:10.1007/s00262-020-02657-x [Epub ahead of print].

It has been suggested that Fusobacterium nucleatum (Fn) may differentially impact tumor immune responses according to microsatellite instability (MSI) status in colorectal cancers (CRCs). We aimed to reveal the detailed relationship between intratumoral Fn and immune microenvironmental features in MSI-high CRCs. A total of 126 MSI-high CRCs were subjected to analyses for intratumoral Fn DNA load using quantitative PCR and for densities of tumor-infiltrating immune cells, including CD3+ T cells, CD4+ T cells, CD8+ T cells, FoxP3+ T cells, CD68+ macrophages, CD163+ macrophages, and CD177+ neutrophils, at invasive margin (IM) and center of tumor (CT) areas using computational image analysis of immunohistochemistry. Based on the Fn load, the 126 MSI-high CRCs were classified into Fn-high, -low, and -negative subgroups. The Fn-high subset of MSI-high CRCs was significantly correlated with larger tumor size and advanced invasion depth (p = 0.017 and p = 0.034, respectively). Compared with the Fn-low/negative subgroup, Fn-high tumors demonstrated significantly lower density of FoxP3+ cells in both IM and CT areas (p = 0.002 and p = 0.003, respectively). Additionally, Fn-high was significantly associated with elevated CD163+ cell to CD68+ cell ratio in only CT areas of MSI-high CRCs (p = 0.028). In conclusion, the Fn-enriched subset of MSI-high CRCs is characterized by increased tumor growth and invasion and distinct immune microenvironmental features, including decreased FoxP3+ T cells throughout the tumor and increased proportion of M2-polarized macrophages in the tumor center. These findings collectively support that Fn may be linked to pro-tumoral immune responses in MSI-high CRCs.

RevDate: 2020-07-05

Kaur H, Golovko S, Golovko MY, et al (2020)

Effects of Probiotic Supplementation on Short Chain Fatty Acids in the AppNL-G-F Mouse Model of Alzheimer's Disease.

Journal of Alzheimer's disease : JAD pii:JAD200436 [Epub ahead of print].

BACKGROUND: The intestinal microbiota and its metabolites, particularly short-chain fatty acids (SCFAs), have been implicated in immune function, host metabolism, and even behavior.

OBJECTIVE: This study was performed to investigate whether probiotic administration influences levels of intestinal microbiota and their metabolites in a fashion that may attenuate brain changes in a mouse model of Alzheimer's disease (AD).

METHODS: C57BL/6 wild-type (WT) mice were compared to AppNL-G-Fmice. The animals were treated with either vehicle or probiotic (VSL#3) for 8 weeks. Fecal microbiome analysis along with Aβ, GFAP, Iba-1, c-Fos, and Ki-67 immunohistochemistry was done. SCFAs were analyzed in serum and brains using UPLC-MS/MS.

RESULTS: Probiotic (VSL#3) supplementation for 2 months resulted in altered microbiota in both WT and AppNL-G-Fmice. An increase in serum SCFAs acetate, butyrate, and lactate were found in both genotypes following VSL#3 treatment. Propionate and isobutyrate were only increased in AppNL-G-Fmice. Surprisingly, VSL#3 only increased lactate and acetate in brains of AppNL-G-Fmice. No significant differences were observed between vehicle and VSL#3 fed AppNL-G-Fhippocampal immunore activities of Aβ, GFAP, Iba-1, and Ki-67. However, hippocampal c-Fos staining increased in VSL#3 fed AppNL-G-Fmice.

CONCLUSION: These data demonstrate intestinal dysbiosis in the AppNL-G-Fmouse model of AD. Probiotic VSL#3 feeding altered both serum and brain levels of lactate and acetate in AppNL-G-Fmice correlating with increased expression of the neuronal activity marker, c-Fos.

RevDate: 2020-07-05

Sulaiman I, Schuster S, LN Segal (2020)

Perspectives in lung microbiome research.

Current opinion in microbiology, 56:24-29 pii:S1369-5274(20)30072-2 [Epub ahead of print].

Our understanding of the existence and role of the lung microbiome has grown at a slower pace than other microbiome research areas. This is likely a consequence of the original dogma that the lung was a sterile environment although there are other barriers that are worth discussing. Here we will not be conducting an exhaustive review of the current literature on the lung microbiome, but rather we will focus on what we see as some important challenges that the field needs to face in order to improve our mechanistic understanding of the lung microbiome and its role on human health.

RevDate: 2020-07-05

Koo BS, Hwang EH, Kim G, et al (2020)

Prevalence and characterization of Clostridium perfringens isolated from feces of captive cynomolgus monkeys (Macaca fascicularis).

Anaerobe pii:S1075-9964(20)30092-5 [Epub ahead of print].

Clostridium perfringens is ubiquitous in the environment and the gastrointestinal tract of warm-blooded animals. While part of the gut microbiome, abnormal growth of C. perfringens causes histotoxic, neurologic, and enteric diseases in a variety of animal species, including humans, due to the production of toxins. There is extremely limited information on C. perfringens infection in non-human primates. Presently, 10 strains were successfully isolated from 126 monkeys and confirmed by molecular and biochemical analyses. All isolates were genotype A based on molecular analysis. Alpha toxin was identified in all isolates. Beta 2 toxin was detected in only three isolates. No other toxins, including enterotoxin, beta, iota, epsilon, and net B toxin, were identified in any isolate. All isolates were highly susceptible to β-lactam antibiotics. Double hemolysis and lecithinase activity were commonly observed in all strains. Biofilm formation, which can increase antibiotic resistance, was identified in 90% of the isolates. The data are the first report the prevalence and characteristics of C. perfringens isolated from captive cynomolgus monkeys.

RevDate: 2020-07-04

Geir B, Lyudmila P, Maryam D, et al (2020)

Gastrointestinal Alterations in Autism Spectrum Disorder: What Do We Know?.

Neuroscience and biobehavioral reviews pii:S0149-7634(20)30460-7 [Epub ahead of print].

There is an emerging body of evidence associating children having autism spectrum disorder (ASD) with gastrointestinal (GI) symptoms, such as abdominal pain, chronic diarrhea, constipation, vomiting, gastroesophageal reflux, intestinal infections, and increased intestinal permeability. Moreover, in many studies, large differences in the composition of intestinal microbiota and metabolic products between ASD patients and controls were reported. Deepening the role and the biology of the gut microbiome may be fundamental to elucidate the onset of GI symptoms in ASD individuals and their etiopathogenetic causes. The gut-brain axis may affect brain development and behaviors through the neuroendocrine, neuroimmune, and autonomic nervous systems.

RevDate: 2020-07-04

Lv N, Ajilore OA, Ronneberg CR, et al (2020)

The ENGAGE-2 study: Engaging self-regulation targets to understand the mechanisms of behavior change and improve mood and weight outcomes in a randomized controlled trial (Phase 2).

Contemporary clinical trials pii:S1551-7144(20)30150-6 [Epub ahead of print].

Despite evidence for effective integrated behavior therapy for treating comorbid obesity and depression, treatment response is highly variable and the underlying neurobiological mechanisms remain unknown. This hampers efforts to identify mechanistic targets in order to optimize treatment precision and potency. Funded within the NIH Science of Behavior Change (SOBC) Research Network, the 2-phased ENGAGE research project applies an experimental precision medicine approach to address this gap. The Phase 1 study focused on demonstrating technical feasibility, target engagement and potential neural mechanisms of responses to an integrated behavior therapy. This therapy combines a video-based behavioral weight loss program and problem-solving therapy for depression, with as-needed intensification of antidepressant medications, and its clinical effectiveness was demonstrated within a parent randomized clinical trial. Here, we describe the ENGAGE Phase 2 (ENGAGE-2) study protocol which builds on Phase 1 in 2 ways: (1) pilot testing of an motivational interviewing-enhanced, integrated behavior therapy in an independent, primarily minority patient sample, and (2) evaluation of a priori defined neural targets, specifically the negative affect (threat and sadness) circuits which demonstrated engagement and malleability in Phase 1, as mediators of therapeutic outcomes. Additionally, the Phase 2 study includes a conceptual and methodological extension to explore the role of microbiome-gut-brain and systemic immunological pathways in integrated behavioral treatment of obesity and depression. This protocol paper documents the conceptualization, design and the transdisciplinary methodologies in ENGAGE-2, which can inform future clinical and translational research in experimental precision medicine for behavior change and chronic disease management. Trial registration: #NCT03841682.

RevDate: 2020-07-04

Su SC, Chang LC, Huang HD, et al (2020)

Oral microbial dysbiosis and its performance in predicting oral cancer.

Carcinogenesis pii:5867492 [Epub ahead of print].

Dysbiosis of oral microbiome may dictate the progression of oral squamous cell carcinoma (OSCC). Yet, the composition of oral microbiome fluctuates by saliva and distinct sites of oral cavity and is affected by risky behaviors (smoking, drinking, and betel quid chewing) and individuals' oral health condition. To characterize the disturbances in the oral microbial population mainly due to oral tumorigenicity, we profiled the bacteria within the surface of OSCC lesion and its contralateral normal tissue from discovery (n=74) and validation (n=42) cohorts of male patients with cancers of the buccal mucosa. Significant alterations in the bacterial diversity and relative abundance of specific oral microbiota (most profoundly, an enrichment for genus Fusobacterium and the loss of genus Streptococcus in the tumor sites) were identified. Functional prediction of oral microbiome shown that microbial genes related to the metabolism of terpenoids and polyketides were differentially enriched between the control and tumor group, indicating a functional role of oral microbiome in formulating a tumor microenvironment via attenuated biosynthesis of secondary metabolites with anti-cancer effects. Furthermore, the vast majority of microbial signatures detected in the discovery cohort was generalized well to the independent validation cohort, and the clinical validity of these OSCC-associated microbes was observed and successfully replicated. Overall, our analyses reveal signatures (a profusion of Fusobacterium nucleatum CTI-2 and a decrease in Streptococcus pneumoniae) and functions (decreased production of tumor-suppressive metabolites) of oral microbiota related to oral cancer.

RevDate: 2020-07-04

Bourgonje AR, Feelisch M, Faber KN, et al (2020)

Oxidative Stress and Redox-Modulating Therapeutics in Inflammatory Bowel Disease.

Trends in molecular medicine pii:S1471-4914(20)30157-X [Epub ahead of print].

Inflammatory bowel disease (IBD) is associated with the production of reactive species that target cysteine redox switches in proteins, thereby affecting gene regulation, DNA damage, ion transport, intermediary metabolism, and mitochondrial function. Precursors of reactive species are derived from organic and inorganic compounds and their cofactors, including amino acids, vitamins, oxygen, nitrite, and sulfate. Nutrition and the gut microbiome fuel this process to a significant extent. The production of reactive species in IBD is reflected by a reduction in systemic free thiols, the major components of the antioxidant machinery. Systemic free thiols are amenable to nutritional or therapeutic intervention. This opens up future avenues for therapeutic modulation of redox status in IBD.

RevDate: 2020-07-04

Bellissimo MP, Ziegler TR, Jones DP, et al (2020)

Plasma high-resolution metabolomics identifies linoleic acid and linked metabolic pathways associated with bone mineral density.

Clinical nutrition (Edinburgh, Scotland) pii:S0261-5614(20)30277-6 [Epub ahead of print].

BACKGROUND & AIMS: There is a considerable degree of variation in bone mineral density (BMD) within populations. Use of plasma metabolomics may provide insight into established and novel determinants of BMD variance, such as nutrition and gut microbiome composition, to inform future prevention and treatment strategies for loss of BMD. Using high-resolution metabolomics (HRM), we examined low-molecular weight plasma metabolites and nutrition-related metabolic pathways associated with BMD.

METHODS: This cross-sectional study included 179 adults (mean age 49.5 ± 10.3 yr, 64% female). Fasting plasma was analyzed using ultra-high-resolution mass spectrometry with liquid chromatography. Whole body and spine BMD were assessed by dual energy X-ray absorptiometry and expressed as BMD (g/cm2) or Z-scores. Multiple linear regression, pathway enrichment, and module analyses were used to determine key plasma metabolic features associated with bone density.

RESULTS: Of 10,210 total detected metabolic features, whole body BMD Z-score was associated with 710 metabolites, which were significantly enriched in seven metabolic pathways, including linoleic acid, fatty acid activation and biosynthesis, and glycerophospholipid metabolism. Spine BMD was associated with 970 metabolites, significantly enriched in pro-inflammatory pathways involved in prostaglandin formation and linoleic acid metabolism. In module analyses, tryptophan- and polyamine-derived metabolites formed a network that was significantly associated with spine BMD, supporting a link with the gut microbiome.

CONCLUSIONS: Plasma HRM provides comprehensive information relevant to nutrition and components of the microbiome that influence bone health. This data supports pro-inflammatory fatty acids and the gut microbiome as novel regulators of postnatal bone remodeling.

RevDate: 2020-07-04

Bello S, Vengoechea JJ, Ponce-Alonso M, et al (2020)

Core Microbiota in Central Lung Cancer With Streptococcal Enrichment as a Possible Diagnostic Marker.

Archivos de bronconeumologia pii:S0300-2896(20)30192-7 [Epub ahead of print].

BACKGROUND: Dysbiosis in lung cancer has been underexplored. The aim of this study was to define the bacterial and fungal microbiota of the bronchi in central lung cancer and to compare it with that of the oral and intestinal compartments.

METHODS: Twenty-five patients with central lung cancer and sixteen controls without antimicrobial intake during the previous month were recruited. Bacterial and fungal distribution was determined by massive sequencing of bronchial biopsies and saliva and faecal samples. Complex computational analysis was performed to define the core lung microbiota.

RESULTS: Affected and contralateral bronchi of patients have almost identical microbiota dominated by Streptococcus, whereas Pseudomonas was the dominant genera in controls. Oral and pulmonary ecosystems were significantly more similar in patients, probably due to microaspirations. Streptococcal abundance in the bronchi differentiated patients from controls according to a ROC curve analysis (90.9% sensitivity, 83.3% specificity, AUC=0.897). The saliva of patients characteristically showed a greater abundance of Streptococcus, Rothia, Gemella and Lactobacillus. The mycobiome of controls (Candida) was significantly different from that of patients (Malassezia). Cancer patients' bronchial mycobiome was similar to their saliva, but different from their contralateral bronchi.

CONCLUSIONS: The central lung cancer microbiome shows high levels of Streptococcus, and differs significantly in its composition from that of control subjects. Changes are not restricted to tumour tissue, and seem to be the consequence of microaspirations from the oral cavity. These findings could be useful in the screening and even diagnosis of this disease.

RevDate: 2020-07-04

Shah RD, Tang ZZ, Chen G, et al (2020)

Soy food intake associates with changes in the metabolome and reduced blood pressure in a gut microbiota dependent manner.

Nutrition, metabolism, and cardiovascular diseases : NMCD pii:S0939-4753(20)30155-1 [Epub ahead of print].

BACKGROUND AND AIMS: Consumption of soy foods has been associated with protection against cardiometabolic disease, but the mechanisms are incompletely understood. We hypothesized that habitual soy food consumption associates with gut microbiome composition, metabolite production, and the interaction between diet, microbiota and metabolites.

METHODS AND RESULTS: We analyzed dietary soy intake, plasma and stool metabolites, and gut microbiome data from two independent cross-sectional samples of healthy US individuals (N = 75 lean or overweight, and N = 29 obese). Habitual soy intake associated with several circulating metabolites. There was a significant interaction between soy intake and gut microbiome composition, as defined by gut enterotype, on metabolites in plasma and stool. Soy consumption associated with reduced systolic blood pressure, but only in a subset of individuals defined by their gut microbiome enterotype, suggesting that responsiveness to soy may be dependent on microbiome composition. Soy intake was associated with differences in specific microbial taxa, including two taxa mapping to genus Dialister and Prevotella which appeared to be suppressed by high soy intake We identified context-dependent effects of these taxa, where presence of Prevotella was associated with higher blood pressure and a worse cardiometabolic profile, but only in the absence of Dialister.

CONCLUSIONS: The gut microbiome is an important intermediate in the interplay between dietary soy intake and systemic metabolism. Consumption of soy foods may shape the microbiome by suppressing specific taxa, and may protect against hypertension only in individuals with soy-responsive microbiota.


RevDate: 2020-07-04

Reuter B, JS Bajaj (2020)

Microbiome: Emerging Concepts in Patients with Chronic Liver Disease.

Clinics in liver disease, 24(3):493-520.

The gut microbiome is an exciting new area of research in chronic liver disease. It has shown promise in expanding our understanding of these complicated disease processes and has opened up new treatment modalities. The aim of this review is to increase understanding of the microbiome and explain the collection and analysis process in the context of liver disease. It also looks at our current understanding of the role of the microbiome in the wide spectrum of chronic liver diseases and how it is being used in current therapies and treatments.

RevDate: 2020-07-04

Clerissi C, Guillou L, Escoubas JM, et al (2020)

Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers.

BMC microbiology, 20(1):193 pii:10.1186/s12866-020-01860-1.

BACKGROUND: Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far.

RESULTS: To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples.

CONCLUSIONS: Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.

RevDate: 2020-07-04

Creswell R, Tan J, Leff JW, et al (2020)

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans.

Genome medicine, 12(1):59 pii:10.1186/s13073-020-00758-x.

BACKGROUND: Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consistency and temporal responses of the gut microbiome to glycans is critical for rationally developing and deploying these compounds as therapeutics.

METHODS: We investigated the effect of two chemically distinct glycans (fructooligosaccharides and polydextrose) through three clinical studies conducted with 80 healthy volunteers. Stool samples, collected at dense temporal resolution (~ 4 times per week over 10 weeks) and analyzed using shotgun metagenomic sequencing, enabled detailed characterization of participants' microbiomes. For analyzing the microbiome time-series data, we developed MC-TIMME2 (Microbial Counts Trajectories Infinite Mixture Model Engine 2.0), a purpose-built computational tool based on nonparametric Bayesian methods that infer temporal patterns induced by perturbations and groups of microbes sharing these patterns.

RESULTS: Overall microbiome structure as well as individual taxa showed rapid, consistent, and durable alterations across participants, regardless of compound dose or the order in which glycans were consumed. Significant changes also occurred in the abundances of microbial carbohydrate utilization genes in response to polydextrose, but not in response to fructooligosaccharides. Using MC-TIMME2, we produced detailed, high-resolution temporal maps of the microbiota in response to glycans within and across microbiomes.

CONCLUSIONS: Our findings indicate that dietary glycans cause reproducible, dynamic, and differential alterations to the community structure of the human microbiome.

RevDate: 2020-07-04

Wang Y, Wang K, Huang L, et al (2020)

Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle.

Microbiome, 8(1):106 pii:10.1186/s40168-020-00879-w.

BACKGROUND: Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice.

RESULTS: Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery.

CONCLUSIONS: Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.

RevDate: 2020-07-04

Zhang J, Zhu Z, Zuo X, et al (2020)

The role of NTHi colonization and infection in the pathogenesis of neutrophilic asthma.

Respiratory research, 21(1):170 pii:10.1186/s12931-020-01438-5.

Asthma is a complex heterogeneous disease. The neutrophilic subtypes of asthma are described as persistent, more severe and corticosteroid-resistant, with higher hospitalization and mortality rates, which seriously affect the lives of asthmatic patients. With the development of high-throughput sequencing technology, an increasing amount of evidence has shown that lower airway microbiome dysbiosis contributes to the exacerbation of asthma, especially neutrophilic asthma. Nontypeable Haemophilus influenzae is normally found in the upper respiratory tract of healthy adults and is one of the most common strains in the lower respiratory tract of neutrophilic asthma patients, in whom its presence is related to the occurrence of corticosteroid resistance. To understand the pathogenic mechanism by which nontypeable Haemophilus influenzae colonization leads to the progression of neutrophilic asthma, we reviewed the previous literature on nontypeable Haemophilus influenzae colonization and subsequent aggravation of neutrophilic asthma and corticosteroid resistance. We discussed nontypeable Haemophilus influenzae as a potential therapeutic target to prevent the progression of neutrophilic asthma.

RevDate: 2020-07-03

Huang J, Jiang Z, Wang Y, et al (2020)

Modulation of gut microbiota to overcome resistance to immune checkpoint blockade in cancer immunotherapy.

Current opinion in pharmacology, 54:1-10 pii:S1471-4892(20)30027-8 [Epub ahead of print].

Immune checkpoint blockade therapies that target CTLA-4 and PD-1/PD-L1 have ushered in a new era of cancer treatment. Nevertheless, a significant proportion of patients demonstrated primary or acquired resistance. Harnessing gut microbiota has been an emerging novel therapeutic strategy to overcome resistance. Here we summarized the current research status of gut microbiota in immune checkpoint blockade therapies, clinical trials, underlying mechanisms and challenges of microbiome research in checkpoint immunotherapy. Findings from preclinical models, standardized microbiome analysis and progress of multi-omic approaches may better disclose the interaction between gut microbiota and immune checkpoint inhibitors (ICIs) and traditional Chinese medicine can be a potential microbiome modulator to sensitize the response to ICIs.

RevDate: 2020-07-03

Ren XM, Kuo Y, B Blumberg (2020)

Agrochemicals and obesity.

Molecular and cellular endocrinology pii:S0303-7207(20)30226-4 [Epub ahead of print].

Obesity has become a very large concern worldwide, reaching pandemic proportions over the past several decades. Lifestyle factors, such as excess caloric intake and decreased physical activity, together with genetic predispositions, are well-known factors related to obesity. There is accumulating evidence suggesting that exposure to some environmental chemicals during critical windows of development may contribute to the rapid increase in the incidence of obesity. Agrochemicals are a class of chemicals extensively used in agriculture, which have been widely detected in human. There is now considerable evidence linking human exposure to agrochemicals with obesity. This review summarizes human epidemiological evidence and experimental animal studies supporting the association between agrochemical exposure and obesity and outlines possible mechanistic underpinnings for this link.

RevDate: 2020-07-03

Ganley JG, Pandey A, Sylvester K, et al (2020)

A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity.

Cell chemical biology pii:S2451-9456(20)30227-0 [Epub ahead of print].

Advances in infectious disease control strategies through genetic manipulation of insect microbiomes have heightened interest in microbially produced small molecules within mosquitoes. Herein, 33 mosquito-associated bacterial genomes were mined and over 700 putative biosynthetic gene clusters (BGCs) were identified, 135 of which belong to known classes of BGCs. After an in-depth analysis of the 135 BGCs, iron-binding siderophores were chosen for further investigation due to their high abundance and well-characterized bioactivities. Through various metabolomic strategies, eight siderophore scaffolds were identified in six strains of mosquito-associated bacteria. Among these, serratiochelin A and pyochelin were found to reduce female Anopheles gambiae overall fecundity likely by lowering their blood-feeding rate. Serratiochelin A and pyochelin were further found to inhibit the Plasmodium parasite asexual blood and liver stages in vitro. Our work supplies a bioinformatic resource for future mosquito-microbiome studies and highlights an understudied source of bioactive small molecules.

RevDate: 2020-07-03

Reitmeier S, Kiessling S, Clavel T, et al (2020)

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.

Cell host & microbe pii:S1931-3128(20)30343-7 [Epub ahead of print].

Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance and identified 13 taxa with disrupted rhythmicity in type 2 diabetes (T2D). Cross-validated prediction models based on this signature similarly classified T2D. In an independent cohort (FoCus), disruption of microbial oscillation and the model for T2D classification was confirmed in 1,363 subjects. This arrhythmic risk signature was able to predict T2D in 699 KORA subjects 5 years after initial sampling, being most effective in combination with BMI. Shotgun metagenomic analysis functionally linked 26 metabolic pathways to the diurnal oscillation of gut bacteria. Thus, a cohort-specific risk pattern of arrhythmic taxa enables classification and prediction of T2D, suggesting a functional link between circadian rhythms and the microbiome in metabolic diseases.

RevDate: 2020-07-03

Zhang C, He X, Sheng Y, et al (2020)

Allicin-induced host-gut microbe interactions improves energy homeostasis.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology [Epub ahead of print].

Allicin (diallylthiosulfinate) is a natural food compound with multiple biological and pharmacological functions. However, the mechanism of beneficial role of Allicin on energy homeostasis is not well studied. Gut microbiota (GM) profoundly affects host metabolism via microbiota-host interactions and coevolution. Here, we investigated the interventions of beneficial microbiome induced by Allicin on energy homeostasis, particularly obesity, and related complications. Interestingly, Allicin treatment significantly improved GM composition and induced the most significant alteration enrichment of Bifidobacterium and Lactobacillus. Importantly, transplantation of the Allicin-induced GM to HFD mice (AGMT) played a remarkable role in decreasing adiposity, maintaining glucose homeostasis, and ameliorating hepatic steatosis. Furthermore, AGMT was effective in modulating lipid metabolism, activated brown adipose tissues (BATs), induced browning in sWAT, reduced inflammation, and inhibited the degradation of intestinal villi. Mechanically, AGMT significantly increased Blautia [short-chain fatty acids (SCFAs)-producing microbiota] and Bifidobacterium in HFD mice, also increased the SCFAs in the cecum, which has been proved many beneficial effects on energy homeostasis. Our study highlights that Allicin-induced host-gut microbe interactions plays an important role in regulating energy homeostasis, which provides a promising potential therapy for obesity and metabolic disorders based on host-microbe interactions.

RevDate: 2020-07-03

Mason LM, Eagar A, Patel P, et al (2020)

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest.

Journal of applied microbiology [Epub ahead of print].

AIMS: The soil microbial community plays a critical role in increasing phosphorus (P) availability in low-P, weathered soils by "mining" recalcitrant organic P through the production of phosphatase enzymes. However, there is a lack of data on the fungal and bacterial taxa which are directly involved in P mining, which could also serve as potential microbial bioindicators of low P availability.

METHODS AND RESULTS: Leveraging a 5-year P enrichment experiment on low-P forest soils, high-throughput sequencing was used to profile the microbial community to determine which taxa associate closely with P availability. We hypothesized that there would be a specialized group of soil microorganisms that could access recalcitrant P and whose presence could serve as a bioindicator of P mining. Community profiling revealed several candidate bioindicators of P mining (Russulales, Acidobacteria Subgroup 2, Acidobacteriales, Obscuribacterales, and Solibacterales), whose relative abundance declined with elevated P and had a significant, positive association with phosphatase production. In addition, we identified candidate bioindicators of high P availability (Mytilinidales, Sebacinales, Chitinophagales, Cytophagales, Saccharimonadales, Opitulales, and Gemmatales).

CONCLUSIONS: This research provides evidence that mitigating P limitation in this ecosystem may be a specialized trait and is mediated by a few microbial taxa.

Here, we characterize Orders of soil microbes associated with manipulated phosphorus availability in forest soils to determine bioindicator candidates for phosphorus. Likewise, we provide evidence that the microbial trait to utilize recalcitrant organic forms of P (e.g. P mining) is likely a specialized trait and not common to all members of the soil microbial community. This work further elucidates the role that a complex microbial community plays in the cycling of P in low-P soils, and provides evidence for future studies on microbial linkages to human-induced ecosystem changes.

RevDate: 2020-07-03

Iqbal Z, Adam S, Ho JH, et al (2020)

Metabolic and cardiovascular outcomes of bariatric surgery.

Current opinion in lipidology [Epub ahead of print].

PURPOSE OF REVIEW: Bariatric surgery is an effective therapy for morbid obesity that also improves weight-related metabolic parameters and reduces morbidity and mortality. The purpose of this review is to consolidate our current understanding of metabolic, macrovascular and microvascular benefits of bariatric surgery and to provide an update.

RECENT FINDINGS: Early resolution of insulin resistance and type 2 diabetes mellitus (T2DM) varies by type of bariatric surgery and appears to be mediated by changes in secretion of gut hormones, metabolism of bile acids, expression of glucose transporters and the gut microbiome. Dyslipidaemia, atherosclerosis, microvascular complications of obesity and diabetes, systemic and tissue-level inflammation show evidence of regression and hypertension improves significantly after bariatric surgery.

SUMMARY: Bariatric surgery leads to improvements in obesity-related metabolic comorbidities such as dyslipidaemia, HDL functionality, hypertension, T2DM, insulin resistance and inflammation. It slows the atherosclerotic process and reduces cardiovascular and all-cause mortality. Recent data have demonstrated regression of the microvascular complications of obesity and diabetes including the regeneration of small nerve fibres. The magnitude of change in short-term metabolic effects depends on the surgical procedure whilst longer term effects are related to the amount of sustained excess weight loss.

RevDate: 2020-07-03

Craven L, Rahman A, Nair Parvathy S, et al (2020)

Allogenic Fecal Microbiota Transplantation in Patients With Nonalcoholic Fatty Liver Disease Improves Abnormal Small Intestinal Permeability: A Randomized Control Trial.

The American journal of gastroenterology, 115(7):1055-1065.

INTRODUCTION: Nonalcoholic fatty liver disease (NAFLD) is an obesity-related disorder that is rapidly increasing in incidence and is considered the hepatic manifestation of the metabolic syndrome. The gut microbiome plays a role in metabolism and maintaining gut barrier integrity. Studies have found differences in the microbiota between NAFLD and healthy patients and increased intestinal permeability in patients with NAFLD. Fecal microbiota transplantation (FMT) can be used to alter the gut microbiome. It was hypothesized that an FMT from a thin and healthy donor given to patients with NAFLD would improve insulin resistance (IR), hepatic proton density fat fraction (PDFF), and intestinal permeability.

METHODS: Twenty-one patients with NAFLD were recruited and randomized in a ratio of 3:1 to either an allogenic (n = 15) or an autologous (n = 6) FMT delivered by using an endoscope to the distal duodenum. IR was calculated by HOMA-IR, hepatic PDFF was measured by MRI, and intestinal permeability was tested using the lactulose:mannitol urine test. Additional markers of metabolic syndrome and the gut microbiota were examined. Patient visits occurred at baseline, 2, 6 weeks, and 6 months post-FMT.

RESULTS: There were no significant changes in HOMA-IR or hepatic PDFF in patients who received the allogenic or autologous FMT. Allogenic FMT patients with elevated small intestinal permeability (>0.025 lactulose:mannitol, n = 7) at baseline had a significant reduction 6 weeks after allogenic FMT.

DISCUSSION: FMT did not improve IR as measured by HOMA-IR or hepatic PDFF but did have the potential to reduce small intestinal permeability in patients with NAFLD.

RevDate: 2020-07-03

Li W, ZS Ma (2020)

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques.

FEMS microbiology ecology pii:5866839 [Epub ahead of print].

Human gut microbiome could translocate to other tissues, and the relocation triggered by HIV/SIV infection has received increasing attention. However, the underlying mode of this translocation, whether it is deterministic or random (passive) process, is not clear, not to mention quantitative estimation of the relocation probability and rates. Using multi-tissue microbiome datasets collected from SIV-infected macaques, originally reported by Klase et al. (2015), we apply Hubbell's unified neutral theory of biodiversity (UNTB) implemented by Harris et al. (2015) in the form of multi-site neutral (MSN) model to explore the translocation mode and rates of the gut microbiome. We found that (i) The translocation from gastrointestinal tract to tissues was driven by stochastic (neutral) forces as revealed by 100% neutrality-passing rates with MSN testing; (ii) The translocation probability from gastrointestinal tract to tissues is significantly larger than the baseline dispersal rates occurring within gastrointestinal tract (0.234 vs. 0.006 at the phylum level, p<0.001). (iii) Approximately 23% of phyla and 55% of genera were migrated from gastrointestinal tract to the tissues (liver and mesenteric lymph nodes). Our findings offer the first interpretation of the microbial translocation mode from gastrointestinal tract to tissues, and the first estimates of the translocation probability and level.

RevDate: 2020-07-03

Ippolito MM, Denny JE, Nenortas E, et al (2020)

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice.

The American journal of tropical medicine and hygiene [Epub ahead of print].

The antimalarial drug lumefantrine (LF) exhibits erratic pharmacokinetics (PK). Intersubject variability might be attributed, in part, to differences in the gut microbiome-mediated drug metabolism. We assessed LF disposition in healthy mice stratified by enterotype to explore associations between the gut microbiota and LF PK. Gut microbiota enterotypes were classified according to abundance and diversity indices from 16S rRNA sequencing. Pharmacokinetic parameters were computed using noncompartmental analysis. Two distinctive enterotypes were identified. Maximal concentration (Cmax) and total drug exposure measured as the area under the drug concentration-time curve (AUC0-24) differed significantly between the groups. The mean and SD of Cmax were 660 ± 220 ng/mL versus 390 ± 59 ng/mL (P = 0.02), and AUC0-24 was 9,600 ± 2,800 versus 5,800 ± 810 ng × h/mL (P = 0.01). In healthy mice intragastrically dosed with the antimalarial drug LF in combination with artemether, LF exposure was associated with the gut bacterial community structure. Studies of xenobiotic-microbiota interactions can inform drug posology and elucidate mechanisms of drug disposition.

RevDate: 2020-07-03

Huang G, Wang X, Hu Y, et al (2020)

Diet drives convergent evolution of gut microbiomes in bamboo-eating species.

Science China. Life sciences pii:10.1007/s11427-020-1750-7 [Epub ahead of print].

Gut microbiota plays a critical role in host physiology and health. The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche. Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota. However, the relative contribution of each factor in shaping the structure of gut microbiota remains unclear. The giant (Ailuropoda melanoleuca) and red (Ailurus styani) pandas belong to different families of order Carnivora. They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution. Here, we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing. We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives. This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea. Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis. These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.

RevDate: 2020-07-03

Weinrauch AM, Folkerts EJ, Blewett TA, et al (2020)

Impacts of low salinity exposure and antibiotic application on gut transport activity in the Pacific spiny dogfish, Squalus acanthias suckleyi.

Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology pii:10.1007/s00360-020-01291-4 [Epub ahead of print].

The role of the marine elasmobranch gastrointestinal tract in nitrogen-recycling and osmotic homeostasis has become increasingly apparent, with the gut microbial community likely playing a significant role converting urea, an important osmolyte in elasmobranchs, into ammonia. The Pacific spiny dogfish can experience and tolerate reduced environmental salinities, yet how this environmental challenge may affect the microbiome, and consequently nitrogen transport across the gut, is as of yet unknown. In the present study, excised gut sac preparations were made from dogfish acclimated to the following: full-strength seawater (C), low salinity for 7 days (LS), and after acute transfer of LS-acclimated fish to full-strength SW for 6 h (AT). Significantly reduced microbial derived urease activity was observed in the mucosal saline of gut sac preparations from the LS (by 81%) and AT (by 89%) treatments relative to the C treatment. Microbial derived cellulase activity from mucosal saline samples tended to follow similar patterns. To further ensure an effective decrease in the spiral valve microbial population, an antibiotic cocktail was applied to the mucosal saline used for in vitro measurements of ion, water, and nitrogen flux in these gut sac preparations. This caused a further 57-61% decrease in the mucosal saline urease activity of the C and LS treatments. Overall, we observed relatively little flux across the stomach for all measured parameters aside from water movement, which switched from a net efflux in control fish to a net influx in acutely transferred fish, indicative of drinking. While no significant differences were observed in terms of nitrogen flux (urea or ammonia), we tended to see the accumulation of ammonia in the spiral valve lumen and a switch from efflux to influx of urea in control versus acutely transferred fish. The increased ammonia production likely occurs as a result of heightened metabolism in a challenging environment, while the retention and acquisition of urea is suggestive of nitrogen scavenging under nitrogen-limiting conditions.

RevDate: 2020-07-03

Jang SW, Yoou MH, Hong WJ, et al (2020)

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition.

Rice (New York, N.Y.), 13(1):44 pii:10.1186/s12284-020-00403-6.

Rice (Oryza sativa. L) has been intensively studied to ensure a stable global supply of this commodity in the face of rapid global climate change. A critical factor that decreases crop yield is drought, which has been analyzed in various ways through many researches. Microbiome-based studies of rice investigate the symbiosis between rice and bacteria, which has been proposed as a way to overcome problems caused by drought. Several rice-associated metagenomic profiles obtained under drought conditions have been reported since the advent of next generation sequencing (NGS) technology. To elucidate the future diversity of plants and microorganisms and to promote sustainable agriculture, we reanalyzed 64 of the publicly available 16S amplicon sequencing data produced under drought condition. In the process of integrating data sets, however, we found an inconsistency that serves as a bottleneck for microbiome-based sustainability research. While this report provides clues about the composition of the microbiome under the drought conditions, the results are affected by differences in the location of the experiments, sampling conditions, and analysis protocols. Re-analysis of amplicon sequencing data of the soil microbiome in rice fields suggests that microbial composition shifts in response to drought condition and the presence of plants. Among the bacteria involved, the phylum Proteobacteria appears to play the most important role in the survival of rice under drought condition.

RevDate: 2020-07-03

Miao F, Zhao Z, Li Q, et al (2020)

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota.

Current microbiology pii:10.1007/s00284-020-02108-x [Epub ahead of print].

Tri-spine horseshoe crabs (HSCs) Tachypleus tridentatus have been facing the threat of population depletion for decades, and the physiology and microbiology of their early life stages are lacking. To explore what directs the change of juvenile T. tridentatus gut microbiota and how gut microbiota change, by using 16S rRNA sequencing of gut samples we detected the intestinal microbiome of juvenile HSCs and compared the impact of initial molting and initial feeding, as well as the effect of environment. Results showed that the predominant phyla in the gut microbial community of juvenile HSCs are Proteobacteria and Bacteroidetes. The richness and diversity of intestinal microbes greatly decreased after initial molting. Microbial-mediated functions predicted by PICRUSt showed that "Signal Transduction", "Cellular Processes and Signaling", "Infective Diseases" and "Digestive System" pathways significantly increased in 2nd instars. As for the effect of environment, the connection between living environment and the intestinal microbiome started to manifest after initial molting. Unexpectedly, initial feeding treatment slightly affected the intestinal microbiome of T. tridentatus in the early life stage, whereas the effect of initial molting was significant. The present study provided the first insight into the gut microbiota of T. tridentatus, and the findings led a new sight to explain what guide the change of gut microbiota.

RevDate: 2020-07-03

Peter I, Maldonado-Contreras A, Eisele C, et al (2020)

A dietary intervention to improve the microbiome composition of pregnant women with Crohn's disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design.

Contemporary clinical trials communications, 18:100573 pii:100573.

Crohn's disease (CD), a type of inflammatory bowel disease (IBD), is a chronic condition of the gastrointestinal tract that is caused by the loss of mucosal tolerance towards the commensal bacteria resulting in inflammatory responses. It has long been postulated that the gut microbiota, a complex and dynamic population of microorganisms, plays a key role in the pathogenesis of IBD. Maternal diagnosis of IBD has been identified as the greatest risk factor for IBD in offspring increasing the odds of developing the disease >4.5-fold. Moreover, babies born to mothers with IBD have demonstrated reduced gut bacterial diversity. There is accumulating evidence that the early life microbiota colonization is informed by maternal diet within the 3rd trimester of pregnancy. While babies born to mothers with IBD would pose an ideal cohort for intervention, no primary prevention measures are currently available. Therefore, we designed the MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial to test whether the IBD-AID™ dietary intervention during the last trimester of pregnancy can beneficially shift the microbiome of CD patients and their babies, thereby promoting a strong, effective immune system during a critical time of the immune system development. We will also test if favorable changes in the microbiome can lead to a reduced risk of postpartum CD relapse and lower mucosal inflammation in the offspring. This study will help create new opportunities to foster a healthy microbiome in the offspring at high risk of other immune-mediated diseases, potentially reducing their risk later in life.

RevDate: 2020-07-03

Zhu C, Yuan C, Wei FQ, et al (2020)

Comparative evaluation of peptidome and microbiota in different types of saliva samples.

Annals of translational medicine, 8(11):686.

Background: Clinical and research interest in salivary peptidome and microbiota is ever-growing owing to its great value for diagnosis, risk assessment and prediction of prognosis in oral and systemic diseases. Saliva can be stimulated for the purpose of rapid collection, but currently there are no studies systematically addressing the similarities and differences of salivary peptidome and microbiota in different types of samples. The purpose of this study was to investigate the variations of salivary peptidome and microbial profiles in response to different stimulating conditions.

Methods: Unstimulated saliva and three types of stimulated saliva samples (olfaction, gustation, and mastication stimulated saliva) were collected from 10 systematically and orally healthy donors. The peptidome profiles were detected by weak cation exchange magnetic beads and analyzed through matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS), while their microbial profiles were analyzed by 16S rDNA V3-V4 hypervariable region amplicon sequencing utilizing the Illumina MiSeq PE300 platform. The distance matrixes of salivary peptidome and microbial profiles were generated and the intra-individual distances were extracted, then the variations brought by different sampling conditions and repeated collections were compared.

Results: By comparisons of the overall salivary peptidome and microbial profiles, olfactory stimulation led to minimal variations comparing with that of unstimulated saliva, but appreciable variations were observed between saliva samples collected with gustatory/masticatory stimulation and unstimulated saliva. The three types of stimulated saliva exhibited significantly different peptidome and microbial profiles.

Conclusions: Stimulated saliva collected in response to olfactory stimulation is an appropriate alternative to unstimulated saliva, whereas gustatory/masticatory stimulation introduced appreciable variations. It is suggested that only one type of stimulating method should be used throughout one peptidome/microbiome research, which provides comprehensive insight into the optimization of sampling methods for salivaomic studies in the future.

RevDate: 2020-07-03

McClure RS, Lee JY, Chowdhury TR, et al (2020)

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations.

Scientific reports, 10(1):10882 pii:10.1038/s41598-020-67878-7.

The soil environment is constantly changing due to shifts in soil moisture, nutrient availability and other conditions. To contend with these changes, soil microorganisms have evolved a variety of ways to adapt to environmental perturbations, including regulation of gene expression. However, it is challenging to untangle the complex phenotypic response of the soil to environmental change, partly due to the absence of predictive modeling frameworks that can mechanistically link molecular-level changes in soil microorganisms to a community's functional phenotypes (or metaphenome). Towards filling this gap, we performed a combined analysis of metabolic and gene co-expression networks to explore how the soil microbiome responded to changes in soil moisture and nutrient conditions and to determine which genes were expressed under a given condition. Our integrated modeling approach revealed previously unknown, but critically important aspects of the soil microbiomes' response to environmental perturbations. Incorporation of metabolomic and transcriptomic data into metabolic reaction networks identified condition-specific signature genes that are uniquely associated with dry, wet, and glycine-amended conditions. A subsequent gene co-expression network analysis revealed that drought-associated genes occupied more central positions in a network model of the soil community, compared to the genes associated with wet, and glycine-amended conditions. These results indicate the occurrence of system-wide metabolic coordination when soil microbiomes cope with moisture or nutrient perturbations. Importantly, the approach that we demonstrate here to analyze large-scale multi-omics data from a natural soil environment is applicable to other microbiome systems for which multi-omics data are available.

RevDate: 2020-07-03

Allers K, Stahl-Hennig C, Fiedler T, et al (2020)

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage.

Scientific reports, 10(1):10887 pii:10.1038/s41598-020-67843-4.

The intesinal microbiome is considered important in human immunodeficiency virus (HIV) pathogenesis and therefore represents a potential therapeutic target to improve the patients' health status. Longitudinal alterations in the colonic mucosa-associated microbiome during simian immunodeficiency virus (SIV) infection were investigated using a 16S rRNA amplicon approach on the Illumina sequencing platform and bioinformatics analyses. Following SIV infection of six animals, no alterations in microbial composition were observed before the viral load peaked in the colon. At the time of acute mucosal SIV replication, the phylum Bacteroidetes including the Bacteroidia class as well as the phylum Firmicutes and its families Ruminococcaceae and Eubacteriaceae became more abundant. Enrichment of Bacteroidetes was maintained until the chronic phase of SIV infection. The shift towards Bacteroidetes in the mucosa-associated microbiome was associated with the extent of SIV infection-induced mucosal CD4+ T cell depletion and correlated with increasing rates of enterocyte damage. These observations suggest that Bacteroidetes strains increase during virus-induced mucosal immune destruction. As Bacteroidetes belong to the lipopolysaccharide- and short chain fatty acids-producing bacteria, their rapid enrichment may contribute to inflammatory tissue damage and metabolic alterations in SIV/HIV infection. These aspects should be considered in future studies on therapeutic interventions.

RevDate: 2020-07-03

de Brito LCN, Doolittle-Hall J, Lee CT, et al (2020)

The apical root canal system microbial communities determined by next-generation sequencing.

Scientific reports, 10(1):10932 pii:10.1038/s41598-020-67828-3.

The aim of this study was to explore the microbial communities of endodontic infections at their apical portion by 16S rRNA Illumina sequencing and delineate the core microbiome of root canal infections and that of their associated clinical symptomatology. Samples were collected from fifteen subjects presenting one tooth with a root canal infection, and their associated symptoms were recorded. Samples were collected from the apical third of roots using a #10 K file and then amplified using multiple displacement amplification and PCR-amplified with universal primers. Amplicons were sequenced (V3-V4 hypervariable region of the 16S rRNA gene) using MiSeq (Illumina, CA). The microbial composition of the samples was determined using QIIME and HOMINGS. Data were analyzed using t tests and ANOVA. A total of 1,038,656 good quality sequences were obtained, and OTUs were assigned to 10 bacterial phyla, led by Bacteroidetes (51.2%) and Firmicutes (27.1%), and 94 genera were represented primarily by Prevotella (17.9%) and Bacteroidaceae G-1 (14.3%). Symptomatic teeth were associated with higher levels of Porphyromonas (p < 0.05) and Prevotella. P. endodontalis and P. oris were present in both cores. The present study demonstrated the complexity of the root canal microbiome and the "common denominators" of root canal infections and identified taxa whose virulence properties should be further explored. The polymicrobial etiology of endodontic infections has long been established. However, few studies have focused on expanding the breadth and depth of coverage of microbiome-infected root canals at their apical portion.

RevDate: 2020-07-03

Hyde J, Correa MA, Hughes GL, et al (2020)

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes.

Scientific reports, 10(1):10880 pii:10.1038/s41598-020-67811-y.

The microbiome is an assemblage of microorganisms living in association with a multicellular host. Numerous studies have identified a role for the microbiome in host physiology, development, immunity, and behaviour. The generation of axenic (germ-free) and gnotobiotic model systems has been vital to dissecting the role of the microbiome in host biology. We have previously reported the generation of axenic Aedes aegypti mosquitoes, the primary vector of several human pathogenic viruses, including dengue virus and Zika virus. In order to better understand the influence of the microbiome on mosquitoes, we examined the transcriptomes of axenic and conventionally reared Ae. aegypti before and after a blood meal. Our results suggest that the microbiome has a much lower effect on the mosquito's gene expression than previously thought with only 170 genes influenced by the axenic state, while in contrast, blood meal status influenced 809 genes. The pattern of expression influenced by the microbiome is consistent with transient changes similar to infection rather than sweeping physiological changes. While the microbiome does seem to affect some pathways such as immune function and metabolism, our data suggest the microbiome is primarily serving a nutritional role in development with only minor effects in the adult.

RevDate: 2020-07-03

Kaur S, Sarma SJ, Marshall BL, et al (2020)

Developmental exposure of California mice to endocrine disrupting chemicals and potential effects on the microbiome-gut-brain axis at adulthood.

Scientific reports, 10(1):10902 pii:10.1038/s41598-020-67709-9.

Xenoestrogens are chemicals found in plant products, such as genistein (GEN), and in industrial chemicals, e.g., bisphenol A (BPA), present in plastics and other products that are prevalent in the environment. Early exposure to such endocrine disrupting chemicals (EDC) may affect brain development by directly disrupting neural programming and/or through the microbiome-gut-brain axis. To test this hypothesis, California mice (Peromyscus californicus) offspring were exposed through the maternal diet to GEN (250 mg/kg feed weight) or BPA (5 mg/kg feed weight, low dose- LD or 50 mg/kg, upper dose-UD), and dams were placed on these diets two weeks prior to breeding, throughout gestation, and lactation. Various behaviors, gut microbiota, and fecal metabolome were assessed at 90 days of age. The LD but not UD of BPA exposure resulted in individuals spending more time engaging in repetitive behaviors. GEN exposed individuals were more likely to exhibit such behaviors and showed socio-communicative disturbances. BPA and GEN exposed females had increased number of metabolites involved in carbohydrate metabolism and synthesis. Males exposed to BPA or GEN showed alterations in lysine degradation and phenylalanine and tyrosine metabolism. Current findings indicate cause for concern that developmental exposure to BPA or GEN might affect the microbiome-gut-brain axis.

RevDate: 2020-07-03

Yan Z, Wu H, Zhou H, et al (2020)

Integrated metabolomics and gut microbiome to the effects and mechanisms of naoxintong capsule on type 2 diabetes in rats.

Scientific reports, 10(1):10829 pii:10.1038/s41598-020-67362-2.

Naoxintong Capsule (NXT) is a Traditional Chinese Medicine formulation which has been widely applied in treating cardiovascular and cerebrovascular diseases. Previous studies also reported the potential effects of NXT against diabetes and certain complications, yet its mechanisms remain largely obscured. Herein, in this study, we investigated the anti-diabetic effects of NXT as well as its potential mechanisms. Type 2 diabetes (T2D) was induced in rats by 10-week high-fat diet in companion with a low-dose streptozotocin injection. NXT was administrated for additional 8 weeks. The results showed that NXT exerted potent efficacy against T2D by alleviating hyperglycemia and hyperlipidemia, ameliorating insulin resistance, mitigating inflammation, relieving hypertension, and reducing myocardial injuries. To investigate its mechanisms, by integrating sequencing of gut microbiota and serum untargeted metabolomics, we showed that NXT could significantly recover the disturbances of gut microbiota and metabolic phenotypes in T2D rats. Several feature pathways, such as arachidonic acid metabolism, fatty acid β-oxidation and glycerophospholipid metabolism, were identified as the potential mechanisms of NXT in vivo. In summary, our study has comprehensively revealed the anti-diabetic effects of NXT which could be considered as a promising strategy for treating metabolic disorders, T2D and diabetic related complications in clinical practice.

RevDate: 2020-07-03

Coker MO, Mongodin EF, El-Kamary SS, et al (2020)

Immune status, and not HIV infection or exposure, drives the development of the oral microbiota.

Scientific reports, 10(1):10830 pii:10.1038/s41598-020-67487-4.

Even with antiretroviral therapy, children born to HIV-infected (HI) mothers are at a higher risk of early-life infections and morbidities including dental disease. The increased risk of dental caries in HI children suggest immune-mediated changes in oral bacterial communities, however, the impact of perinatal HIV exposure on the oral microbiota remains unclear. We hypothesized that the oral microbiota of HI and perinatally HIV-exposed-but-uninfected (HEU) children will significantly differ from HIV-unexposed-and-uninfected (HUU) children. Saliva samples from 286 child-participants in Nigeria, aged ≤ 6 years, were analyzed using 16S rRNA gene sequencing. Perinatal HIV infection was significantly associated with community composition (HI vs. HUU-p = 0.04; HEU vs. HUU-p = 0.11) however, immune status had stronger impacts on bacterial profiles (p < 0.001). We observed age-stratified associations of perinatal HIV exposure on community composition, with HEU children differing from HUU children in early life but HEU children becoming more similar to HUU children with age. Our findings suggest that, regardless of age, HIV infection or exposure, low CD4 levels persistently alter the oral microbiota during this critical developmental period. Data also indicates that, while HIV infection clearly shapes the developing infant oral microbiome, the effect of perinatal exposure (without infection) appears transient.

RevDate: 2020-07-03

Seppey M, Manni M, EM Zdobnov (2020)

LEMMI: A continuous benchmarking platform for metagenomics classifiers.

Genome research pii:gr.260398.119 [Epub ahead of print].

Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the method's release and its adoption in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to metagenome composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark designed to be continuously open to new submissions. This allows developers to be proactive regarding comparative evaluations and guarantees that any promising methods can be assessed side-by-side with established tools quickly after their release. Moreover, LEMMI enforces an effective distribution through software containers to ensure long term availability of all methods. Here, we detail the LEMMI workflow and discuss the performances of some previously unevaluated tools. We see this platform eventually as a community-driven effort where method developers can showcase novel approaches and get unbiased benchmarks for publications, while users can make informed choices and obtain standardized and easy-to-use tools.

RevDate: 2020-07-03

Terada T, Nii T, Isobe N, et al (2020)

Effect of antibiotic treatment on microbial composition and expression of antimicrobial peptides and cytokines in the chick cecum.

Poultry science, 99(7):3385-3392.

The aim of this study was to confirm whether the expression of innate immune molecules in the chick cecum is altered in association with changes in the composition of the intestinal microbiome that are regulated by treatment with antibiotics. Broiler chicks were administered with antibiotics (penicillin and streptomycin) daily, and the composition of the microbiota, expression of innate immune molecules, and localization of antimicrobial peptides in the chick cecum were examined at day 7 and day 14 using real-time PCR and immunohistochemistry. The oral administration of antibiotics caused an increase in the relative frequency of the Enterobacteriaceae family and a decrease in some gram-negative (Barnesiellaceae) and gram-positive bacterial (Clostridiaceae and Erysipelotrichaceae) families. The gene expression levels of immune molecules, including 4 Toll-like receptors (TLR) (TLR 2, 4, 5, and 21), inflammation-related cytokines (IL-1β, TGFβ3, TGFβ4, and IL-8), and antimicrobial peptides (avian β-defensins and cathelicidins) showed a tendency to decrease with antibiotic treatment at day 7. However, expression levels of TLR21 and some cytokines (IL-1β, TGFβ3, and IL-8) were higher in the cecum or cecal tonsils of the antibiotic-treated group than in those of the control at day 14. The immunoreactive avian β-defensin 2 and cathelicidin 1 proteins were localized in the leukocyte-like cells in the lamina propria, and they were aggregated in the form of small islands. We conclude that the expression of innate immune molecules, including TLR, inflammation-related cytokines, and antimicrobial peptides, in the cecum are altered in association with changes in the density or composition of the luminal microbiota during the early phase of life in chicks.

RevDate: 2020-07-03

Chen L, Chen MY, Shao L, et al (2020)

Panax notoginseng saponins prevent colitis-associated colorectal cancer development: the role of gut microbiota.

Chinese journal of natural medicines, 18(7):500-507.

Gut microbiota dysbiosis is a risk factor for colorectal cancer (CRC) in inflammatory bowel disease (IBD). In this study, the effects of Panax notoginseng saponins (PNS) on colitis-associated CRC progression were evaluated on an azoxymethane (AOM)/dextran sulfate sodium (DSS) mouse model. In vivo, PNS significantly relieved AOM/DSS-induced colon tumorigenesis and development by reducing the disease activity index (DAI) scores and colon tumor load. The 16S rRNA data of fecal samples showed that the microbiome community was obviously destructed, while PNS could recover the richness and diversity of gut microbiota. Especially, PNS could increase the abundance of Akkermansia spp. which was significantly decreased in model group and negatively correlated with the progression of CRC. Moreover, ginsenoside compound K (GC-K) was evaluated on the effects of human CRC cells, which was the main bio-transformed metabolite of PNS by gut microbiota. Our data showed that PNS played important role in the prevention of the progression of CRC, due to their regulation on the microbiome balance and microbial bio-converted product with anti-CRC activity.

RevDate: 2020-07-03

Le Sciellour M, Zemb O, Serviento AM, et al (2020)

Transient effect of single or repeated acute deoxynivalenol and zearalenone dietary challenge on fecal microbiota composition in female finishing pigs.

Animal : an international journal of animal bioscience pii:S1751731120001299 [Epub ahead of print].

Mycotoxins are a major contaminant of pig feed and have negative effects on health and performance. The present study investigated the impact of single or repeated acute challenges with a diet naturally contaminated with deoxynivalenol (DON) and zearalenone (ZEN) on growth performances of finishing pigs and their fecal microbiota composition. A total of 160 pigs (castrated males and females) in two successive batches were randomly divided into four experimental groups of 40 pigs each. The control group received a control finisher diet from 99 to 154 days of age. Challenged groups were subjected to a 7-day acute challenge by being fed a DON- and ZEN-contaminated diet (3.02 mg DON/kg feed and 0.76 mg ZEN/kg feed) at 113 days (group DC), 134 days (group CD) or both 113 and 134 days (group DD). Microbiota composition was analyzed via 16S rRNA sequencing from fecal samples collected from the 80 females at 99, 119, 140 and 154 days. Challenged pigs (i.e. groups DC, CD and DD) reduced their average daily feed intake by 25% and 27% (P < 0.001) and feed efficiency by 34% and 28% (P < 0.05) during the first and second mycotoxin exposure, respectively. Microbiota composition was affected by mycotoxin exposure (P = 0.07 during the first exposure and P = 0.01 during the second exposure). At the family level, mycotoxin exposure significantly (P < 0.05) decreased the relative abundances of Ruminococcaceae, Streptococcaceae and Veillonellaceae and increased that of Erysipelotrichaceae at both 119 and 140 days of age. After the 7-day DON/ZEN challenge, the relative abundance of 6 to 148 operational taxonomic units (OTUs) differed among the treatment groups. However, none of these OTUs changed in all treatment groups. Using 27 functional pathways, pigs exposed to DON/ZEN challenges could be distinguished from control pigs using sparse partial least squares discriminant analysis, with a 15% misclassification rate. Regarding the functionality of these predictors, two pathways were involved in detoxifying mycotoxins: drug metabolism and xenobiotic metabolism by cytochrome P450. In challenged pigs, microbiota composition returned to the initial state within 3 weeks after the end of a single or repeated DON/ZEN challenge, highlighting the resilience of the gut microbiome. The feeding and growth performances of the pigs during challenge periods were significantly correlated with biological pathways related to health problems and modifications in host metabolism. To conclude, short-term DON/ZEN challenges resulted in transient modifications in the composition and functions of fecal microbiota.

RevDate: 2020-07-03

Ames NJ, Barb JJ, Schuebel K, et al (2020)

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity.

Gut microbes, 11(6):1608-1631.

Many patients with alcohol use disorder (AUD) consume alcohol chronically and in large amounts that alter intestinal microbiota, damage the gastrointestinal tract, and thereby injure other organs via malabsorption and intestinal inflammation. We hypothesized that alcohol consumption and subsequent abstinence would change the gut microbiome in adults admitted to a treatment program. Stool and oral specimens, diet data, gastrointestinal assessment scores, anxiety, depression measures and drinking amounts were collected longitudinally for up to 4 weeks in 22 newly abstinent inpatients with AUD who were dichotomized as less heavy drinkers (LHD, <10 drinks/d) and very heavy drinkers (VHD, 10 or more drinks/d). Next-generation 16 S rRNA gene sequencing was performed to measure the gut and oral microbiome at up to ten time points/subject and LHD and VHD were compared for change in principal components, Shannon diversity index and specific genera. The first three principal components explained 46.7% of the variance in gut microbiome diversity across time and all study subjects, indicating the change in gut microbiome following abstinence. The first time point was an outlier in three-dimensional principal component space versus all other time points. The gut microbiota in LHD and VHD were significantly dissimilar in change from day 1 to day 5 (p = .03) and from day 1 to week 3 (p = .02). The VHD drinking group displayed greater change from baseline. The Shannon diversity index of the gut microbiome changed significantly during abstinence in five participants. In both groups, the Shannon diversity was lower in the oral microbiome than gut. Ten total genera were shared between oral and stool in the AUD participants. These data were compared with healthy controls from the Human Microbiome Project to investigate the concept of a core microbiome. Rapid changes in gut microbiome following abstinence from alcohol suggest resilience of the gut microbiome in AUD and reflects the benefits of refraining from the highest levels of alcohol and potential benefits of abstinence.

RevDate: 2020-07-03

Lee SJ (2020)

Commentary on "The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method".

International neurourology journal, 24(2):182-184.

RevDate: 2020-07-03

Ackerman AL, TC Chai (2019)

The Bladder is Not Sterile: an Update on the Urinary Microbiome.

Current bladder dysfunction reports, 14(4):331-341.

Purpose of Review: The article discusses (1) techniques used to study bacterial urinary microbiota; (2) existence of non-bacterial urinary microbiota; (3) associations between changes in urinary microbiota and various benign lower urinary tract disorders.

Recent Findings: Urine harbors a diverse microbial community that resides within it. A multitude of studies have identified differences in these communities associated with urologic conditions, suggesting that microbial communities may maintain normal bladder homeostasis. Technological advances in analytic approaches have improved our understanding of the urinary microbiome. The choice of urine sampling method (voided, catheterized, or aspirated) will significantly influence microbiome findings. Sex and age highly influence urinary microbiota; in addition to rigorous inclusion criteria, microbial studies must be sufficiently powered to overcome the substantial interindividual variability of urinary microbiota. Regardless of these complicating factors, studies have identified microbial patterns correlating with both urologic diagnoses and treatment responses.

Summary: Without a clear understanding of the variability of and exogenous influences on the urinary microbiota in the absence of disease, it has been challenging to reveal the microbial patterns responsible for disease pathophysiology. Host mechanisms in response to the urinary microbiome are also poorly understood. Additional research can address whether the manipulation of urinary microbiota will benefit lower urinary tract health.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )