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16 Jan 2020 at 01:43
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Bibliography on: Microbiome


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RJR: Recommended Bibliography 16 Jan 2020 at 01:43 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: 2020-01-14

O' Donovan CM, Connor B, Madigan SM, et al (2020)

Instances of altered gut microbiomes among Irish cricketers over periods of travel in the lead up to the 2016 World Cup: A sequencing analysis.

Travel medicine and infectious disease pii:S1477-8939(20)30003-X [Epub ahead of print].

BACKGROUND: Changes and stresses experienced during travel have the potential to impact the gut microbiome, with travel implicated in the spread of antibiotic resistance genes across continents. The possibility of gut microbiome-mediated negative impacts arising from travel, and consequences for peak performance, would be of particular concern for elite athletes.

METHODS: Faecal samples were collected from male (N = 14) and female (N = 7) cricket players during the build-up to the 2016 Cricket World Cup. Baseline and post-travel samples were collected from all participants and subjected to 16S rRNA amplicon sequencing. Samples from a subset of participants (N = 4) were analysed by shotgun metagenomic sequencing.

RESULTS: Analysis revealed a single travel time point as having the potential to have an impact on the gut microbiome. Reductions in alpha diversity following travel were observed, accompanied by shifts in the taxonomic profile of the gut microbiome. Antibiotic resistance and virulence genes were also identified as undergoing changes following travel.

CONCLUSIONS: This study reveals that periods of travel, in particular following gastrointestinal distress, may result in gut microbiome disruption. While this analysis was completed in athletes, the findings are applicable to all travelling individuals and considerations should be made surrounding travel in an attempt to reduce these changes.

RevDate: 2020-01-14

Fredensborg BL, Fossdal Í Kálvalíð I, Johannesen TB, et al (2020)

Parasites modulate the gut-microbiome in insects: A proof-of-concept study.

PloS one, 15(1):e0227561 pii:PONE-D-19-25437.

Host-parasite interactions may be modulated by host- or parasite-associated microbes, but the role of these are often overlooked. Particularly for parasites with intestinal stages (either larval or adult), the host gut microbiome may play a key role for parasite establishment; moreover, the microbiome may change in response to invading parasites. Hypothesis testing at the organismal level may be hampered, particularly in mammalian definitive hosts, by ethical, logistical, and economical restrictions. Thus, invertebrates naturally serving as intermediate hosts to parasites with complex life cycles may inform the development of mammalian models as an early-stage host-parasite model. In addition, several important pathogens are vectored by insects, and insect gut microbiome-pathogen interactions may provide essential base-line knowledge, which may be used to control vectorborne pathogens. Here, we used the grain beetle, Tenebrio molitor, a host of the tapeworm Hymenolepis diminuta, to explore interactions between infection status and resident gut microbiota at two pre-determined time points (day two and seven) post infection. Using 16S/18S microbial profiling, we measured key parameters of the composition, relative abundance, and diversity of the host gut bacteriome and mycobiome. In addition, we quantified the systemic beetle immune response to infection by Phenoloxidase activity and hemocyte abundance. We found significant changes in the gut bacteriome and mycobiome in relation to infection status and beetle age. Thus, the relative abundance of Proteobacteria was significantly higher in the gut of infected beetles and driven mostly by an increased abundance of Acinetobacter. In addition, the mycobiome was less abundant in infected beetles but maintained higher Shannon diversity in infected compared with non-infected beetles. Beetles treated with a broad-spectrum antibiotic (Tetracycline) exhibited significantly reduced parasite establishment compared with the untreated control group, indicating that the host microbiome may greatly influence hatching of eggs and subsequent establishment of H. diminuta larvae. Our results suggest that experimental work using invertebrates may provide a platform for explorative studies of host-parasite-microbe interactions and their underlying mechanisms.

RevDate: 2020-01-14

Simon H, Vartanian V, Wong MH, et al (2020)

OGG1 deficiency alters the intestinal microbiome and increases intestinal inflammation in a mouse model.

PloS one, 15(1):e0227501 pii:PONE-D-19-24784.

OGG1-deficient (Ogg1-/-) animals display increased propensity to age-induced and diet-induced metabolic diseases, including insulin resistance and fatty liver. Since the intestinal microbiome is increasingly understood to play a role in modulating host metabolic responses, we examined gut microbial composition in Ogg1-/- mice subjected to different nutritional challenges. Interestingly, Ogg1-/- mice had a markedly altered intestinal microbiome under both control-fed and hypercaloric diet conditions. Several microbial species that were increased in Ogg1-/- animals were associated with increased energy harvest, consistent with their propensity to high-fat diet induced weight gain. In addition, several pro-inflammatory microbes were increased in Ogg1-/- mice. Consistent with this observation, Ogg1-/- mice were significantly more sensitive to intestinal inflammation induced by acute exposure to dextran sulfate sodium. Taken together, these data indicate that in addition to their proclivity to obesity and metabolic disease, Ogg1-/- mice are prone to colonic inflammation. Further, these data point to alterations in the intestinal microbiome as potential mediators of the metabolic and intestinal inflammatory response in Ogg1-/- mice.

RevDate: 2020-01-14

Nel Van Zyl K, Whitelaw AC, M Newton-Foot (2020)

The effect of storage conditions on microbial communities in stool.

PloS one, 15(1):e0227486 pii:PONE-D-19-27079.

Microbiome research has experienced a surge of interest in recent years due to the advances and reduced cost of next-generation sequencing technology. The production of high quality and comparable data is dependent on proper sample collection and storage and should be standardized as far as possible. However, this becomes challenging when samples are collected in the field, especially in resource-limited settings. We investigated the impact of different stool storage methods common to the TB-CHAMP clinical trial on the microbial communities in stool. Ten stool samples were subjected to DNA extraction after 48-hour storage at -80°C, room temperature and in a cooler-box, as well as immediate DNA extraction. Three stool DNA extraction kits were evaluated based on DNA yield and quality. Quantitative PCR was performed to determine the relative abundance of the two major gut phyla Bacteroidetes and Firmicutes, and other representative microbial groups. The bacterial populations in the frozen group closely resembled the immediate extraction group, supporting previous findings that storage at -80°C is equivalent to the gold standard of immediate DNA extraction. More variation was seen in the room temperature and cooler-box groups, which may be due to the growth temperature preferences of certain bacterial populations. However, for most bacterial populations, no significant differences were found between the storage groups. As seen in other microbiome studies, the variation between participant samples was greater than that related to differences in storage. We determined that the risk of introducing bias to microbial community profiling through differences in storage will likely be minimal in our setting.

RevDate: 2020-01-14

Kashef MT, RK Aziz (2020)

Drug Factory Microbiome: Top Three Actionable Challenges and Prospects.

Omics : a journal of integrative biology, 24(1):55-56.

RevDate: 2020-01-14

El Hage R, Hernandez-Sanabria E, Calatayud Arroyo M, et al (2020)

Supplementation of a propionate-producing consortium improves markers of insulin resistance in an in vitro model of gut-liver axis.

American journal of physiology. Endocrinology and metabolism [Epub ahead of print].

Gut-liver crosstalk is an important determinant of human health with profound effects on energy homeostasis. While gut microbes produce a huge range of metabolites, specific compounds such as short chain fatty acids (SCFA) can enter the portal circulation and reach the liver, a central organ involved in glucose homeostasis and diabetes control. Propionate is a major SCFA involved in activation of intestinal gluconeogenesis (IGN), thereby regulating food intake, enhancing insulin sensitivity and leading to metabolic homeostasis. Although microbiome modulating strategies may target the increased microbial production of propionate, it is not clear whether such effect spreads through to the hepatic cellular level. Here, we designed a propionate-producing consortium using a selection of commensal gut bacteria, and we investigated how their delivered metabolites impact an in vitro enterohepatic model of insulin resistance. Glycogen storage on hepatocyte-like cells and inflammatory markers associated with insulin resistance were evaluated to understand the role of gut metabolites on gut-liver crosstalk in a simulated scenario of insulin resistance. The metabolites produced by our consortium increased glycogen synthesis by approximately 57% and decreased pro-inflammatory markers such as IL-8 by 12%, thus elucidating the positive effect of our consortium on metabolic function and low-grade inflammation. Our results suggest that microbiota-derived products can be a promising multipurpose strategy to modulate energy homeostasis, with potential ability to assist in managing metabolic diseases due to their adaptability.

RevDate: 2020-01-14

Sviridova AA, Kabaeva AR, Rogovskii VS, et al (2019)

[Norepinephrine and intestinal microbiome in the early stages of demyelination: clinical-immunological parallels].

Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova, 119(10. Vyp. 2):28-34.

Biogenic amines are key mediators of neuroimmune interaction and may influence on multiple sclerosis (MS) pathogenesis and MS course. At the same time, the role of biogenic amines in immunoregulation of early stages of demyelination, in particular clinically isolated syndrome (CIS) and radiologically isolated syndrome (RIS) is still unclear. This literature review addresses a role of norepinephrine in the regulation of neuroimmune interactions in the early stages of the demyelination. Neuropsychological disorders, immunological characteristics, gut-brain axis as well as the role of norepinephrine in these interactions in patients with CIS, RIS and early MS are discussed.

RevDate: 2020-01-14

Da Silva CC, Monteil MA, EM Davis (2020)

Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota.

Childhood obesity (Print) [Epub ahead of print].

Background: Obesity in children continues to be a global epidemic. Given the recent focus on the potential role gut microbiota play in the development of obesity and the continuous rise of obesity in childhood worldwide, it has become necessary that the association between gut microbes and weight is explored in previously unexplored regions such as the Caribbean island of Trinidad. As such, our objective was to characterize the composition of the gut microbiota in children with obesity/overweight and children of normal weight to determine if there are any gut microbes associated with overweight and obesity. Methods: Fifty-one children provided stool samples and their BMIs were calculated and classified. 16S amplicons from stool samples were individually barcoded and sequenced in multiplex in the NextSeq 500 platform in a 150 bp paired-end modality and a complete gut microbiome profile was generated. Results: The relative abundance and diversity of the microbiota of the lean and children with obesity/overweight were analyzed against each other and showed that children with obesity/overweight recorded significantly more (p = 0.001) Firmicutes and significantly less Bifidobacterium (p = 0.039) than the children of normal weight. Children with obesity/overweight also recorded significantly (p = 0.009) reduced alpha diversity compared with the lean children. Conclusion: This study has shown associations of Firmicutes to obesity/overweight and Bifidobacterium species with healthy weight in children.

RevDate: 2020-01-14

Orłowska A, Iwan E, Smreczak M, et al (2019)

Evaluation of Direct Metagenomics and Target Enriched Approaches for High-throughput Sequencing of Field Rabies Viruses.

Journal of veterinary research, 63(4):471-479 pii:jvetres-2019-0067.

Introduction: High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs).

Material and Methods: The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes.

Results: Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71.

Conclusion: Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.

RevDate: 2020-01-14

Aden K, W Reindl (2019)

The Gut Microbiome in Inflammatory Bowel Diseases: Diagnostic and Therapeutic Implications.

Visceral medicine, 35(6):332-337.

The incidence of chronic inflammatory bowel diseases (IBD) is rising worldwide, and the interaction between the mucosal immune system and the intestinal microbiota is crucial for the understanding of these diseases. Due to new technologies, the data published on the intestinal microbiota has increased rapidly in the recent years. While many findings are descriptive, reporting associations between disease and microbial populations, recent advancement in technology made it possible to ask and answer more functional questions and to elucidate complex interactions between the intestinal microbiota and the mucosal immune system. In addition, first trials influenced the intestinal microbiota with the intention to treat IBD. This review summarizes aspects of the physiological function as well as the inflammation-induced changes of the gut microbiota and the association between the gut microbiota and pathogenesis in IBD. In addition, diagnostic and therapeutic options for treating IBD are reviewed.

RevDate: 2020-01-14

Hadadi N, Pandey V, Chiappino-Pepe A, et al (2020)

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models.

NPJ systems biology and applications, 6:1 pii:121.

Understanding the adaptive responses of individual bacterial strains is crucial for microbiome engineering approaches that introduce new functionalities into complex microbiomes, such as xenobiotic compound metabolism for soil bioremediation. Adaptation requires metabolic reprogramming of the cell, which can be captured by multi-omics, but this data remains formidably challenging to interpret and predict. Here we present a new approach that combines genome-scale metabolic modeling with transcriptomics and exometabolomics, both of which are common tools for studying dynamic population behavior. As a realistic demonstration, we developed a genome-scale model of Pseudomonas veronii 1YdBTEX2, a candidate bioaugmentation agent for accelerated metabolism of mono-aromatic compounds in soil microbiomes, while simultaneously collecting experimental data of P. veronii metabolism during growth phase transitions. Predictions of the P. veronii growth rates and specific metabolic processes from the integrated model closely matched experimental observations. We conclude that integrative and network-based analysis can help build predictive models that accurately capture bacterial adaptation responses. Further development and testing of such models may considerably improve the successful establishment of bacterial inoculants in more complex systems.

RevDate: 2020-01-14

Yu W, Gao D, Wang Z, et al (2019)

Probiotics alleviate cognitive dysfunction associated with neuroinflammation in cardiac surgery.

American journal of translational research, 11(12):7614-7626.

Neuroinflammation plays a key role in the progression and pathogenesis of postoperative cognitive dysfunction, but it does not always occur in the local response to primary injury. In this study, we revealed that probiotics alleviate cognitive dysfunction associated with neuroinflammation in cardiac surgery. Rats were administered a probiotic or placebo once a day by gavage for 2 weeks until the day of surgery. Cardiac surgery was induced by ischemia/reperfusion of the left coronary artery. Key factors, such as the gut microbiome, the gut barrier and the blood-brain barrier (BBB), were systematically investigated to determine whether changes in the gut microbiome lead to neuroinflammation. We used 16S rDNA sequencing to confirm that cardiac surgery induced intestinal flora dysbiosis by altering the number of organisms rather than the structure in the cecum microbiome, which occurs at the same time as damage to the gut barrier. Cardiac surgery also increased BBB permeability, suggesting that disruption of the microbiome may increase the likelihood of neuroinflammation. Probiotics-induced alterations in the intestinal flora significantly reduced the level of inflammatory cytokines (IL-6 and IL-1β). Importantly, we found that the administration of probiotics significantly improved spatial memory impairment in rats after cardiac surgery, as measured by the Morris water maze. Overall, dysbiosis of the gut flora may aggravate cognitive impairment associated with neuroinflammation after cardiac surgery, and probiotics may attenuate this effect.

RevDate: 2020-01-14

Shi TT, Hua L, Wang H, et al (2019)

The Potential Link between Gut Microbiota and Serum TRAb in Chinese Patients with Severe and Active Graves' Orbitopathy.

International journal of endocrinology, 2019:9736968.

Background and Objective: A previous study reported alterations in the intestinal microbiota in patients with Graves' orbitopathy (GO). Thyrotropin receptor autoantibody (TRAb) stimulates orbital and periorbital tissues and plays a pivotal role in the development of GO. However, the association between gut microbiota and TRAb in GO patients has still remained elusive. In this study, we explored the relationships between gut microbiota and GO-related traits, in which we applied a metabolic-network-driven analysis to identify GO trait-related modules and extracted significant operational taxonomic units (OTUs).

Methods: In the present study, we profiled gut microbiota using 16S rRNA gene sequencing in 31 GO patients. We performed metabolic-network-driven analysis to investigate the association between gut microbiota and GO-related traits (e.g., TRAb, TGAb, and TPOAb) in the combination of microbial effects.

Results: Applying microbiome network analysis of cooccurrence patterns and analysis of topological properties, we found that s_Prevotella_copri and f_Prevotellaceae showed a significant correlation with TRAb. In particular, we applied the latent class model to explore the association between gut microbiota and GO-related traits in the combination of microbial effects. It was revealed that the subjects involved in the latent class model with the higher abundance of s_Prevotella_copri and g_Bacteroides had a higher TRAb level.

Conclusions: Our results revealed the potential relationships between gut microbiota and GO-related traits in the combination of microbial effects. This study may provide a new insight into the interaction between the intestinal microbiota and TRAb-associated immune responses in GO patients.

RevDate: 2020-01-14

Charlesworth RP (2020)

Diagnosing coeliac disease: Out with the old and in with the new?.

World journal of gastroenterology, 26(1):1-10.

Coeliac disease (CD) is a complex condition resulting from an interplay between genetic and environmental factors. When diagnosing the condition, serological testing and genotyping are useful in excluding CD, although the gold standard of testing is currently histopathological examination of the small intestine. There are drawbacks associated with this form of testing however and because of this, novel forms of testing are currently under investigation. Before we develop completely novel tests though, it is important to ask whether or not we can simply use the data we gather from coeliac patients more effectively and build a more accurate snapshot of CD through statistical analysis of combined metrics. It is clear that not one single test can accurately diagnose CD and it is also clear that CD patients can no longer be defined by discrete classifications, the continuum of patient presentation needs to be recognised and correctly captured to improve diagnostic accuracy. This review will discuss the current diagnostics for CD and then outline novel diagnostics under investigation for the condition. Finally, improvements to current protocols will be discussed with the need for a holistic "snapshot" of CD using a number of metrics simultaneously.

RevDate: 2020-01-14

Liu J, Lahousse L, Nivard MG, et al (2020)

Integration of epidemiologic, pharmacologic, genetic and gut microbiome data in a drug-metabolite atlas.

Nature medicine, 26(1):110-117.

Progress in high-throughput metabolic profiling provides unprecedented opportunities to obtain insights into the effects of drugs on human metabolism. The Biobanking BioMolecular Research Infrastructure of the Netherlands has constructed an atlas of drug-metabolite associations for 87 commonly prescribed drugs and 150 clinically relevant plasma-based metabolites assessed by proton nuclear magnetic resonance. The atlas includes a meta-analysis of ten cohorts (18,873 persons) and uncovers 1,071 drug-metabolite associations after evaluation of confounders including co-treatment. We show that the effect estimates of statins on metabolites from the cross-sectional study are comparable to those from intervention and genetic observational studies. Further data integration links proton pump inhibitors to circulating metabolites, liver function, hepatic steatosis and the gut microbiome. Our atlas provides a tool for targeted experimental pharmaceutical research and clinical trials to improve drug efficacy, safety and repurposing. We provide a web-based resource for visualization of the atlas (http://bbmri.researchlumc.nl/atlas/).

RevDate: 2020-01-14

Gunasekera DC, Ma J, Vacharathit V, et al (2020)

The development of colitis in Il10-/- mice is dependent on IL-22.

Mucosal immunology pii:10.1038/s41385-019-0252-3 [Epub ahead of print].

Mice deficient in the IL-10 pathway are the most widely used models of intestinal immunopathology. IL-17A is strongly implicated in gut disease in mice and humans, but conflicting evidence has drawn IL-17's role in the gut into question. IL-22 regulates antimicrobial and repair activities of intestinal epithelial cells (IECs) and is closely associated with IL-17A responses but it's role in chronic disease is uncertain. We report that IL-22, like IL-17A, is aberrantly expressed in colitic Il10-/- mice. While IL-22+ Th17 cells were elevated in the colon, IL-22-producing ILC3s were highly enriched in the small intestines of Il10-/- mice. Remarkably, Il10-/-Il22-/- mice did not develop colitis despite retaining high levels of Th17 cells and remaining colonized with colitogenic Helicobacter spp. Accordant with IL-22-induced IEC proliferation, the epithelia hyperplasia observed in Il10-/- animals was reversed in Il10-/-Il22-/- mice. Also, the high levels of antimicrobial IL-22-target genes, including Reg3g, were normalized in Il10-/-Il22-/- mice. Consistent with a heightened antimicrobial environment, Il10-/- mice had reduced diversity of the fecal microbiome that was reestablished in Il10-/-Il22-/- animals. These data suggest that spontaneous colitis in Il10-/- mice is driven by IL-22 and implicates an underappreciated IL-10/IL-22 axis in regulating intestinal homeostasis.

RevDate: 2020-01-14

Boling L, Cuevas DA, Grasis JA, et al (2020)

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome.

Gut microbes [Epub ahead of print].

The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.

RevDate: 2020-01-13

Paniagua AT, Paranjape K, Hu M, et al (2019)

Impact of temperature on Legionella pneumophila, its protozoan host cells, and the microbial diversity of the biofilm community of a pilot cooling tower.

The Science of the total environment, 712:136131 pii:S0048-9697(19)36127-3 [Epub ahead of print].

Legionella pneumophila is a waterborne bacterium known for causing Legionnaires' Disease, a severe pneumonia. Cooling towers are a major source of outbreaks, since they provide ideal conditions for L. pneumophila growth and produce aerosols. In such systems, L. pneumophila typically grow inside protozoan hosts. Several abiotic factors such as water temperature, pipe material and disinfection regime affect the colonization of cooling towers by L. pneumophila. The local physical and biological factors promoting the growth of L. pneumophila in water systems and its spatial distribution are not well understood. Therefore, we built a lab-scale cooling tower to study the dynamics of L. pneumophila colonization in relationship to the resident microbiota and spatial distribution. The pilot was filled with water from an operating cooling tower harboring low levels of L. pneumophila. It was seeded with Vermamoeba vermiformis, a natural host of L. pneumophila, and then inoculated with L. pneumophila. After 92 days of operation, the pilot was disassembled, the water was collected, and biofilm was extracted from the pipes. The microbiome was studied using 16S rRNA and 18S rRNA genes amplicon sequencing. The communities of the water and of the biofilm were highly dissimilar. The relative abundance of Legionella in water samples reached up to 11% whereas abundance in the biofilm was extremely low (≤0.5%). In contrast, the host cells were mainly present in the biofilm. This suggests that L. pneumophila grows in host cells associated with biofilm and is then released back into the water following host cell lysis. In addition, water temperature shaped the bacterial and eukaryotic community of the biofilm, indicating that different parts of the systems may have different effects on Legionella growth.

RevDate: 2020-01-13

Radulescu CI, Garcia-Miralles M, Sidik H, et al (2020)

Reprint of: Manipulation of microbiota reveals altered callosal myelination and white matter plasticity in a model of Huntington disease.

Neurobiology of disease pii:S0969-9961(20)30019-X [Epub ahead of print].

Structural and molecular myelination deficits represent early pathological features of Huntington disease (HD). Recent evidence from germ-free (GF) animals suggests a role for microbiota-gut-brain bidirectional communication in the regulation of myelination. In this study, we aimed to investigate the impact of microbiota on myelin plasticity and oligodendroglial population dynamics in the mixed-sex BACHD mouse model of HD. Ultrastructural analysis of myelin in the corpus callosum revealed alterations of myelin thickness in BACHD GF compared to specific-pathogen free (SPF) mice, whereas no differences were observed between wild-type (WT) groups. In contrast, myelin compaction was altered in all groups when compared to WT SPF animals. Levels of myelin-related proteins were generally reduced, and the number of mature oligodendrocytes was decreased in the prefrontal cortex under GF compared to SPF conditions, regardless of genotype. Minor differences in commensal bacteria at the family and genera levels were found in the gut microbiota of BACHD and WT animals housed in standard living conditions. Our findings indicate complex effects of a germ-free status on myelin-related characteristics, and highlight the adaptive properties of myelination as a result of environmental manipulation.

RevDate: 2020-01-13

Casals-Pascual C, González A, Vázquez-Baeza Y, et al (2020)

Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations: Statistical Power for Microbiome Studies.

RevDate: 2020-01-13

Li HZ, Li N, Wang JJ, et al (2019)

Dysbiosis of gut microbiome affecting small intestine morphology and immune balance: a rhesus macaque model.

Zoological research, 41(1):20-31.

There is a growing appreciation for the specific health benefits conferred by commensal microbiota on their hosts. Clinical microbiota analysis and animal studies in germ-free or antibiotic-treated mice have been crucial for improving our understanding of the role of the microbiome on the host mucosal surface; however, studies on the mechanisms involved in microbiome-host interactions remain limited to small animal models. Here, we demonstrated that rhesus monkeys under short-term broad-spectrum antibiotic treatment could be used as a model to study the gut mucosal host-microbiome niche and immune balance with steady health status. Results showed that the diversity and community structure of the gut commensal bacteria in rhesus monkeys were both disrupted after antibiotic treatment. Furthermore, the 16S rDNA amplicon sequencing results indicated that Escherichia-Shigella were predominant in stool samples 9 d of treatment, and the abundances of bacterial functional genes and predicted KEGG pathways were significantly changed. In addition to inducing aberrant morphology of small intestinal villi, the depletion of gut commensal bacteria led to increased proportions of CD3 + T, CD4 + T, and CD16 + NK cells in peripheral blood mononuclear cells (PBMCs), but decreased numbers of Treg and CD20 + B cells. The transcriptome of PBMCs from antibiotic-treated monkeys showed that the immune balance was affected by modulation of the expression of many functional genes, including IL-13, VCAM1, and LGR4.

RevDate: 2020-01-13

Judkins TC, Archer DL, Kramer DC, et al (2020)

Probiotics, Nutrition, and the Small Intestine.

Current gastroenterology reports, 22(1):2 pii:10.1007/s11894-019-0740-3.

PURPOSE OF REVIEW: Probiotics are promising remedial treatments for symptoms of small intestine (SI) diseases and promoters of overall good health. Probiotics play an important role in supporting a healthy SI microbiome (eubiosis), and in preventing establishment of unhealthy microbiota. SI eubiosis promotes optimal nutrient uptake, and optimal nutritional status maintains a healthy SI, reducing the likelihood of SI diseases. It is important to understand the advantages and limitations of probiotic therapies.

RECENT FINDINGS: Microbial dysbiosis decreases the capacity of the small bowel to utilize and absorb dietary compounds. In some studies, probiotic supplements containing lactic acid bacteria and Bifidobacterium have been demonstrated effective in supporting beneficial microbes in the SI while improving barrier integrity and reducing nutrient malabsorption and SI disease-related pathology. Strain-specific probiotic therapy may be a natural and effective approach to restoring SI barrier integrity and eubiosis, resulting in improved nutrient absorption and better health, including reducing the incidence of and severity of SI diseases.

RevDate: 2020-01-13

Ghaly S, Kaakoush NO, PH Hart (2020)

Effects of UVR exposure on the gut microbiota of mice and humans.

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology [Epub ahead of print].

Many alterations to the skin microbiome by exposure to UV radiation (UVR) have been postulated and may contribute to the ability of UVR phototherapy to regulate skin inflammatory diseases. Very recently, an effect of sub-erythemal narrowband UVB radiation (311 nm) on the gut microbiome of healthy individuals was reported. The relative abundance of Firmicutes and Proteobacteria increased in faecal samples of those receiving three exposures to narrowband UVB radiation; the Bacteroidetes phyla were reduced by UVB. In mice chronically exposed to sub-erythemal broadband UVR, similar faecal changes in Firmicutes and Bacteroidetes have been reported. Murine studies have allowed a further dissection of the relative ability of UVR and dietary vitamin D to modulate the gut microbiome by analysis of relative bacterial abundance in mice with similar 25-hydroxy vitamin D levels obtained by UVR exposure or from their diet, respectively. The studies of mice recovering from colitis suggested that dietary vitamin D could stimulate greater faecal abundance of Rikenellaceae, whilst exposure to UVR was necessary for changes to the abundance of Lachnospiraceae and Desulfovibrionaceae. Both human and murine studies report that multiple exposures to sub-erythemal UVR can increase the diversity of the gut microbiome, which in turn may be beneficial to the health of the host.

RevDate: 2020-01-13

Stollman N, Picchio M, Biondo S, et al (2020)

Critical Issues on Diverticular Disease.

Journal of gastrointestinal and liver diseases : JGLD, 28 suppl.1:35-38.

In this session diverse critical issues in diverticular disease were considered, including "In or outpatient management of uncomplicated diverticulitis?", "Segmental colitis associated with diverticulosis: what is it?"and "Diverticular inflammation is a risk factor for colorectal cancer?". The conclusions drawn are outlined in the statements but in summary, outpatient management is safe in selected patients, as long as correct diagnosis and stage are assured, and this can allow a cost effective treatment. Non-antibiotic management is also safe but should be confined as an outpatient treatment in carefully selected patients. Segmental colitis associated with diverticulosis (SCAD) is a defined pathological entity (only diagnosed on biopsy) characterized by an inflammatory bowel disease-like pathology, occurring principally in the sigmoid colon, with rectal and right colon sparing. The pathogenesis is unclear but may include a genetic predisposition, microbiome alteration and ischaemia. Treatment can last months, and depends on severity, options include antibiotics, 5 ASA and probiotics for mild cases. Severe disease needs systemic steroids or even anti TNFα treatment. Whether diverticular inflammation is a risk factor for colorectal cancer was debated and the conclusion that within the first eighteen months of diagnosis of diverticular disease associations with cancer are found, likely due to similar symptoms and misclassification of disease. After that time, diverticular disease does not increase the risk of colorectal cancer. Therefore, this is recommended to exclude cancer with imaging and colonoscopy after healing of the first episode of diverticulitis.

RevDate: 2020-01-13

Coryell M, Roggenbeck BA, ST Walk (2019)

The Human Gut Microbiome's Influence on Arsenic Toxicity.

Current pharmacology reports, 5(6):491-504.

Purpose of Review: Arsenic exposure is a public health concern of global proportions with a high degree of interindividual variability in pathologic outcomes. Arsenic metabolism is a key factor underlying toxicity, and the primary purpose of this review is to summarize recent discoveries concerning the influence of the human gut microbiome on the metabolism, bioavailability, and toxicity of ingested arsenic. We review and discuss the current state of knowledge along with relevant methodologies for studying these phenomena.

Recent Findings: Bacteria in the human gut can biochemically transform arsenic-containing compounds (arsenicals). Recent publications utilizing culture-based approaches combined with analytical biochemistry and molecular genetics have helped identify several arsenical transformations by bacteria that are at least possible in the human gut and are likely to mediate arsenic toxicity to the host. Other studies that directly incubate stool samples in vitro also demonstrate the gut microbiome's potential to alter arsenic speciation and bioavailability. In vivo disruption or elimination of the microbiome has been shown to influence toxicity and body burden of arsenic through altered excretion and biotransformation of arsenicals. Currently, few clinical or epidemiological studies have investigated relationships between the gut microbiome and arsenic-related health outcomes in humans, although current evidence provides strong rationale for this research in the future.

Summary: The human gut microbiome can metabolize arsenic and influence arsenical oxidation state, methylation status, thiolation status, bioavailability, and excretion. We discuss the strength of current evidence and propose that the microbiome be considered in future epidemiologic and toxicologic studies of human arsenic exposure.

RevDate: 2020-01-13

Xin Y, Diling C, Tianlu C, et al (2019)

Oligosaccharides from Morinda officinalis Slow the Progress of Aging Mice by Regulating the Key Microbiota-Metabolite Pairs.

Evidence-based complementary and alternative medicine : eCAM, 2019:9306834.

The gut microbiota is considered an important factor in the progression of Alzheimer's disease (AD). Active research on the association between the metabolome and the gut microbiome is ongoing and can provide a large amount of beneficial information about the interactions between the microbiome and the metabolome. Previous studies have shown that the oligosaccharides from Morinda officinalis (OMO) can delay the progress of AD in model animals by regulating the diversity of the gut microbiome and metabolic components, and the correlation between the gut microbiome and metabolic components still needs to be further verified. This study applied a new two-level strategy to investigate and ensure the accuracy and consistency of the results. This strategy can be used to determine the association between the gut microbiome and serum metabolome in APP/PS1 transgenic mice and C57BL/6J male mice. The "4C0d-2 spp.-Cholesterol," "CW040 spp.-L-valine," "CW040 spp.-L-acetylcarnitine," "RF39 spp.-L-valine," "TM7-3 spp.-L-valine," and "TM7-3 spp.-L-acetylcarnitine" associations among specific "microbiota-metabolite" pairs were further identified based on univariate and multivariate correlation analyses and functional analyses. The key relevant pairs were verified by an independent oligosaccharide intervention study, and the gut microbiome and serum metabolome of the OMO intervention group were similar to those of the normal group. The results indicate that OMO can significantly suppress Alzheimer's disease by regulating the key microbiota-metabolite pairs. Therefore, this two-level strategy is effective in identifying the principal correlations in large datasets obtained from combinations of multiomic studies and further enhancing our understanding of the correlation between the brain and gut in patients with AD.

RevDate: 2020-01-13

Chen WS, Huang S, Plugge CM, et al (2020)

Concurrent use of methanol and ethanol for chain-elongating short chain fatty acids into caproate and isobutyrate.

Journal of environmental management, 258:110008 pii:S0301-4797(19)31726-8 [Epub ahead of print].

Microbial chain elongation (MCE) is a bioprocess that could utilise a mixed-culture fermentation to valorise organic waste. MCE converting ethanol and short chain fatty acids (SCFA; derived from organic waste) to caproate has been studied extensively and implemented. Recent studies demonstrated the conversion of SCFAs and methanol or ethanol into isomerised fatty acids as novel products, which may expand the MCE application and market. Integrating caproate and isomerised fatty acid production in one reactor system is theoretically feasible given the employment of a mixed culture and may increase the economic competence of MCE; however, the feasibility of such has never been demonstrated. This study investigated the feasibility of using two electron donors, i.e. methanol and ethanol, for upgrading SCFAs into isobutyrate and caproate concurrently in MCE Results show that supplying methanol and ethanol in MCE simultaneously converted acetate and/or butyrate into caproate and isobutyrate, by a mixed-culture microbiome. The butyrate supplement stimulated the caproate production rate from 1.5 to 2.6 g/L.day and induced isobutyrate production (1.5 g/L.day). Further increasing ethanol feeding rate from 140 to 280 mmol carbon per litre per day enhanced the direct use of butyrate for caproate production, which improved the caproate production rate to 5.9 g/L.day. Overall, the integration of two electron donors, i.e. ethanol and methanol, in one chain-elongation reactor system for upgrading SCFAs was demonstrated. As such, MCE could be applied to valorise organic waste (water) streams into a wider variety of value-added biochemical.

RevDate: 2020-01-13

Zeisel SH (2020)

Precision (Personalized) Nutrition: Understanding Metabolic Heterogeneity.

Annual review of food science and technology [Epub ahead of print].

People differ in their requirements for and responses to nutrients and bioactive molecules in the diet. Many inputs contribute to metabolic heterogeneity (including variations in genetics, epigenetics, microbiome, lifestyle, diet intake, and environmental exposure). Precision nutrition is not about developing unique prescriptions for individual people but rather about stratifying people into different subgroups of the population on the basis of biomarkers of the above-listed sources of metabolic variation and then using this stratification to better estimate the different subgroups' dietary requirements, thereby enabling better dietary recommendations and interventions. The hope is that we will be able to subcategorize people into ever-smaller groups that can be targeted in terms of recommendations, but we will never achieve this at the individual level, thus, the choice of precision nutrition rather than personalized nutrition to designate this new field. This review focuses mainly on genetically related sources of metabolic heterogeneity and identifies challenges that need to be overcome to achieve a full understanding of the complex interactions between the many sources of metabolic heterogeneity that make people differ from one another in their requirements for and responses to foods. It also discusses the commercial applications of precision nutrition. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 11 is March 25, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

RevDate: 2020-01-13

Lazado CC (2020)

The 1st international symposium on mucosal health in aquaculture - MHA2019.

Tissue barriers [Epub ahead of print].

The 1st International Symposium on Mucosal Health and Aquaculture (MHA2019) was held on 11-13 September 2019 in Oslo, Norway. This was the first platform of its kind that gathered people from academia, R&D institutes, and industry to discuss the state-of-the-art and future directions of mucosal health research in aquaculture. The symposium was divided into four scientific sessions: Session 1, Mucosal structures and functions; Session 2, Mucosal health and nutrition; Session 3, Mucosal health and microbiome; and Session 4, Mucosal health and the changing environment. A plenary talk from a prominent authority in the field opened each session. The papers presented at MHA2019 exemplified the dynamic evolution of the field of mucosal health in aquaculture - from an area solely explored from an immunological aspect about 20 years ago, to the multidisciplinary field it is today. Moreover, papers presented highlighted the complementary application of both classical (e.g., histology) and modern platforms (e.g., omics, artificial intelligence) to characterize mucosal health. The interactive discussion during the meeting underscored the importance of mucosal health research in modern aquaculture and collectively emphasized the role of both fundamental and applied approaches in advancing this timely and highly relevant field. The symposium was organized by Nofima, The Norwegian Institute of Food, Fisheries, and Aquaculture Research, with support from the Research Council of Norway.

RevDate: 2020-01-13

Bowerman KL, Varelias A, Lachner N, et al (2020)

Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice.

Gut microbes [Epub ahead of print].

Objective: The gut microbiome plays a key role in the development of acute graft-versus-host disease (GVHD) following allogeneic hematopoietic stem cell transplantation. Here we investigate the individual contribution of the pre- and post-transplant gut microbiome to acute GVHD using a well-studied mouse model.Design: Wild-type mice were cohoused with IL-17RA-/ - mice, susceptible to hyperacute GVHD, either pre- or post-transplant alone or continuously (i.e., pre- and post-transplant). Fecal samples were collected from both WT and IL-17RA-/ - mice pre- and post-cohousing and post-transplant and the microbiome analyzed using metagenomic sequencing.Results: Priming wild-type mice via cohousing pre-transplant only is insufficient to accelerate GVHD, however, accelerated disease is observed in WT mice cohoused post-transplant only. When mice are cohoused continuously, the effect of priming and exacerbation is additive, resulting in a greater acceleration of disease in WT mice beyond that seen with cohousing post-transplant only. Metagenomic analysis of the microbiome revealed pre-transplant cohousing is associated with the transfer of specific species within two as-yet-uncultured genera of the bacterial family Muribaculaceae; CAG-485 and CAG-873. Post-transplant, we observed GVHD-associated blooms of Enterobacteriaceae members Escherichia coli and Enterobacter hormaechei subsp. steigerwaltii, and hyperacute GVHD gut microbiome distinct from that associated with delayed-onset disease (>10 days post-transplant).Conclusion: These results clarify the importance of the peri-transplant microbiome in the susceptibility to acute GVHD post-transplant and demonstrate the species-specific nature of this association.

RevDate: 2020-01-13

Ye Z, Wu C, Zhang N, et al (2020)

Altered gut microbiome composition in patients with Vogt-Koyanagi-Harada disease.

Gut microbes [Epub ahead of print].

Background: Vogt-Koyanagi-Harada (VKH) disease is a multisystemic autoimmune disorder characterized by granulomatous panuveitis. Gut microbiome has been considered to play a role in the pathogenesis of this disease but whether the alternation of gut microbiome was involved is unclear. This study was set up to identify abnormalities of gut microbiome composition in VKH disease.Results: Depleted butyrate-producing bacteria, lactate-producing bacteria and methanogens as well as enriched Gram-negative bacteria were identified in the active VKH patients, as well as in VKH patients of Mix enterotype and Bacteroides enterotype. Changes of gut microbiome in the VKH patients were partially restored after an immunosuppressive treatment. The disease susceptibility genotype HLA-DRA was associated with Bacteroides sp.2.1.33B, Paraprevotella clara, Alistipes finegoldii and Eubacterium eligens. A microbial marker profile including 40 disease-associated species was established to differentiate patients from controls. Another microbial marker profile including 37 species was found to be associated with the response to treatment. An animal experiment showed that transfer of gut microbiome from VKH patients could significantly exacerbate disease activity clinically and pathologically in the recipient mice.Conclusion: Our results revealed a distinct gut microbiome signature in VKH patients and showed an exacerbating effect of this gut microbiome on experimental autoimmune uveitis (EAU). We also developed two microbial marker profiles in differentiating VKH patients from healthy controls as well as predicting the effectiveness of treatment.

RevDate: 2020-01-13

Zemb O, Achard CS, Hamelin J, et al (2020)

Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard.

MicrobiologyOpen [Epub ahead of print].

Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.

RevDate: 2020-01-13

Bardanzellu F, Peroni DG, V Fanos (2020)

Human Breast Milk: Bioactive Components, from Stem Cells to Health Outcomes.

Current nutrition reports pii:10.1007/s13668-020-00303-7 [Epub ahead of print].

PURPOSE OF REVIEW: Breast milk (BM) is a peculiar fluid owing unique properties and resulting the ideal food during early neonatal period. As widely known, it can improve the outcome of both neonate and lactating mother, influencing their whole life. BM is characterized by several beneficial components; among these, a great role is played by BM own and specific microbiome, deeply investigated in many studies. Moreover, the use of metabolomics in BM analysis allowed a better characterization of its metabolic pathways that vary according to lactation stage and neonatal gestational age. The aim of this review is to describe growth factors, cytokines, immunity mediators, and stem cells (SCs) contained in BM and investigate their functions and effects on neonatal outcome, especially focusing on immuno- and neurodevelopment.

RECENT FINDINGS: We evaluated recent and updated literature on this field. The article that we analyzed to write this review have been found in MEDLINE using breast milk-derived stem cells, biofactors, growth factors, breastfeeding-related outcomes, neurodevelopment, and neonatal immunological system as keywords. Discovering and characterizing BM components could result very useful to clarify the pathophysiology of their influence on neonatal growth and even to improve artificial formulations' composition. Moreover, since SCs abilities and their involvement in the development of several diseases, they could help to discover specific targets for new therapies. It could be useful to characterize BM-derived SC markers, properties, and variations during lactation stages, to understand their potential role in therapeutic applications, since they could be noninvasively isolated from BM. More studies will help to describe more in detail the characteristics of mother-to-child communication through breastfeeding and its potential role in the next future.

RevDate: 2020-01-13

Mueller NT, Zhang M, Juraschek SP, et al (2020)

Effects of high-fiber diets enriched with carbohydrate, protein, or unsaturated fat on circulating short chain fatty acids: results from the OmniHeart randomized trial.

The American journal of clinical nutrition pii:5700785 [Epub ahead of print].

BACKGROUND: short chain fatty acids (SCFAs; e.g., acetate, propionate, and butyrate) are produced by microbial fermentation of fiber in the colon. Evidence is lacking on how high-fiber diets that differ in macronutrient composition affect circulating SCFAs.

OBJECTIVES: We aimed to compare the effects of 3 high-fiber isocaloric diets differing in %kcal of carbohydrate, protein, or unsaturated fat on circulating SCFAs. Based on previous literature, we hypothesized that serum acetate, the main SCFA in circulation, increases on all high-fiber diets, but differently by macronutrient composition of the diet.

METHODS: OmniHeart is a randomized crossover trial of 164 men and women (≥30 y old); 163 participants with SCFA data were included in this analysis. We provided participants 3 isocaloric high-fiber (∼30 g/2100 kcal) diets, each for 6 wk, in random order: a carbohydrate-rich (Carb) diet, a protein-rich (Prot) diet (protein predominantly from plant sources), and an unsaturated fat-rich (Unsat) diet. We used LC-MS to quantify SCFA concentrations in fasting serum, collected at baseline and the end of each diet period. We fitted linear regression models with generalized estimating equations to examine change in ln-transformed SCFAs from baseline to the end of each diet; differences between diets; and associations of changes in SCFAs with cardiometabolic parameters.

RESULTS: From baseline, serum acetate concentrations were increased by the Prot (β: 0.24; 95% CI: 0.12, 0.35), Unsat (β: 0.21; 95% CI: 0.10, 0.33), and Carb (β: 0.12; 95% CI: 0.01, 0.24) diets; between diets, only Prot compared with Carb was significant (P = 0.02). Propionate was decreased by the Carb (β: -0.10; 95% CI: -0.16, -0.03) and Unsat (β: -0.10; 95% CI: -0.16, -0.04) diets, not the Prot diet; between diet comparisons of Carb vs. Prot (P = 0.006) and Unsat vs. Prot (P = 0.002) were significant. The Prot diet increased butyrate (β: 0.05; 95% CI: 0.00, 0.09) compared with baseline, but not compared with the other diets. Increases in acetate were associated with decreases in insulin and glucose; increases in propionate with increases in leptin, LDL cholesterol, and blood pressure; and increases in butyrate with increases in insulin and glucose, and decreases in HDL cholesterol and ghrelin (Ps < 0.05).

CONCLUSIONS: Macronutrient composition of high-fiber diets affects circulating SCFAs, which are associated with measures of appetite and cardiometabolic health. This trial was registered at clinicaltrials.gov as NCT00051350.

RevDate: 2020-01-13

Boehlke C, Rupf S, Tenniswood M, et al (2020)

Caries and periodontitis associated bacteria are more abundant in human saliva compared to other great apes.

Archives of oral biology, 111:104648 pii:S0003-9969(19)30866-0 [Epub ahead of print].

OBJECTIVE: Caries and periodontitis are uncommon in free ranging great apes but a major oral disease in humans. The aim was to analyze abundance and diversity of oral bacteria of western humans and their closest relatives, to examine if zoo apes feeding on diet other than in their natural habitat show caries and periodontitis associated salivary bacteria and comparable susceptibility for oral civilization diseases as humans.

DESIGN: Bacterial composition of human and great ape saliva samples were compared by analyzing the V3 region of the bacteria 16S rRNA gene by Next Generation Sequencing with Ion Torrent.

RESULTS: Results show species-specific differences in the salivary bacteria phyla and genera composition among all apes. Moreover, salivary bacterial composition within non-human apes showed higher intra-individual differences than within humans. Human saliva exhibited lowest bacteria diversity. Different behavioral patterns including (oral) hygiene standards of humans and non-human apes might cause differences. All species differed in diversity and abundance of caries associated bacteria genera. Human saliva revealed higher abundance of caries and periodontitis relevant bacteria in contrast to other great apes, which might be supported by higher consume of refined cariogenic food items, possibly raising their risk for oral disease susceptibility.

CONCLUSIONS: The study offers first clues on caries and periodontitis relevant bacteria of captive great ape species in comparison to humans. Higher susceptibility to oral diseases for humans than for their closest relatives, leads to the question, if the oral microbiome changed during evolution and how it is influenced by the human life style.

RevDate: 2020-01-13

Tikka C, Manthari RK, Ommati MM, et al (2020)

Immune disruption occurs through altered gut microbiome and NOD2 in arsenic induced mice: Correlation with colon cancer markers.

Chemosphere, 246:125791 pii:S0045-6535(19)33032-2 [Epub ahead of print].

The gut microbial compositions are easily affected by the environmental chemicals like arsenic (As) leading to dysbiosis. The dysbiosis of gut microbiome has associated with numerous diseases; among which cancer is one of the major diseases. The meticulous mechanism underlying As- altered gut microbiome, Nucleotide domine containing protein 2 (NOD2) and how altered gut microbiome disturbs the intestinal homeostasis to regulate colon cancer markers remains unclear. For this, one hundred twenty 8-week old age male mice were divided into two exposure periods (3 and 6 months), and each exposure group animals were further divided into four groups as control (received only distilled H2O), low (0.15 mg As2O3/L), medium (1.5 mg As2O3/L) and high (15 mg As2O3/L) dose (each group containing 15 mice) administrated for 3 and 6 months. The results showed that As exposure highly altered gut microbiome with a significant depletion in NOD2 in contrast to control groups. Moreover, the dendritic cells (CD11a, CD103, CX3CR1) and macrophages (F4/80) were significantly increased by As exposure. Interestingly, increased trend of inflammatory cytokines (TNF-α, IFN-γ, IL-17) and depleted anti-inflammatory cytokines (IL-10) was observed in As exposed mice. Furthermore, the colon cancer markers β-catenin has increased while APC was arrested by As both in 3 and 6 months treated animals. Many studies reported that As altered gut microbial compositions, in this study, our results suggested that altered gut microbiome indirectly regulates colon cancer marker through immune system destruction mediated by inflammatory cytokines.

RevDate: 2020-01-13

Ma J, Sheng GD, Chen QL, et al (2020)

Do combined nanoscale polystyrene and tetracycline impact on the incidence of resistance genes and microbial community disturbance in Enchytraeus crypticus?.

Journal of hazardous materials, 387:122012 pii:S0304-3894(19)31966-1 [Epub ahead of print].

It has been proved that nanoplastics can effectively adsorb pollutants and thus influence their behavior and availability. The combined toxic effects of nanoplastic and its adsorbed pollutant on the soil fauna are still not well known. We used high-throughput quantitative PCR to explore the effects of oral nanoscale polystyrene and tetracycline exposure on antibiotic resistance genes in the soil invertebrate Enchytraeus crypticus, and used bacterial 16S rRNA gene amplification sequencing to examine the response of the microbiome of E. crypticus. After 14 days of tetracycline and nanoscale polystyrene exposure, we terminated exposure and monitored the restoration of ARGs and microbiome in the E. crypticus. Results showed that the number of ARGs, especially macrolide-lincosamide-streptogramin B (MLSB), tetracycline ARGs, as well as multidrug ARGs, increased with exposure to nanoscale polystyrene and tetracycline. The abundance of Aminoglycoside and Beta_Lactamase ARGs in E. crypticus also significantly increased. The exposure significantly perturbed the abundance of families Microbacteriaceae, Streptococcaceae, Enterobacteriaceae, Rhodocyclaceae and Sphinomonadaceae. After terminating exposure for 14 days, the diversity and abundance of ARGs were not completely restored, while the microbiome was not permanently changed but reversibly impacted.

RevDate: 2020-01-13

Torchia MT, Amakiri I, Werth P, et al (2020)

Characterization of native knee microorganisms using next-generation sequencing in patients undergoing primary total knee arthroplasty.

The Knee pii:S0968-0160(19)30324-2 [Epub ahead of print].

BACKGROUND: Next-generation sequencing (NGS) offers improved sensitivity compared to culture-based methods for identifying organisms from synovial joints. It remains unclear whether native microorganisms exist in a joint, and positive NGS results may be interpreted as pathologic when in fact they may represent this native microbiome. The purpose of this study was to characterize the native knee microorganism profile in patients undergoing primary total knee arthroplasty (TKA).

METHODS: Forty consecutive patients with osteoarthritis undergoing primary total knee arthroplasty were enrolled prospectively. During TKA surgery but prior to arthrotomy, the native knee was aspirated and the fluid was sent for NGS analysis. Immediately after arthrotomy, four separate tissue samples were also sent for NGS analysis. All microbes identified by NGS were recorded.

RESULTS: Twelve out of forty patients (30%) had at least one positive organism identified by NGS from their native knee. Of those with positive NGS results, 9/12 (75%) had more than one organism identified (range two to 11). There were no significant differences in demographics, comorbidities, or incidence of prior knee injections between the two groups. There were 48 unique organisms identified from all patients, and the average number of organisms identified by NGS was 4.6 per patient. Four sterile water controls were all negative for organisms.

CONCLUSION: A proportion of patients with osteoarthritis undergoing primary total knee arthroplasty have organisms identified in their joint by NGS at the time of surgery. Organisms identified after TKA by NGS when concern for periprosthetic joint infection exists may represent the native microbiome rather than pathogenic microbes.

RevDate: 2020-01-13

Mays ZJS, Chappell TC, NU Nair (2020)

Quantifying and Engineering Mucus Adhesion of Probiotics.

ACS synthetic biology [Epub ahead of print].

Mucus in the gastrointestinal (GI) tract is the primary point-of-interaction between humans and their gut microbiota. This intimates that mucus not only ensures protection against endogenous and exogenous opportunists but also provisions for the human microbiota to reside and flourish. With the emergence of living therapeutics, engineered microbes can deliver and produce increasingly complex medicine, and controlling the mucoadhesive properties of different microbial chassis can dictate dose-response in a patient. Here we present a redesigned, in vitro, plate-based assay to measure the mucus adhesion of various probiotics. Cell-mucus interactions were isolated by immobilizing mucus to the plate surface. Binding parameters were derived for each probiotic strain by measuring cell adhesion over a wide range of cell concentrations, providing dose-dependent adhesion metrics. Surface proteins and cell components known to influence mucoadhesion were then heterologously expressed or altered in Lactococcus lactis MG1363 and Escherichia coli Nissle 1917 to control mucus-binding capacity, avidity, and cooperativity.

RevDate: 2020-01-11

Edge TA, Baird DJ, Bilodeau G, et al (2019)

The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.

The Science of the total environment, 710:135906 pii:S0048-9697(19)35901-7 [Epub ahead of print].

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.

RevDate: 2020-01-11

Zhang L, Rimal B, Nichols RG, et al (2020)

Perfluorooctane Sulfonate Alters Gut Microbiota-Host Metabolic Homeostasis in Mice.

Toxicology pii:S0300-483X(20)30003-2 [Epub ahead of print].

Perfluorooctane sulfonate (PFOS) is a persistent environmental chemical whose biological effects are mediated by multiple mechanisms. Recent evidence suggests that the gut microbiome may be directly impacted by and/or alter the fate and effects of environmental chemicals in the host. Thus, the aim of this study was to determine whether PFOS influences the gut microbiome and its metabolism, and the host metabolome. Four groups of male C57BL/6 J mice were fed a diet with or without 0.003%, 0.006%, or 0.012% PFOS, respectively. 16S rRNA gene sequencing, metabolomic, and molecular analyses were used to examine the gut microbiota of mice after dietary PFOS exposure. Dietary PFOS exposure caused a marked change in the gut microbiome compared to controls. Dietary PFOS also caused dose-dependent changes in hepatic metabolic pathways including those involved in lipid metabolism, oxidative stress, inflammation, TCA cycle, glucose, and amino acid metabolism. Changes in the metabolome correlated with changes in genes that regulate these pathways. Integrative analyses also demonstrated a strong correlation between the alterations in microbiota composition and host metabolic profiles induced by PFOS. Further, using isolated mouse cecal contents, PFOS exposure directly affected the gut microbiota metabolism. Results from these studies demonstrate that the molecular and biochemical changes induced by PFOS are mediated in part by the gut microbiome, which alters gene expression and the host metabolome in mice.

RevDate: 2020-01-11

Altman MC, Beigelman A, Ciaccio C, et al (2020)

Evolving Concepts in how Viruses Impact Asthma.

The Journal of allergy and clinical immunology pii:S0091-6749(20)30002-6 [Epub ahead of print].

Over the last decade, there have been substantial advances in our understanding about how viral infections regulate asthma (Table 1). Important lessons have been learned from birth cohort studies examining viral infections and subsequent asthma, understanding the relationships between host genetics and viral infections, the contributions of respiratory viral infections to patterns of immune development, the impact of environmental exposure on severity of viral infections, and how the viral genome influences host immune responses to viral infections. Further, there has been major progress in our knowledge about how bacteria regulate host immune responses in asthma pathogenesis. In this article, we also examine the dynamics of respiratory tract bacterial colonization during viral upper respiratory tract infection, in addition to the relationship of the gut and respiratory microbiomes with respiratory viral infections. Finally, we focus on potential interventions that could decrease virus-induced wheezing and asthma. There are emerging therapeutic options to decrease severity of wheezing exacerbations caused by respiratory viral infections. Primary prevention is a major goal and a strategy toward this end is considered.

RevDate: 2020-01-11

Rojas CA, Holekamp KE, Winters AD, et al (2020)

Body-site specific microbiota reflect sex and age-class among wild spotted hyenas.

FEMS microbiology ecology pii:5700710 [Epub ahead of print].

Host-associated microbial communities, henceforth 'microbiota', can affect the physiology and behavior of their hosts. In mammals, host ecological, social, and environmental variables are associated with variation in microbial communities. Within individuals in a given mammalian species, the microbiota also partitions by body-site. Here, we build on this work and sequence the bacterial 16S rRNA gene to profile the microbiota at six distinct body-sites (ear, nasal and oral cavities, prepuce, rectum, and anal scent gland) in a population of wild spotted hyenas (Crocuta crocuta), which are highly social, large African carnivores. We inquired whether microbiota at these body-sites vary with host sex or social rank among juvenile hyenas, and whether they differ between juvenile females and adult females. We found that the scent gland microbiota differed between juvenile males and juvenile females, whereas the prepuce and rectal microbiota differed between adult females and juvenile females. Social rank, however, was not a significant predictor of microbiota profiles. Additionally, the microbiota varied considerably among the six sampled body-sites and exhibited strong specificity among individual hyenas. Thus, our findings suggest that site-specific niche selection is a primary driver of microbiota structure in mammals, but endogenous host factors may also be influential.

RevDate: 2020-01-11

Nakano T, Ochiai S, Suzuki S, et al (2020)

Breastfeeding promotes egg white sensitization in early infancy.

A recent systematic review indicates that food sensitization in early childhood is a risk factor, not only for food allergies, but also for developing an allergic march which can lead to airway allergic diseases1 . Over the past few decades, many groups have studied risk factors for allergic diseases, including sensitization. These risks include eczema, gut microbiome, timing of introduction of solid food, Vitamin D, etc.

RevDate: 2020-01-11

Xu J, Bian G, Zheng M, et al (2020)

Fertility factors affect the vaginal microbiome in women of reproductive age.

American journal of reproductive immunology (New York, N.Y. : 1989) [Epub ahead of print].

PROBLEM: For women of reproductive age, achieving a successful pregnancy requires both the normal functioning of reproductive endocrine and the health of the reproductive tract environment. We aimed to study how these fertility factors, such as female age, baseline sexual hormone levels, tubal patency, and vaginal pH, affect the composition of vaginal microbiome.

METHOD OF STUDY: The 16S rRNA sequencing was carried on vaginal microbiome samples from 85 women of reproductive age without vaginal infections or reproductive endocrine diseases. The detailed correlations between fertility factors and vaginal microbiome were quantified by Spearman's rank tests. A linear discriminant analysis was carried out to explore the effects of fertility factors on the relative abundances of vaginal bacterial species.

RESULTS: The vaginal pH, levels of basal E2, LH, and FSH all had significant effects on the distribution of vaginal microbiome. The relative abundances of vaginal bacterial species, including Escherichia coli, Streptococcus agalactiae, and Prevotella intermedia, were significantly different due to the host's state of reproductive endocrine and tubal patency. It was worth noting that women with tubal obstruction, or prolonged menstrual cycle, or antral follicle count > 15, or vaginal pH > 4.5 all had a higher abundance of Escherichia coli in vagina.

CONCLUSIONS: The fertility factors associated with the reproductive endocrine and the genital tract environment affected vaginal microbiome in women of reproductive age. The species Escherichia coli, Streptococcus agalactiae, Prevotella intermedia, et al. could be used as biomarkers to reflect the pathological state of reproductive endocrine and genital tract.

RevDate: 2020-01-11

Cenci-Goga BT, Sechi P, Karama M, et al (2020)

Cross-sectional study to identify risk factors associated with the occurrence of antimicrobial resistance genes in honey bees Apis mellifera) in Umbria, Central Italy.

Environmental science and pollution research international pii:10.1007/s11356-020-07629-3 [Epub ahead of print].

The use antimicrobials for therapeutic and metaphylactic purpose in humans and agriculture exerts selective pressure on animal and environmental microbiota resulting in the survival and spread of antimicrobial resistance genes among bacteria and subsequent development of resistance in bacteria. Previous studies have shown that honey bees' microbiota (Apis mellifera) can accumulate antimicrobial resistance genes in their microbiome and act as collectors and disseminators of resistance genes. The aim of this study was to investigate to what extent honey bees act as reservoir of select antimicrobial resistance genes. This study was conducted on 35 groups of bees. Bees were collected from 35 sites in Umbria, Italy. PCR was used to screen pooled ground bees' specimens for genes that code for resistance against antimicrobials that are commonly used in humans and in veterinary medicine including aminoglycosides (aph), beta-lactams (blaZ), tetracycline (tetM) and sulphonamides (sul1 and sul2). Twenty-four samples out of 35 (68.57%) were positive for at least one antimicrobial resistance gene. Two samples were positive for the aph, 5.71%; eight for blaZ, 22.86%; three for tetM, 8.57%; ten for sul1, 28.57% and eighteen for sul2, 51.43%. Positivity to more than one antimicrobial resistance gene was observed in nine samples, 25.71%. The multivariate analysis identified "presence of farms nearby" as the factor most closely related to PCR positivity. Honey bees (Apis mellifera) from Umbria, Italy, carry antimicrobial resistance genes and can be used as indicators of the presence of resistance genes in the environment.

RevDate: 2020-01-11

Gupta S, Mortensen MS, Schjørring S, et al (2019)

Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing.

Communications biology, 2(1):291 pii:10.1038/s42003-019-0540-1.

Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare the diagnostic efficiency of the two methods using a large number of samples (n = 1,748 fecal and n = 1,790 hypopharyngeal), among healthy children at different time points. Here we show that bacteria identified by NGS represented 75.70% of the unique bacterial species cultured in each sample, while TCM only identified 23.86% of the bacterial species found by amplicon sequencing. We discuss the pros and cons of both methods and provide perspective on how NGS can be implemented effectively in clinical settings.

RevDate: 2020-01-11

Kaliannan K, Li XY, Wang B, et al (2019)

Multi-omic analysis in transgenic mice implicates omega-6/omega-3 fatty acid imbalance as a risk factor for chronic disease.

Communications biology, 2(1):276 pii:10.1038/s42003-019-0521-4.

An unbalanced increase in dietary omega-6 (n-6) polyunsaturated fatty acids (PUFA) and decrease in omega-3 (n-3) PUFA in the Western diet coincides with the global rise in chronic diseases. Whether n-6 and n-3 PUFA oppositely contribute to the development of chronic disease remains controversial. By using transgenic mice capable of synthesizing PUFA to eliminate confounding factors of diet, we show here that alteration of the tissue n-6/n-3 PUFA ratio leads to correlated changes in the gut microbiome and fecal and serum metabolites. Transgenic mice able to overproduce n-6 PUFA and achieve a high tissue n-6/n-3 PUFA ratio exhibit an increased risk for metabolic diseases and cancer, whereas mice able to convert n-6 to n-3 PUFA, and that have a lower n-6/n-3 ratio, show healthy phenotypes. Our study demonstrates that n-6 PUFA may be harmful in excess and suggests the importance of a low tissue n-6/n-3 ratio in reducing the risk for chronic diseases.

RevDate: 2020-01-11

Sato Y, Hori T, Koike H, et al (2019)

Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism.

Communications biology, 2(1):179 pii:10.1038/s42003-019-0418-2.

Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.

RevDate: 2020-01-11

Rampelli S, Guenther K, Turroni S, et al (2018)

Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity.

Communications biology, 1(1):222 pii:10.1038/s42003-018-0221-5.

It is widely accepted that the intestinal microbiome is connected to obesity, as key mediator of the diet impact on the host metabolic and immunological status. To investigate whether the individual gut microbiome has a potential in predicting the onset and progression of diseases, here we characterized the faecal microbiota of 70 children in a two-time point prospective study, within a four-year window. All children had normal weight at the beginning of this study, but 36 of them gained excessive weight at the subsequent check-up. Microbiome data were analysed together with the hosts' diet information, physical activity, and inflammatory parameters. We find that the gut microbiota structures were stratified into a discrete number of groups, characterized by different biodiversity that correlates with inflammatory markers and dietary habits, regardless of age, gender, and body weight. Collectively, our data underscore the importance of the microbiome-host-diet configuration as a possible predictor of obesity.

RevDate: 2020-01-11

Douglas CA, Ivey KL, Papanicolas LE, et al (2020)

DNA extraction approaches substantially influence the assessment of the human breast milk microbiome.

Scientific reports, 10(1):123 pii:10.1038/s41598-019-55568-y.

In addition to providing nutritional and bioactive factors necessary for infant development, human breast milk contains bacteria that contribute to the establishment of commensal microbiota in the infant. However, the composition of this bacterial community differs considerably between studies. We hypothesised that bacterial DNA extraction methodology from breast milk samples are a substantial contributor to these inter-study differences. We tested this hypothesis by applying five widely employed methodologies to a mock breast milk sample and four individual human breast milk samples. Significant differences in DNA yield and purity were observed between methods (P < 0.05). Microbiota composition, assessed by 16S rRNA gene amplicon sequencing, also differed significantly with extraction methodology (P < 0.05), including in the contribution of contaminant signal. Concerningly, many of the bacterial taxa identified here as contaminants have been reported as components of the breast milk microbiome in other studies. These findings highlight the importance of using stringent, well-validated, DNA extraction methodologies for analysis of the breast milk microbiome, and exercising caution interpreting microbiota data from low-biomass contexts.

RevDate: 2020-01-11

Suttner BJ, Johnston ER, Orellana LH, et al (2020)

Potential and limitations of metagenomics as a public health risk assessment tool in a study of natural creek sediments influenced by agricultural and livestock runoff.

Applied and environmental microbiology pii:AEM.02525-19 [Epub ahead of print].

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens originating from these practices such as Shiga Toxin-producing Escherichia coli (STEC) remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley of California was sampled over a nine-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and comparable to the functional and taxonomic diversity observed in soils. With our sequencing effort (∼4Gbp per library), we were unable to detect any pathogenic E. coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low abundance. Further, there were no significant differences in the abundance of human- or cow-specific gut microbiome sequences in the downstream, impacted sites compared to upstream, more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, a high number of metagenomic reads carrying antibiotic resistance genes (ARGs) was found in all samples that was significantly higher compared to ARG reads in other available freshwater and soil metagenomes, suggesting that these communities may be natural reservoirs of ARGs. The work presented here should serve as guide for sampling volumes, amount of sequencing to apply, and what bioinformatics analyses to perform when using metagenomics for public health risk studies of environmental samples such as sediments.IMPORTANCE Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food and water-borne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health is assessed by culture-based tests for the intestinal bacterium, E. coli However, the accuracy of these traditional methods (e.g., low accuracy in quantification, and false positive signal when PCR-based) and their suitability for sediments remains unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the U.S. in order to assess how agricultural runoff affects the native microbial communities and if the presence of STEC in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.

RevDate: 2020-01-11

Jnana A, Muthuraman V, Varghese VK, et al (2020)

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals.

Applied and environmental microbiology pii:AEM.02608-19 [Epub ahead of print].

Diabetic foot ulcer (DFU) is a major complication of diabetes with high morbidity and mortality rates. Pathogenesis of DFUs is governed by a complex milieu of environmental and host factors. The empirical treatment is initially based on wound severity since culturing and profiling the antibiotic sensitivity of wound-associated microbes is time consuming. Hence, a thorough and rapid analysis of the microbial landscape is a major requirement towards devising evidence-based interventions. Towards this, 122 wound (100 diabetic and 22 non-diabetic) samples were sampled for their bacterial community structure using both culture-based and next-generation 16S rRNA based metagenomics approach. Both the approaches showed that the Gram-negative microbes were more abundant in the wound microbiome. The core microbiome consisted of bacterial genera including Alcaligenes, Pseudomonas, Burkholderia, and Corynebacterium in decreasing order of average relative abundance. Despite the heterogenous nature and extensive sharing of microbes, an inherent community structure was apparent as revealed by a cluster analysis based on Euclidean distances. Facultative anaerobes (26.5%) were predominant in Wagner grade 5 while strict anaerobes were abundant in Wagner grade 1 (26%). A non-metric dimensional scaling analysis could not clearly discriminate samples based on HbA1c levels. Sequencing approach revealed the presence of major culturable species even in samples with no bacterial growth in culture-based approach. Our study indicates that a) composition of core microbial community varies with wound severity, b) polymicrobial species distribution is individual-specific, and c) antibiotic susceptibility varies with individuals. Our study suggests the need to evolve better-personalized care for better wound management therapies.IMPORTANCE: Chronic non-healing diabetic foot ulcers (DFU) is a serious complication of diabetes and is further exacerbated by bacterial colonization. Microbial burden in the wound of each individual displays diverse morphological and physiological characteristics with unique patterns of host-pathogen interactions, antibiotic resistance and virulence. Treatment involves empirical decisions until definitive results on the causative wound pathogens and their antibiotic susceptibility profiles are available. Hence, there is a need for rapid and accurate detection of these polymicrobial communities for effective wound management. Deciphering microbial communities will aid clinicians to tailor their treatment specifically to the microbes prevalent in the DFU at the time of assessment. This may reduce DFU associated morbidity and mortality while impeding the rise of multi drug resistant microbes.

RevDate: 2020-01-11

Jackson EW, Pepe-Ranney C, Johnson MR, et al (2020)

A highly prevalent and pervasive densovirus discovered among sea stars from the North American Atlantic Coast.

Applied and environmental microbiology pii:AEM.02723-19 [Epub ahead of print].

The etiology of Sea Star Wasting Syndrome is hypothesized to be caused by a densovirus, SSaDV, that has previously been reported on the Pacific and Atlantic coasts of the United States. In this study, we reevaluated the presence of SSaDV among sea stars from the North American Atlantic Coast and in doing so discovered a novel densovirus we have named Asterias forbesi associated densovirus (AfaDV) that shares 78% nucleotide pairwise identity to SSaDV. In contrast to previous studies, SSaDV was not detected in sea stars from the North American Atlantic Coast. Using a variety of PCR-based techniques, we investigated the tissue tropism, host specificity, and prevalence of AfaDV among populations of sea stars at five locations along the Atlantic Coast. AfaDV was detected in three sea star species (Asterias forbesi, Asterias rubens, and Henricia sp) found in this region and was highly prevalent (>80% of individuals tested, n=134), among sampled populations. AfaDV was detected in the body wall, gonads, and pyloric caeca (digestive gland) of specimens but was not detected in their coelomic fluid. A significant difference in viral load was found between tissue types with the pyloric caeca having the highest viral loads. Further investigation of Asterias forbesi gonad tissue found germline cells (oocytes) to be virus positive, suggesting a potential route of vertical transmission. Taken together, these observations show that the presence of AfaDV is not an indicator of Sea Star Wasting Syndrome because AfaDV is a common constituent of these animals' microbiome, regardless of health.Importance Sea Star Wasting Syndrome is a disease primarily observed on the Pacific and Atlantic coast of North America that has significantly impacted sea star populations. The etiology of this disease is unknown though hypothesized to be caused by a densovirus, SSaDV. However, previous studies have not found a correlation between SSaDV to Sea Star Wasting Syndrome on the North American Atlantic Coast. This study suggests that this observation may be explained by the presence of a genetically similar densovirus, AfaDV, that may have confounded previous studies. SSaDV was not present in sea stars screened in this study, and instead AfaDV was commonly found in sea star populations across the New England region with no apparent signs of disease. These results suggest that sea star densoviruses may be common constituents of the animal's microbiome, and the diversity and extent of these viruses among wild populations may be greater than previously recognized.

RevDate: 2020-01-11

Lee YH (2020)

Causal association of gut microbiome on the risk of rheumatoid arthritis: a Mendelian randomisation study.

RevDate: 2020-01-11

Inamo J (2020)

Response to: 'Causal association of gut microbiome on the risk of rheumatoid arthritis: a Mendelian randomisation study' by Lee.

Annals of the rheumatic diseases pii:annrheumdis-2019-216767 [Epub ahead of print].

RevDate: 2020-01-11

Shomorony I, Cirulli ET, Huang L, et al (2020)

An unsupervised learning approach to identify novel signatures of health and disease from multimodal data.

Genome medicine, 12(1):7 pii:10.1186/s13073-019-0705-z.

BACKGROUND: Modern medicine is rapidly moving towards a data-driven paradigm based on comprehensive multimodal health assessments. Integrated analysis of data from different modalities has the potential of uncovering novel biomarkers and disease signatures.

METHODS: We collected 1385 data features from diverse modalities, including metabolome, microbiome, genetics, and advanced imaging, from 1253 individuals and from a longitudinal validation cohort of 1083 individuals. We utilized a combination of unsupervised machine learning methods to identify multimodal biomarker signatures of health and disease risk.

RESULTS: Our method identified a set of cardiometabolic biomarkers that goes beyond standard clinical biomarkers. Stratification of individuals based on the signatures of these biomarkers identified distinct subsets of individuals with similar health statuses. Subset membership was a better predictor for diabetes than established clinical biomarkers such as glucose, insulin resistance, and body mass index. The novel biomarkers in the diabetes signature included 1-stearoyl-2-dihomo-linolenoyl-GPC and 1-(1-enyl-palmitoyl)-2-oleoyl-GPC. Another metabolite, cinnamoylglycine, was identified as a potential biomarker for both gut microbiome health and lean mass percentage. We identified potential early signatures for hypertension and a poor metabolic health outcome. Additionally, we found novel associations between a uremic toxin, p-cresol sulfate, and the abundance of the microbiome genera Intestinimonas and an unclassified genus in the Erysipelotrichaceae family.

CONCLUSIONS: Our methodology and results demonstrate the potential of multimodal data integration, from the identification of novel biomarker signatures to a data-driven stratification of individuals into disease subtypes and stages-an essential step towards personalized, preventative health risk assessment.

RevDate: 2020-01-11

Morshedi M, Saghafi-Asl M, ES Hosseinifard (2020)

The potential therapeutic effects of the gut microbiome manipulation by synbiotic containing-Lactobacillus plantarum on neuropsychological performance of diabetic rats.

Journal of translational medicine, 18(1):18 pii:10.1186/s12967-019-02169-y.

BACKGROUND: The manipulation of gut microbiota as a target has been suggested to reduce the risks for a number of diseases such as type 2 diabetes mellitus (T2DM). Conversely, T2DM is associated with complications such as gut and brain disorders. Furthermore, the impact of probiotics and prebiotics to improve T2DM complications are reported. Thus, the present study seeks to investigate the therapeutic and neuropsychological effects of L. plantarum and inulin in diabetic rats.

METHODS: Throughout the investigation, L. plantarum, inulin or their combination (synbiotic) was administered to diabetic rats. in the end, fecal samples were collected to evaluate the gut microbial composition. Then behavioral tests were conducted. Subsequently, the obtainment of the prefrontal cortex (PFC) and hippocampal samples.

RESULTS: Our data demonstrated that administration of L. plantarum and inulin could improve gut dysbiosis and oxidative stress status. In addition, it could ameliorate serotonin and BDNF/TrkB signaling pathway. Notably, a strong correlation between the gut microbiota changes and cognition responses was observed. Interestingly, synbiotics intake exploited a rather powerful effect on oxidative stress markers.

CONCLUSION: The findings confirm that there is a beneficial therapeutic potential of supplements, especially symbiotic. Moreover, neuropsychological improvement associated with balanced gut microbiome.

RevDate: 2020-01-11

Triplett J, Ellis D, Braddock A, et al (2020)

Temporal and region-specific effects of sleep fragmentation on gut microbiota and intestinal morphology in Sprague Dawley rats.

Gut microbes [Epub ahead of print].

Sleep is a fundamental biological process, that when repeatedly disrupted, can result in severe health consequences. Recent studies suggest that both sleep fragmentation (SF) and dysbiosis of the gut microbiome can lead to metabolic disorders, though the underlying mechanisms are largely unclear. To better understand the consequences of SF, we investigated the effects of acute (6 days) and chronic (6 weeks) SF on rats by examining taxonomic profiles of microbiota in the distal ileum, cecum and proximal colon, as well as assessing structural and functional integrity of the gastrointestinal barrier. We further assayed the impact of SF on a host function by evaluating inflammation and immune response. Both acute and chronic SF induced microbial dysbiosis, more dramatically in the distal ileum (compared to other two regions studied), as noted by significant perturbations in alpha- and beta-diversity; though, specific microbial populations were significantly altered throughout each of the three regions. Furthermore, chronic SF resulted in increased crypt depth in the distal ileum and an increase in the number of villi lining both the cecum and proximal colon. Additional changes were noted with chronic SF, including: decreased microbial adhesion and penetration in the distal ileum and cecum, elevation in serum levels of the cytokine KC/GRO, and depressed levels of corticotropin. Importantly, our data show that perturbations to microbial ecology and intestinal morphology intensify in response to prolonged SF and these changes are habitat specific. Together, these results reveal consequences to gut microbiota homeostasis and host response following acute and chronic SF in rats.

RevDate: 2020-01-10

Martino A, Giuliani A, Todde V, et al (2019)

Metabolic networks classification and knowledge discovery by information granulation.

Computational biology and chemistry, 84:107187 pii:S1476-9271(19)30244-0 [Epub ahead of print].

Graphs are powerful structures able to capture topological and semantic information from data, hence suitable for modelling a plethora of real-world (complex) systems. For this reason, graph-based pattern recognition gained a lot of attention in recent years. In this paper, a general-purpose classification system in the graphs domain is presented. When most of the information of the available patterns can be encoded in edge labels, an information granulation-based approach is highly discriminant and allows for the identification of semantically meaningful edges. The proposed classification system has been tested on the entire set of organisms (5299) for which metabolic networks are known, allowing for both a perfect mirroring of the underlying taxonomy and the identification of most discriminant metabolic reactions and pathways. The widespread diffusion of graph (network) structures in biology makes the proposed pattern recognition approach potentially very useful in many different fields of application. More specifically, the possibility to have a reliable metric to compare different metabolic systems is instrumental in emerging fields like microbiome analysis and, more in general, for proposing metabolic networks as a universal phenotype spanning the entire tree of life and in direct contact with environmental cues.

RevDate: 2020-01-10

Tsonis O, Gkrozou F, Harrison E, et al (2019)

Female genital tract microbiota affecting the risk of preterm birth: What do we know so far? A review.

European journal of obstetrics, gynecology, and reproductive biology, 245:168-173 pii:S0301-2115(19)30571-8 [Epub ahead of print].

Spontaneous Preterm birth (SPTB) is a common obstetric complication affecting 12.9 million births worldwide and is the leading cause of neonatal morbidity and mortality. Disruption in the vaginal microbiota has an impact on the maternal immunological profile leading to SPTBs. Scientists have struggled to link maternal infectious agents with the dysregulation of the maternal immune response in cases of SPTBs. Throughout the last decade, important findings regarding the role of microbiota and its genome, the so-called microbiome, have linked alterations within the population of the microorganisms in our bodies with changes in nutrition, immunity, behaviour and diseases. In this review, evidence regarding the female genital tract microbiota and microbiome has been examined to help further our understanding of its role in disrupting the maternal immune system resulting in spontaneous preterm birth.

RevDate: 2020-01-10

Wang CN, Wu RL, Li YY, et al (2019)

Effects of pesticide residues on bacterial community diversity and structure in typical greenhouse soils with increasing cultivation years in Northern China.

The Science of the total environment, 710:136321 pii:S0048-9697(19)36317-X [Epub ahead of print].

The understanding of soil microbiome is important for sustainable cultivation, especially under greenhouse conditions. Here, we investigated the changes in soil pesticide residues and microbial diversity and community structure at different cultivation years under a greenhouse system. The 9-to-14 years sites were found to have the least diversity/rich microbial population as compared to sites under 8 years and over 16 years, as analyzed with alpha diversity index. In total, 42 bacterial phyla were identified across soils with different pesticide residues and cultivation ages. Proteobacteria, Acidobacteria, and Bacteroidetes represented the dominant phyla, that accounted for 34.2-43.4%, 9.7-19.3% and 9.2-16.5% of the total population, respectively. Our data prove that certain pesticides contribute to variation in soil microbial community and that soil bacteria respond differently to cultivation years under greenhouse conditions. Thus, this study provides an insight into microbial community structure changes by pesticides under greenhouse systems and natural biodegradation may have an important part in pesticides soil decontamination.

RevDate: 2020-01-10

Singh KP, Dhruva A, Flowers E, et al (2020)

Alterations in Patterns of Gene Expression and Perturbed Pathways in the Gut-Brain Axis Are Associated With Chemotherapy-Induced Nausea.

Journal of pain and symptom management pii:S0885-3924(19)31057-7 [Epub ahead of print].

CONTEXT: Despite current advances in antiemetic treatments, approximately 50% of oncology patients experience chemotherapy-induced nausea (CIN).

OBJECTIVES: The purpose of this study was to evaluate for differentially expressed genes and perturbed pathways associated with the gut-brain axis (GBA) across two independent samples of oncology patients who did and did not experience CIN.

METHODS: Oncology patients (n=735) completed study questionnaires in the week prior to their second or third cycle of chemotherapy (CTX). CIN occurrence was assessed using the Memorial Symptom Assessment Scale. Gene expression analyses were performed in two independent samples using RNA-sequencing (sample 1, n=357) and microarray (sample 2, n=352) methodologies. Fisher's combined probability method was used to determine genes that were differentially expressed and pathways that were perturbed between the two nausea groups across both samples.

RESULTS: CIN was reported by 63.6% of the patients in sample 1 and by 48.9% of the patients in sample 2. Across the two samples, 703 genes were differentially expressed and 37 pathways were found to be perturbed between the two CIN groups. We identified nine perturbed pathways that are involved in mechanisms associated with alterations in the GBA (i.e., mucosal inflammation, disruption of gut microbiome).

CONCLUSIONS: Persistent CIN remains a significant clinical problem. Our study is the first to identify novel GBA-related pathways associated with the occurrence of CIN. Our findings warrant confirmation and suggest directions for future clinical studies to decrease CIN occurrence.

RevDate: 2020-01-10

Zuluaga MYA, Lima Milani KM, Azeredo Gonçalves LS, et al (2020)

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum.

PloS one, 15(1):e0227422 pii:PONE-D-19-29936.

Studies of the interactions between plants and their microbiome have been conducted worldwide in the search for growth-promoting representative strains for use as biological inputs for agriculture, aiming to achieve more sustainable agriculture practices. With a focus on the isolation of plant growth-promoting (PGP) bacteria with ability to alleviate N stress, representative strains that were found at population densities greater than 104 cells g-1 and that could grow in N-free semisolid media were isolated from soils under different management conditions and from the roots of tomato (Solanum lycopersicum) and lulo (Solanum quitoense) plants that were grown in those soils. A total of 101 bacterial strains were obtained, after which they were phylogenetically categorized and characterized for their basic PGP mechanisms. All strains belonged to the Proteobacteria phylum in the classes Alphaproteobacteria (61% of isolates), Betaproteobacteria (19% of isolates) and Gammaproteobacteria (20% of isolates), with distribution encompassing nine genera, with the predominant genus being Rhizobium (58.4% of isolates). Strains isolated from conventional horticulture (CH) soil composed three bacterial genera, suggesting a lower diversity for the diazotrophs/N scavenger bacterial community than that observed for soils under organic management (ORG) or secondary forest coverture (SF). Conversely, diazotrophs/N scavenger strains from tomato plants grown in CH soil comprised a higher number of bacterial genera than did strains isolated from tomato plants grown in ORG or SF soils. Furthermore, strains isolated from tomato were phylogenetically more diverse than those from lulo. BOX-PCR fingerprinting of all strains revealed a high genetic diversity for several clonal representatives (four Rhizobium species and one Pseudomonas species). Considering the potential PGP mechanisms, 49 strains (48.5% of the total) produced IAA (2.96-193.97 μg IAA mg protein-1), 72 strains (71.3%) solubilized FePO4 (0.40-56.00 mg l-1), 44 strains (43.5%) solubilized AlPO4 (0.62-17.05 mg l-1), and 44 strains produced siderophores (1.06-3.23). Further, 91 isolates (90.1% of total) showed at least one PGP trait, and 68 isolates (67.3%) showed multiple PGP traits. Greenhouse trials using the bacterial collection to inoculate tomato or lulo plants revealed increases in plant biomass (roots, shoots or both plant tissues) elicited by 65 strains (54.5% of the bacterial collection), of which 36 were obtained from the tomato rhizosphere, 15 were obtained from the lulo rhizosphere, and 14 originated from samples of soil that lacked plants. In addition, 18 strains showed positive inoculation effects on both Solanum species, of which 12 were classified as Rhizobium spp. by partial 16S rRNA gene sequencing. Overall, the strategy adopted allowed us to identify the variability in the composition of culturable diazotroph/N-scavenger representatives from soils under different management conditions by using two Solanum species as trap plants. The present results suggest the ability of tomato and lulo plants to enrich their belowground microbiomes with rhizobia representatives and the potential of selected rhizobial strains to promote the growth of Solanum crops under limiting N supply.

RevDate: 2020-01-10

Lee SH, Bang S, Jang HH, et al (2020)

Effects of Allium hookeri on gut microbiome related to growth performance in young broiler chickens.

PloS one, 15(1):e0226833 pii:PONE-D-19-17223.

Healthy food promotes beneficial bacteria in the gut microbiome. A few prebiotics act as food supplements to increase fermentation by beneficial bacteria, which enhance the host immune system and health. Allium hookeri is a healthy food with antioxidant and anti-inflammatory activities. A. hookeri is used as a feed supplement for broiler chickens to improve growth performance. Although the underlying mechanism is unknown, A. hookeri may alter the gut microbiome. In the current study, 16S rRNA sequencing has been carried out using samples obtained from the cecum of broiler chickens exposed to diets comprising different tissue types (leaf and root) and varying amounts (0.3% and 0.5%) of A. hookeri to investigate their impact on gut microbiome. The microbiome composition in the groups supplemented with A. hookeri leaf varied from that of the control group. Especially, exposure to 0.5% amounts of leaf resulted in differences in the abundance of genera compared with diets comprising 0.3% leaf. Exposure to a diet containing 0.5% A. hookeri leaf decreased the abundance of the following bacteria: Eubacterium nodatum, Marvinbryantia, Oscillospira, and Gelria. The modulation of gut microbiome by leaf supplement correlated with growth traits including body weight, bone strength, and infectious bursal disease antibody. The results demonstrate that A. hookeri may improve the health benefits of broiler chickens by altering the gut microbiome.

RevDate: 2020-01-10

Bellaguarda E, S Hanauer (2020)

Checkpoint Inhibitor-Induced Colitis.

The American journal of gastroenterology [Epub ahead of print].

Immune checkpoint inhibitors have revolutionized treatment and overall survival for several different types of cancer. Antibodies to cytotoxic T-lymphocyte-associated protein 4 and to programmed cell death protein 1 and its ligand enhance cytotoxic T-cell survival, thus augmenting antitumor action and consequently inducing immune-related adverse events, of which the most relevant is diarrhea and colitis. This review compiles recent data on pathophysiology, clinical manifestations, and treatment of immune-mediated colitis (IMC). The pathogenesis of IMC is not completely understood, but recent studies have focused on the role of regulatory T cells and interactions with the gut microbiome. While sharing similarities with inflammatory bowel disease, IMC is considered a distinct form of colitis with acute onset and rapid progression leading to potential complications including bowel perforation and death. Prompt recognition and management of IMC is imperative for optimal outcomes. Although prospective clinical trials are lacking to guide therapy, recent guidelines recommend early endoscopic evaluation to establish the diagnosis and prompt initiation of corticosteroids. Response to first-line therapy should be assessed early to determine the need of escalation to biologic agents. With treatment, most patients will experience full resolution of symptoms, and subsequent rechallenge with anti-programmed cell death protein 1 or anti-programmed death-ligand 1 inhibitors can be considered.

RevDate: 2020-01-10

Sela R, M Halpern (2020)

Seasonal dynamics of Chironomus transvaalensis populations and the microbial community composition of their egg masses.

FEMS microbiology letters pii:5700282 [Epub ahead of print].

Chironomids (Diptera; Chironomidae) are the most abundant insects in freshwater environments and are considered natural reservoirs of Vibrio cholerae. We monitored the annual dynamics of chironomid populations along with their microbiota in order to better understand host-microbiota interactions. Chironomus transvaalensis populations peaked biannually in August and May-June. The composition of the endogenous bacterial communities of their egg masses clustered in two groups according to the sampling periods August-November and May-July. Nevertheless, a core bacterial community (43%) was present in all egg-mass samples. The most abundant phyla were: Proteobacteria, Firmicutes, Cyanobacteria and Bacteroidetes. The abundance of several genera (e.g. Rheinheimera and Pseudomonas) was positively correlated with C. transvaalensis population dynamics, while a predator-prey interaction was observed between the relative abundance of Vibrio OTUs and C. transvaalensis population size. Chironomids are known to tolerate toxic and stress conditions, and our results demonstrated that bacterial genera that may protect the insect under these conditions are present in the egg masses. After hatching, the first larval meal is the gelatinous matrix that surrounds the eggs. This meal contains a probiotic consortium that may protect the larva during its metamorphosis. The results provide important insights into the host-microbe interactions of chironomids.

RevDate: 2020-01-10

Cho DY, Skinner D, Lim DJ, et al (2020)

The impact of Lactococcus lactis (probiotic nasal rinse) co-culture on growth of patient-derived strains of Pseudomonas aeruginosa.

International forum of allergy & rhinology [Epub ahead of print].

BACKGROUND: The Lactococcus strain of bacteria has been introduced as a probiotic nasal rinse for alleged salubrious effects on the sinonasal bacterial microbiome. However, data regarding interactions with pathogenic bacteria within the sinuses are lacking. The purpose of this study is to assess the interaction between L. lactis and patient-derived Pseudomonas aeruginosa, an opportunistic pathogen in recalcitrant chronic rhinosinusitis (CRS).

METHODS: Commercially available probiotic suspension containing L. lactis W136 was grown in an anaerobic chamber and colonies were isolated. Colonies were co-cultured with patient-derived P. aeruginosa strains in the presence of porcine gastric mucin (mimicking human mucus) for 72 hours. P. aeruginosa cultures without L. lactis served as controls. Colony forming units (CFUs) were compared.

RESULTS: Six P. aeruginosa isolates collected from 5 CRS patients (3 isolates from cystic fibrosis [CF], 1 mucoid strain) and laboratory strain PAO1 were co-cultured with L. lactis. There was no statistical difference in CFUs of 5 P. aeruginosa isolates grown with L. lactis compared to CFUs without presence of L. lactis. CFU counts were much higher when the mucoid strain was co-cultured with L. lactis (CFU+L.lactis = 1.9 × 108 ± 1.44 × 107, CFU-L.lactis = 1.3 × 108 ± 8.9 × 106, p = 0.01, n = 7). L. lactis suppressed the growth of 1 P. aeruginosa strain (CFU+L.lactis = 2.15 × 108 ± 2.9 × 107, CFU-L.lactis = 3.95 × 108 ± 4.8 × 106, p = 0.03, n = 7).

CONCLUSION: L. lactis suppressed the growth of 1 patient P. aeruginosa isolate and induced growth of another (a mucoid strain) in in vitro co-culture setting in the presence of mucin. Further experiments are required to assess the underlying interactions between L. lactis and P. aeruginosa.

RevDate: 2020-01-10

Zeng SL, Li SZ, Xiao PT, et al (2020)

Citrus polymethoxyflavones attenuate metabolic syndrome by regulating gut microbiome and amino acid metabolism.

Science advances, 6(1):eaax6208 pii:aax6208.

Metabolic syndrome (MetS) is intricately linked to dysregulation of gut microbiota and host metabolomes. Here, we first find that a purified citrus polymethoxyflavone-rich extract (PMFE) potently ameliorates high-fat diet (HFD)-induced MetS, alleviates gut dysbiosis, and regulates branched-chain amino acid (BCAA) metabolism using 16S rDNA amplicon sequencing and metabolomic profiling. The metabolic protective effects of PMFE are gut microbiota dependent, as demonstrated by antibiotic treatment and fecal microbiome transplantation (FMT). The modulation of gut microbiota altered BCAA levels in the host serum and feces, which were significantly associated with metabolic features and actively responsive to therapeutic interventions with PMFE. Notably, PMFE greatly enriched the commensal bacterium Bacteroides ovatus, and gavage with B. ovatus reduced BCAA concentrations and alleviated MetS in HFD mice. PMFE may be used as a prebiotic agent to attenuate MetS, and target-specific microbial species may have unique therapeutic promise for metabolic diseases.

RevDate: 2020-01-10

Zangl I, Pap IJ, Aspöck C, et al (2019)

The role of Lactobacillus species in the control of Candida via biotrophic interactions.

Microbial cell (Graz, Austria), 7(1):1-14 pii:MIC0179E115.

Microbial communities have an important role in health and disease. Candida spp. are ubiquitous commensals and sometimes opportunistic fungal pathogens of humans, colonizing mucosal surfaces of the genital, urinary, respiratory and gastrointestinal tracts and the oral cavity. They mainly cause local mucosal infections in immune competent individuals. However, in the case of an ineffective immune defense, Candida infections may become a serious threat. Lactobacillus spp. are part of the human microbiome and are natural competitors of Candida in the vaginal environment. Lactic acid, low pH and other secreted metabolites are environmental signals sensed by fungal species present in the microbiome. This review briefly discusses the ternary interaction between host, Lactobacillus species and Candida with regard to fungal infections and the potential antifungal and fungistatic effect of Lactobacillus species. Our understanding of these interactions is incomplete due to the variability of the involved species and isolates and the complexity of the human host.

RevDate: 2020-01-10

Corrêa TAF, Rogero MM, Hassimotto NMA, et al (2019)

The Two-Way Polyphenols-Microbiota Interactions and Their Effects on Obesity and Related Metabolic Diseases.

Frontiers in nutrition, 6:188.

Metabolic diseases can change the gut microbiota composition and function, and pathogenic bacteria contribute to the development of metabolic disorders. Polyphenols may act in the gut microbiota to favor the increase of beneficial bacteria and hamper the increase of pathogenic bacteria. In addition, the microbiota may act on polyphenols to increase their bioavailability. This two-way interactions between polyphenols and the gut microbiota could affect human metabolism and reduce cardiometabolic risk. Despite the possible benefits of polyphenols for human health through modulating the microbiome, studies are scarce, and present several limitations. This review provides an overview of the polyphenol-microbiota interactions and its effects on metabolic disorders.

RevDate: 2020-01-10

He Z, Wu J, Xiao B, et al (2019)

The Initial Oral Microbiota of Neonates Among Subjects With Gestational Diabetes Mellitus.

Frontiers in pediatrics, 7:513.

Objective: The objective was to investigate the potential effect of gestational diabetes mellitus on the initial neonatal oral microbiome community structure. Methods: Oral samples were collected from 20 full-term, vaginally delivered newborns with sterile swabs. Nine of them had mothers diagnosed with gestational diabetes mellitus (GDM group), while 11 had non-diabetic mothers (NDM group). The oral microbiota was analyzed using multi-barcode 16S rRNA sequencing on Illumina MiSeq system. Results: The results showed that the birth weight, gestational age and gestational weight gain were significantly higher in NDM group. There was a significant correlation between gestational age and birth weight. Neonatal oral microbiome was composed of five dominant phyla from Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Tenericutes. Compared to NDM group, a higher alpha diversity and reduction of phylum Firmicutes were observed in GDM group. Genus Lactobacillus dominated in NDM group, while Alistipes, Streptococcus, and Faecalibacterium were overabundant in GDM group. Additionally, carbohydrate metabolism increased in NDM group, whereas amino acid metabolism, vitamin metabolism and lipopolysaccharide biosynthesis were more abundant in GDM group. Conclusions: This study showed a distinct oral microbiota profile in neonates born to mothers with GDM, which indicated that maternal diabetes status played an important role in neonatal initial oral microbiota.

RevDate: 2020-01-10

Moynihan M, Sullivan T, Provenzano K, et al (2019)

Urinary Microbiome Evaluation in Patients Presenting with Hematuria with a Focus on Exposure to Tobacco Smoke.

Research and reports in urology, 11:359-367 pii:233386.

Purpose: To better characterize the urinary microbiome in males and contribute to overall understanding of the urinary microbiota specifically in patients undergoing evaluation for possible bladder cancer, stratified by risk exposure to smoking.

Patients and Methods: Recruitment of 43 male patients in a sequential manner presenting for hematuria evaluation to a single institution was undertaken. Mid-stream urine specimen pellets were processed through a DNA isolation protocol before undergoing PCR amplification, purification, and 16S rRNA gene sequencing. Gene sequences were clustered into operational taxonomic units and statistical analysis was performed to determine specimen diversity and phylogenetic trends.

Results: No significant difference in microbial diversity was found between the specimens. On subgroup analysis, no significant difference was observed when stratified by either tobacco smoking history or by newly diagnosed urothelial bladder cancer. Variation in microbial diversity was seen amongst all analyzed specimens.

Conclusion: The results of our analysis of carefully selected subjects help to better characterize the urinary microbiome in males and supplements the limited available information on the interrelationship between the urinary microbiome and development of genitourinary malignancy. No significant difference was observed in our small sample size when stratified by tobacco exposure or newly diagnosed bladder cancer.

RevDate: 2020-01-10

Mirmiran P, Houshialsadat Z, Gaeini Z, et al (2020)

Functional properties of beetroot (Beta vulgaris) in management of cardio-metabolic diseases.

Nutrition & metabolism, 17:3 pii:421.

Red beetroot (Beta vulgaris), as a naturally occurring root vegetable and a rich source of phytochemicals and bioactive compounds, is known for its beneficial roles in the improvement of several clinical and pathologic outcome. Chronic and acute beetroot juice supplementation, as a cost-effective strategy, is proposed to hold promises in controlling diabetes and insulin hemostasis, blood pressure and vascular function, renal health and the possible effect on microbiome abundance. The secondary outcome and physiological response of microbiome abundance modulation included the non- significant fluctuation of systolic and diastolic blood pressures. Also, some studies have suggested a reno-protective property of beetroot juice that is associated with the reduction of mortality rate and favorable changes in kidney's functional parameters among patients with renal disorders. Similarly, it is shown that the persistent consumption of beetroot juice effectively postpones the postprandial glycemic response and decreases the blood glucose peak. The significant blood pressure lowering effect has been seen among normotensive subjects, which tend to be more considerable among hypertensive individuals and progressive among overweight adults. Within this context, this review aims to provide a comprehensive overview on the therapeutic applications of beetroot juice in metabolic disorders and theirs underlying mechanisms. Despite the inconsistencies in the set of results from the reviewed studies, there is no doubt that further contributing factors must be investigated more deeply in future studies.

RevDate: 2020-01-10

Wei F, Zhao L, Xu X, et al (2019)

Cultivar-Dependent Variation of the Cotton Rhizosphere and Endosphere Microbiome Under Field Conditions.

Frontiers in plant science, 10:1659.

Verticillium wilt caused by Verticillium dahliae is a common soil-borne disease worldwide, affecting many economically important crop species. Soil microbes can influence plant disease development. We investigated rhizosphere and endosphere microbiomes in relation to cotton cultivars with differential susceptibility to Verticillium wilt. Soil samples from nine cotton cultivars were assessed for the density of V. dahliae microsclerotia; plants were assessed for disease development. We used amplicon sequencing to profile both bacterial and fungal communities. Unlike wilt severity, wilt inoculum density did not differ significantly among resistant and susceptible cultivars. Overall, there were no significant association of alpha diversity indices with wilt susceptibility. In contrast, there were clear differences in the overall rhizosphere and endosphere microbial communities, particularly bacteria, between resistant and susceptible cultivars. Many rhizosphere and endosphere microbial groups differed in their relative abundance between resistant and susceptible cultivars. These operational taxonomic units included several well-known taxonomy groups containing beneficial microbes, such as Bacillales, Pseudomonadales, Rhizobiales, and Trichoderma, which were higher in their relative abundance in resistant cultivars. Greenhouse studies with sterilized soil supported that beneficial microbes in the rhizosphere contribute to reduced wilt development. These findings suggested that specific rhizosphere and endosphere microbes may contribute to cotton resistance to V. dahliae.

RevDate: 2020-01-10

Coates M, Lee MJ, Norton D, et al (2019)

The Skin and Intestinal Microbiota and Their Specific Innate Immune Systems.

Frontiers in immunology, 10:2950.

The skin and intestine are active organs of the immune system that are constantly exposed to the outside environment. They support diverse microbiota, both commensal and pathogenic, which encompass bacteria, viruses, fungi, and parasites. The skin and intestine must maintain homeostasis with the diversity of commensal organisms present on epithelial surfaces. Here we review the current literature pertaining to epithelial barrier formation, microbial composition, and the complex regulatory mechanisms governing the interaction between the innate immune system and microbiota in the skin and intestine. We also compare and contrast the skin and intestine-two different organ systems responsible creating a protective barrier against the external environment, each of which has unique mechanisms for interaction with commensal populations and host repair.

RevDate: 2020-01-10

Tirone C, Pezza L, Paladini A, et al (2019)

Gut and Lung Microbiota in Preterm Infants: Immunological Modulation and Implication in Neonatal Outcomes.

Frontiers in immunology, 10:2910.

In recent years, an aberrant gastrointestinal colonization has been found to be associated with an higher risk for postnatal sepsis, necrotizing enterocolitis (NEC) and growth impairment in preterm infants. As a consequence, the reasons of intestinal dysbiosis in this population of newborns have increasingly become an object of interest. The presence of a link between the gut and lung microbiome's development (gut-lung axis) is emerging, and more data show as a gut-brain cross talking mediated by an inflammatory milieu, may affect the immunity system and influence neonatal outcomes. A revision of the studies which examined gut and lung microbiota in preterm infants and a qualitative analysis of data about characteristic patterns and related outcomes in terms of risk of growing impairment, Necrotizing Enterocolitis (NEC), Bronchopulmonary Dysplasia (BPD), and sepsis have been performed. Microbiota take part in the establishment of the gut barrier and many data suggest its immune-modulator role. Furthermore, the development of the gut and lung microbiome (gut-lung axis) appear to be connected and able to lead to abnormal inflammatory responses which have a key role in the pathogenesis of BPD. Dysbiosis and the gut predominance of facultative anaerobes appear to be crucial to the pathogenesis and subsequently to the prevention of such diseases.

RevDate: 2020-01-10

Mei C, Yang W, Wei X, et al (2019)

The Unique Microbiome and Innate Immunity During Pregnancy.

Frontiers in immunology, 10:2886.

A successful pregnancy depends on not only the tolerance of the fetal immune system by the mother but also resistance against the threat of hazardous microorganisms. Infection with pathogenic microorganisms during pregnancy may lead to premature delivery, miscarriage, growth restriction, neonatal morbidity, and other adverse outcomes. Moreover, the host also has an intact immune system to avoid these adverse outcomes. It is important to note the presence of normal bacteria in the maternal reproductive tract and the principal role of the maternal-placental-fetal interaction in antimicrobial immunity. Previous studies mainly focused on maternal infection during pregnancy. However, this review summarizes the new views on the study of the maternal microbiome and expounds the innate immune defense mechanism of the maternal vagina and decidua as well as how cytotrophoblasts and syncytiotrophoblasts recognize and kill bacteria in the placenta. Fetal immune systems, thought to be weak, also exhibit an immune defense function that is indispensable for maintaining the safety of the fetus. The skin, lungs, and intestines of the fetus during pregnancy constitute the main immune barriers. These findings will provide a new understanding of the effects of normal microbial flora and how the host resists harmful microbes during pregnancy. We believe that it may also contribute to the reference on the clinical prevention and treatment of gestational infection to avoid adverse pregnancy outcomes.

RevDate: 2020-01-10

Drall KM, Tun HM, Morales-Lizcano NP, et al (2019)

Clostridioides difficile Colonization Is Differentially Associated With Gut Microbiome Profiles by Infant Feeding Modality at 3-4 Months of Age.

Frontiers in immunology, 10:2866.

Colonization with Clostridioides difficile occurs in up to half of infants under the age of 3 months, is strongly influenced by feeding modality and is largely asymptomatic. In spite of this, C. difficile's presence has been associated with susceptibility to chronic disease later in childhood, perhaps by promoting or benefiting from changes in infant gut microbiome development, including colonization with pathogenic bacteria and disrupted production of microbial bioactive metabolites and proteins. In this study, the microbiomes of 1554 infants from the CHILD Cohort Study were described according to C. difficile colonization status and feeding mode at 3-4 months of age. C. difficile colonization was associated with a different gut microbiome profile in exclusively breastfed (EBF) vs. exclusively formula fed (EFF) infants. EBF infants colonized with C. difficile had an increased relative abundance of Firmicutes and Proteobacteria, decreased relative abundance of Bifidobacteriaceae, greater microbiota alpha-diversity, greater detectable fecal short chain fatty acids (SCFA), and lower detectable fecal secretory Immunoglobulin A (sIgA) than those not colonized. Similar but less pronounced differences were seen among partially breastfed infants (PBF) but EFF infants did not possess these differences in the gut microbiome according to colonization status. Thus, breastfed infants colonized with C. difficile appear to possess a gut microbiome that differs from non-colonized infants and resembles that of EFF infants, but the driving force and direction of this association remains unknown. Understanding these compositional differences as drivers of C. difficile colonization may be important to ensure future childhood health.

RevDate: 2020-01-10

De la Fuente M, MacDonald TT, MA Hermoso (2019)

Editorial: Intestinal Homeostasis and Disease: A Complex Partnership Between Immune Cells, Non-Immune Cells, and the Microbiome.

Frontiers in immunology, 10:2775.

RevDate: 2020-01-10

Gereige JD, PJ Maglione (2019)

Current Understanding and Recent Developments in Common Variable Immunodeficiency Associated Autoimmunity.

Frontiers in immunology, 10:2753.

Common variable immunodeficiency (CVID) is the most prevalent symptomatic primary immunodeficiency and comprises a group of disorders with similar antibody deficiency but a myriad of different etiologies, most of which remain undefined. The variable aspect of CVID refers to the approximately half of patients who develop non-infectious complications in addition to heightened susceptibility to infection. The pathogenesis of these complications is poorly understood and somewhat counterintuitive because these patients that are defined by their immune futility simultaneously have elevated propensity for autoimmune disease. There are numerous aspects of immune dysregulation associated with autoimmunity in CVID that have only begun to be studied. These findings include elevations of T helper type 1 and follicular helper T cells and B cells expressing low levels of CD21 as well as reciprocal decreases in regulatory T cells and isotype-switched memory B cells. Recently, advances in genomics have furthered our understanding of the fundamental biology underlying autoimmunity in CVID and led to precision therapeutic approaches. However, these genetic etiologies are also associated with clinical heterogeneity and incomplete penetrance, highlighting the fact that continued research efforts remain necessary to optimize treatment. Additional factors, such as commensal microbial dysbiosis, remain to be better elucidated. Thus, while recent advances in our understanding of CVID-associated autoimmunity have been exciting and substantial, these current scientific advances must now serve as building blocks for the next stages of discovery.

RevDate: 2020-01-10

Haro-Moreno JM, Rodriguez-Valera F, M López-Pérez (2019)

Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics.

Frontiers in microbiology, 10:2926.

We performed an incubation experiment of seawater confined in plastic bottles with samples collected at three depths (15, 60, and 90 m) after retrieval from a single offshore location in the Mediterranean Sea, from a late summer stratified water column. Two samples representative of each depth were collected and stored in opaque bottles after two periods of 7 h. We took advantage of the "bottle effect" to investigate changes in the natural microbial communities (abundant and rare). We recovered 94 metagenome-assembled genomes (MAGs) and 1089 metagenomic viral contigs and examined their abundance using metagenomic recruitment. We detected a significant fast growth of copiotrophic bacteria such as Alteromonas or Erythrobacter throughout the entire water column with different dynamics that we assign to "clonal," "polyclonal," or "multispecies" depending on the recruitment pattern. Results also showed a marked ecotype succession in the phototropic picocyanobacteria that were able to grow at all the depths in the absence of light, highlighting the importance of their mixotrophic potential. In addition, "wall-chain-reaction" hypothesis based on the study of phage-host dynamics showed the higher impact of viral predation on archaea in deeper waters, evidencing their prominent role during incubations. Our results provide a step forward in understanding the mechanisms underlying dynamic patterns and ecology of the marine microbiome and the importance of processing the samples immediately after collection to avoid changes in the community structure.

RevDate: 2020-01-10

Baquero F, Coque TM, Martínez JL, et al (2019)

Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance.

Frontiers in microbiology, 10:2892.

Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.

RevDate: 2020-01-10

Lundgren SN, Madan JC, Karagas MR, et al (2019)

Microbial Communities in Human Milk Relate to Measures of Maternal Weight.

Frontiers in microbiology, 10:2886.

The process of breastfeeding exposes infants to bioactive substances including a diversity of bacteria from breast milk as well as maternal skin. Knowledge of the character of and variation in these microbial communities, as well as the factors that influence them, is limited. We aimed to identify profiles of breastfeeding-associated microbial communities and their association with maternal and infant factors. Bilateral milk samples were collected from women in the New Hampshire Birth Cohort Study at approximately 6 weeks postpartum without sterilization of the skin in order to capture the infant-relevant exposure. We sequenced the V4-V5 hypervariable region of the bacterial 16S rRNA gene in 155 human milk samples. We used unsupervised clustering (partitioning around medoids) to identify microbial profiles in milk samples, and multinomial logistic regression to test their relation with maternal and infant variables. Associations between alpha diversity and maternal and infant factors were tested with linear models. Four breastfeeding microbiome types (BMTs) were identified, which differed in alpha diversity and in Streptococcus, Staphylococcus, Acinetobacter, and Pseudomonas abundances. Higher maternal pre-pregnancy BMI was associated with increased odds of belonging to BMT1 [OR (95% CI) = 1.13 (1.02, 1.24)] or BMT3 [OR (95% CI) = 1.12 (1.01, 1.25)] compared to BMT2. Independently, increased gestational weight gain was related to reduced odds of membership in BMT1 [OR (95% CI) = 0.66 (0.44, 1.00) per 10 pounds]. Alpha diversity was positively associated with gestational weight gain and negatively associated with postpartum sample collection week. There were no statistically significant associations of breastfeeding microbiota with delivery mode. Our results indicate that the breastfeeding microbiome partitions into four profiles and that its composition and diversity is associated with measures of maternal weight.

RevDate: 2020-01-10

Millette G, Langlois JP, Brouillette E, et al (2019)

Despite Antagonism in vitro, Pseudomonas aeruginosa Enhances Staphylococcus aureus Colonization in a Murine Lung Infection Model.

Frontiers in microbiology, 10:2880.

Staphylococcus aureus and Pseudomonas aeruginosa are prevalent lung pathogens in cystic fibrosis (CF). Whereas co-infection worsens the clinical outcome, prototypical strains are usually antagonistic in vitro. We sought to resolve the discrepancy between these in vitro and in vivo observations. In vitro, growth kinetics for co-cultures of co-isolates from CF patients showed that not all P. aeruginosa strains affected S. aureus viability. On solid media, S. aureus slow-growing colonies were visualized around some P. aeruginosa strains whether or not S. aureus viability was reduced in liquid co-cultures. The S. aureus-P. aeruginosa interactions were then characterized in a mouse lung infection model. Lung homogenates were plated on selective media allowing colony counts of either bacterium. Overall, 35 P. aeruginosa and 10 S. aureus strains (clinical, reference, and mutant strains), for a total of 200 co-infections, were evaluated. We observed that S. aureus colonization of lung tissues was promoted by P. aeruginosa and even by strains showing antagonism in vitro. Promotion was proportional to the extent of P. aeruginosa colonization, but no correlation was found with the degree of myeloperoxidase quantification (as marker of inflammation) or with specific virulence-associated factors using known mutant strains of S. aureus and P. aeruginosa. On the other hand, P. aeruginosa significantly increased the expression of two possible cell receptors for S. aureus, i.e., ICAM-1 and ITGA-5 (marker for integrin α5β1) in lung tissue, while mono-infections by S. aureus did not. This study provides insights on polymicrobial interactions that may influence the progression of CF-associated pulmonary infections.

RevDate: 2020-01-10

Lang M, Bei S, Li X, et al (2019)

Rhizoplane Bacteria and Plant Species Co-determine Phosphorus-Mediated Microbial Legacy Effect.

Frontiers in microbiology, 10:2856.

Much effort has been directed toward increasing the availability of soil residual phosphorus (P). However, little information is available for the P fertilization-induced biotic P legacy and its mediation of plant P uptake. We collected microbial inocula from a monoculture maize field site with a 10-year P-fertilization history. A greenhouse experiment was conducted to investigate whether bacterial communities, as a result of different P-fertilization history (nil P, 33 and/or 131 kg P kg ha-1 yr-1), affected the growth of a conspecific (maize) or heterospecific (clover) plant, at two levels of current P application (5 and 30 mg P kg-1 soil; P5 and P30). Deep amplicon sequencing (16S rRNA) was used to determine the maize and clover root-associated bacterial microbiome in different rhizocompartments (rhizoplane, rhizosphere, bulk soil). For both maize and clover, rhizocompartment and host identity were the dominant factors shaping bacterial assemblages, followed by P supply level and the inoculum effect was smallest. Bacterial operational taxonomic unit (OTU) numbers decreased from bulk soil to rhizoplane, whilst specific OTUs were enriched from bulk soil to rhizoplane. A clear hierarchical habitat filtering of bacterial communities was observed in the rhizoplane of the two plant species. The functional prediction of dominant bacterial taxa in the rhizoplane differed between clover and maize, and clover microbiota were more closely associated with P metabolism and maize with carbon cycling. More connected and complex interactions were observed in the clover rhizoplane compared to maize. The microbial legacy effect caused by long-term P fertilization is overridden by host identity and rhizocompartment. Our results highlight the importance of crop diversification in improving P efficiency. The fine-tuning of rhizosphere microbiome in host metabolism indicates that the functions of microbial communities should be integrated into P management to increase P use efficiency and sustainable food production.

RevDate: 2020-01-10

De Cock M, Virgilio M, Vandamme P, et al (2019)

Impact of Sample Preservation and Manipulation on Insect Gut Microbiome Profiling. A Test Case With Fruit Flies (Diptera, Tephritidae).

Frontiers in microbiology, 10:2833.

High-throughput sequencing (HTS) techniques are of great value for the investigation of microbial communities, and have been extensively used to study the gut microbiome. While most studies focus on the human gut, many others have investigated insects. However, because of the rapid spread of HTS techniques, a lot of variation exists in the protocols for sample preparation. In the present study, we investigated the impact of two widely adopted sample-processing procedures preceding library preparation, i.e., preservation of insect tissue in 70% ethanol (EtOH) and sample dissection. We used the fruit fly Ceratitis capitata (Diptera: Tephritidae) as a model organism and set up two experiments, one comparing the effects of sample manipulation and preservation across life stages and the other across fruit samples from different sources. The results of this study showed no major effects of dissection on the outcome of HTS. However, EtOH preservation did have effects on the recovered gut microbiome, the main effect being a significant reduction of the dominant genus, Providencia, in EtOH-preserved samples. Less abundant bacterial groups were also affected resulting in altered microbial profiles obtained from samples preserved in 70% EtOH. These results have important implications for the planning of future studies and when comparing studies that used different sample preparation protocols.

RevDate: 2020-01-10

Latini A, Bacci G, Teodoro M, et al (2019)

The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil.

Frontiers in microbiology, 10:2694.

Biochar shapes the soil environment and plant growth. Nevertheless, the mechanisms associated with an improved plant biomass and soil microbiome in low metal-contaminated soils are still unclear. In this study, the influence of biochar on soil physico-chemical properties, plant performance, and rhizosphere microbiota in durum wheat was investigated at the above- and belowground levels. Two kinds of biochar from different feedstocks (wood chips and wheat straw pellets) and two Italian durum wheat varieties, Duilio and Marco Aurelio, were analyzed in a greenhouse using a low-nutrient gleyic fluvisol containing a very small amount of Pb and Zn. Four different treatments were performed: soil-only control (C), soil amended with woody biochar equilibrated with nutrient solution (B1+) and non-activated (B1-), and soil amended with non-activated (B2-) wheat straw biochar. Seven weeks after seed germination, (1) the physico-chemical properties of soil, biochars, and mixtures were assessed; (2) the fresh and dry weight of aboveground plant tissues and roots and other morphometric traits were measured; and (3) metabarcoding of the 16S rRNA bacterial gene was performed on rhizosphere soil samples. The results showed that the biochar from wheat straw had stronger impact on both durum varieties, with higher electrical conductivity, higher levels of available K and Na, and a substantial increase of dissolved Na+, K+, and Cl- ions in pore water. Generally, biochar amendment decreased Zn availability for the plants. In addition, biochar improved plant growth in the early growth stage, and the more positive effect was achieved by combining wheat straw biochar with Marco Aurelio. Rhizosphere bacterial microbiota showed variation in alpha diversity only due to treatment; on the other hand, the differential analysis showed consistent variation among samples with significant effects on amplicon sequence variant (ASV) abundance due to the specific biochar treatment as well as the genotype. The pure B1-, due to its scarce nutrient content with respect to the richer types (B1+ and B2-), had a negative impact on microbiota richness. Our study highlights that an appropriate combination of biochar feedstock and crop species may lead to superior yield.

RevDate: 2020-01-10

Jackson A, Forsyth CB, Shaikh M, et al (2019)

Diet in Parkinson's Disease: Critical Role for the Microbiome.

Frontiers in neurology, 10:1245.

Background: Parkinson's disease (PD) is the most common movement disorder affecting up to 1% of the population above the age of 60 and 4-5% of those above the age of 85. Little progress has been made on efforts to prevent disease development or halt disease progression. Diet has emerged as a potential factor that may prevent the development or slow the progression of PD. In this review, we discuss evidence for a role for the intestinal microbiome in PD and how diet-associated changes in the microbiome may be a viable approach to prevent or modify disease progression. Methods: We reviewed studies demonstrating that dietary components/foods were related to risk for PD. We reviewed evidence for the dysregulated intestinal microbiome in PD patients including abnormal shifts in the intestinal microbiota composition (i.e., dysbiosis) characterized by a loss of short chain fatty acid (SCFA) bacteria and increased lipopolysaccharide (LPS) bacteria. We also examined several candidate mechanisms by which the microbiota can influence PD including the NLRP3 inflammasome, insulin resistance, mitochondrial function, vagal nerve signaling. Results: The PD-associated microbiome is associated with decreased production of SCFA and increased LPS and it is believed that these changes may contribute to the development or exacerbation of PD. Diet robustly impacts the intestinal microbiome and the Western diet is associated with increased risk for PD whereas the Mediterranean diet (including high intake of dietary fiber) decreases PD risk. Mechanistically this may be the consequence of changes in the relative abundance of SCFA-producing or LPS-containing bacteria in the intestinal microbiome with effects on intestinal barrier function, endotoxemia (i.e., systemic LPS), NLRP3 inflammasome activation, insulin resistance, and mitochondrial dysfunction, and the production of factors such as glucagon like peptide 1 (GLP-1) and brain derived neurotrophic factor (BDNF) as well as intestinal gluconeogenesis. Conclusions: This review summarizes a model of microbiota-gut-brain-axis regulation of neuroinflammation in PD including several new mechanisms. We conclude with the need for clinical trials in PD patients to test this model for beneficial effects of Mediterranean based high fiber diets.

RevDate: 2020-01-10

Kaur H, Bose C, SS Mande (2019)

Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis.

Frontiers in neuroscience, 13:1365.

The link between gut microbiome and brain is being slowly acknowledged due to the speculated role of resident gut microbial community in altering the functions of gut-brain axis (GBA). Recently, a number of microbial metabolites (referred to as neuro-active metabolites) produced through tryptophan metabolism have been suggested to influence the GBA. In view of this, the current study focuses on microbial tryptophan metabolism pathways which produce neuro-active metabolites. An in silico analysis was performed on bacterial genomes as well as publicly available gut microbiome data. The results provide a comprehensive catalog of the analyzed pathways across bacteria. The analysis indicates an enrichment of tryptophan metabolism pathways in five gut-associated phyla, namely, Actinobacteria, Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria. Further, five genera, namely, Clostridium, Burkholderia, Streptomyces, Pseudomonas, and Bacillus have been predicted to be enriched in terms of number of the analyzed tryptophan metabolism pathways, suggesting a higher potential of these bacterial groups to metabolize tryptophan in gut. Analysis of available microbiome data corresponding to gut samples from patients of neurological diseases and healthy individuals suggests probable association of different sets of tryptophan metabolizing bacterial pathways with the etiology of different diseases. The insights obtained from the present study are expected to provide directions toward designing of microbiome based diagnostic and therapeutic approaches for neurological diseases/disorders.

RevDate: 2020-01-10

Bi Y, Marcus AK, Robert H, et al (2020)

The complex puzzle of dietary silver nanoparticles, mucus and microbiota in the gut.

Journal of toxicology and environmental health. Part B, Critical reviews [Epub ahead of print].

Hundreds of consumer and commercial products containing silver nanoparticles (AgNPs) are currently used in food, personal-care products, pharmaceutical, and many other applications. Human exposure to AgNPs includes oral intake, inhalation, and dermal contact. The aim of this review was to focus on oral intake, intentional and incidental of AgNPs where well-known antimicrobial characteristics that might affect the microbiome and mucus in the gastrointestinal tract (GIT). This critical review summarizes what is known regarding the impacts of AgNPs on gut homeostasis. It is fundamental to understand the forms of AgNPs and their physicochemical characterization before and during digestion. For example, lab-synthesized AgNPs differ from "real" ingestable AgNPs used as food additives and dietary supplements. Similarly, the gut environment alters the chemical and physical state of Ag that is ingested as AgNPs. Emerging research on in vitro and in vivo rodent and human indicated complex multi-directional relationships among AgNPs, the intestinal microbiota, and the epithelial mucus. It may be necessary to go beyond today's descriptive approach to a modeling-based ecosystem approach that might quantitatively integrate spatio-temporal interactions among microbial groups, host factors (e.g., mucus), and environmental factors, including lifestyle-based stressors. It is suggested that future research (1) utilize more representative AgNPs, focus on microbe/mucus interactions, (2) assess the effects of environmental stressors for longer and longitudinal conditions, and (3) be integrated using quantitative modeling.

RevDate: 2020-01-10

Xu K, Bai M, Liu H, et al (2020)

Gut microbiota and blood metabolomics in weaning multiparous sows: Associations with oestrous.

Journal of animal physiology and animal nutrition [Epub ahead of print].

This study was conducted to detect the potential relationship between changed plasma metabolites, intestinal microbiota and the weaning-to-oestrous interval in multiparous sows after weaning. Multiparous sows were allocated to two groups after weaning: the oestrous group (n = 15) with a weaning-to-oestrous interval ≤7 days or the anoestrous group (n = 15) with a weaning-to-oestrous interval >14 days. The levels of plasma reproductive hormones: oestradiol, follicle-stimulating hormone and luteinizing hormone, plasma total protein; blood urea nitrogen; cholesterol; high-density lipoprotein; and ammonia (NH3) were significantly lower in the anoestrous sows compared with the oestrous sows (p < .05). The plasma metabolomics analysis identified 14 metabolites (lactose, l-cysteine, cytosine, hydantoin, palmitoleic acid, arachidic acid, linoleic acid methyl ester, α-ketoglutaric acid, N(ε)-trimethyllysine, threo-β-hydroxyaspartate, 3-(3-hydroxyphenyl) propionic acid and others) with lower concentrations and 12 metabolites (noradrenaline, 5-dihydrocortisone, p-cresol, 1,4-cyclohexanedione, 2,3-dimethylsuccinic acid and others) with higher concentrations in the anoestrous group compared with the oestrous group (p < .05). The 16S rRNA pyrosequencing analysis showed the relative increase in abundance of the Prevotella and the Bacteroides at the genus level in the anoestrous group (p < .05). At the phylum level, lower proportions of Firmicutes and Lentisphaerae were observed in the anoestrous group (p < .05). This study provided a comprehensive assessment of metabolic differences in the blood and differences in the gut microbiome composition between anoestrous and oestrous sows. And suggesting that this profiling approach may offer new insights into explaining the alteration of the gut microbiota and blood metabolomics are correlated with sex hormone secretion and the weaning-to-oestrous interval of sows after weaning.

RevDate: 2020-01-10

Davis I, Sevigny J, Kleiner V, et al (2020)

Draft Genome Sequences of 10 Bacterial Strains Isolated from Root Nodules of Alnus Trees in New Hampshire.

Microbiology resource announcements, 9(2): pii:9/2/e01440-19.

Here, we report the draft genome sequences obtained for 10 bacterial strains isolated from root nodules of Alnus trees. These members of the nodule microbiome were sequenced to determine their potential functional roles in plant health. The selected strains belong to the genera Rhodococcus, Kocuria, Rothia, Herbaspirillum, Streptomyces, and Thiopseudomonas.

RevDate: 2020-01-10

Donovan M, Lynch MDJ, Mackey CS, et al (2020)

Metagenome-Assembled Genome Sequences of Five Strains from the Microtus ochrogaster (Prairie Vole) Fecal Microbiome.

Microbiology resource announcements, 9(2): pii:9/2/e01310-19.

The prairie vole (Microtus ochrogaster) is an important model for the study of social monogamy and dual parental care of offspring. Characterization of specific host species-microbe strain interactions is critical for understanding the effects of the microbiota on mood and behavior. The five metagenome-assembled genome sequences reported here represent an important step in defining the prairie vole microbiome.

RevDate: 2020-01-10

Cholewińska P, Czyż K, Nowakowski P, et al (2020)

The microbiome of the digestive system of ruminants - a review.

Animal health research reviews pii:S1466252319000069 [Epub ahead of print].

This review aims to explain the influence and characterization of the microbiome in the ruminant digestive system by presenting the knowledge collected so far. The knowledge presented in this work is focused on the main factors affecting the microbiome and the main dependencies that have been found in it so far. The microbiome in the rumen is the first to come into contact with the biomass of the forage and its main purpose is to decompose into smaller particles or compounds. With the gradual increase in knowledge about the microbiome, there is a chance to manipulate it so that the animal continues to live in a symbiotic relationship with it, while reducing greenhouse gas emissions to the environment as well as increasing feed efficiency. Therefore, understanding the influence of the ruminant microbiome is the main step to achieve such results. However, learning the relationship between microorganisms is only at an early stage, because research focuses mainly on taxonomy. Future research should focus on interactions in the ecosystem which is the microbiome, on explaining individual functions and on influence of environmental factors.

RevDate: 2020-01-10

Song YF, Pei LX, Chen L, et al (2020)

Electroacupuncture Relieves Irritable Bowel Syndrome by Regulating IL-18 and Gut Microbial Dysbiosis in a Trinitrobenzene Sulfonic Acid-Induced Post-Inflammatory Animal Model.

The American journal of Chinese medicine [Epub ahead of print].

Post inflammatory irritable bowel syndrome (PI-IBS), a subset of IBS, is characterized by symptoms of visceral pain, bloating, and changed bowel habits that occur post initial episode of intestinal infection. Gut microbial dysbiosis or inflammation plays a key role in the pathogenesis of abdominal hypersensitivity of PI-IBS. Electroacupuncture (EA) stimulation results in an alleviated PI-IBS-associated symptom. This study investigated the effect of EA on IL-18 and gut microbial dysbiosis in one visceral hypersensitive rat models with PI-IBS. A trinitrobenzene sulfonic acid (TNBS)-induced visceral hypersensitivity rat model was developed. EA stimulation was applied to the ST25 and ST36 acupoints. Animals were assessed using abdominal withdrawal reflex (AWR) scores to determine the development of colonic visceral hypersensitivity. The 16S rRNA was used to correlate microbial diversity. IL-18 expression in colon was quantified by quantitative real-time PCR and western blotting. We identified that model rats had an increased visceral hypersensitivity to colorectal distention at different distention pressures compared with the normal group. Sensitivity to colorectal distention decreased after EA stimulation. The composition of the fecal microbiota was different between groups. Specifically, in the model group Empedobacter, Psychrobacter, Enterococcus, Butyricimonas, Vampirovibrio, Kurthia, Intestinimonas, Neisseria, Falsiporphyromonas, Bilophila, Fusobacterium, Alistipes, Veillonella, Flavonifractor, Clostridium XlVa were more abundant affected genera, whereas Lactobacillus was enriched in normal rats. EA stimulation was correlated with significant decrease in the phyla of Fusobacteria. The mRNA and protein levels of IL-18 were higher in the model group. Meanwhile, EA stimulation attenuated this response. In a word, our findings suggest that PI-IBS is associated with significant increase in IL-18 levels as well as an alteration in microbiome diversity. These changes can be reversed with EA treatment. EA stimulation has a positive effect in alleviating symptoms of visceral hypersensitivity and protecting the gastrointestinal tract.

RevDate: 2020-01-10

Tang X, Kudo Y, Baker JL, et al (2020)

Cariogenic Streptococcus mutans Produces Tetramic Acid Strain-Specific Antibiotics That Impair Commensal Colonization.

ACS infectious diseases [Epub ahead of print].

Streptococcus mutans is a common constituent of dental plaque and a major etiologic agent of dental caries (tooth decay). In this study, we elucidated the biosynthetic pathway encoded by muc, a hybrid polyketide synthase and nonribosomal peptide synthetase (PKS/NRPS) biosynthetic gene cluster (BGC), present in a number of globally distributed S. mutans strains. The natural products synthesized by muc included three N-acyl tetramic acid compounds (reutericyclin and two novel analogues) and an unacylated tetramic acid (mutanocyclin). Furthermore, the enzyme encoded by mucF was identified as a novel class of membrane-associated aminoacylases and was responsible for the deacylation of reutericyclin to mutanocyclin. A large number of hypothetical proteins across a broad diversity of bacteria were homologous to MucF, suggesting that this may represent a large family of unexplored acylases. Finally, S. mutans utilized the reutericyclin produced by muc to impair the growth of neighboring oral commensal bacteria. Since S. mutans must be able to out-compete these health-associated organisms to persist in the oral microbiota and cause disease, the competitive advantage conferred by muc suggests that this BGC is likely to be involved in S. mutans ecology and therefore dental plaque dysbiosis and the resulting caries pathogenesis.

RevDate: 2019-12-23

Rimet CS, Maurer JJ, Berghaus RD, et al (2019)

The Contribution of Eimeria Coinfection and Intestinal Inflammation to Cecal Colonization and Systemic Spread of Salmonella Typhimurium Deficient in Tetrathionate Reductase or Type III Secretion Systems Salmonella Pathogenicity Island 1 or 2.

Avian diseases, 63(4):559-567.

Intestinal inflammation may provide a growth advantage for Salmonella and enhance its systemic spread in chickens. Salmonella triggers intestinal inflammation in the host by using type III secretion systems (T3SS) and produces the inflammatory end product tetrathionate. In mice, tetrathionate respiration confers a growth advantage for Salmonella Typhimurium over the competitive microbiome in the inflamed intestine. Coccidia also promote intestinal inflammation and enhance Salmonella intestinal growth and systemic spread in chickens. The objective of this study was to evaluate the contribution of inflammation, induced by Eimeria spp. or Salmonella Typhimurium, to Salmonella colonization and dissemination in chickens. In addition, the fitness costs associated with defects in tetrathionate reductase and T3SS associated with Salmonella Pathogenicity Island 1 or 2 (SPI-1 or SPI-2) were evaluated in in vivo competition experiments with wild-type Salmonella strain, with or without Eimeria coinfection. One-day-old specific-pathogen-free chickens were orally inoculated with a sham inoculum or with 4 × 102Eimeria oocysts cocktail of Eimeria tenella, Eimeria acervulina, Eimeria maxima, and Eimeria mitis. At 6 days of age, birds were orally administered a 1:1 ratio of Salmonella Typhimurium wild-type and mutant deficient in tetrathionate reductase, SPI-1, or SPI-2 (108 colony forming units/bird). Ceca, livers, and drumsticks were collected at 3, 7, 14, and 42 days after Salmonella infection, for bacteriology. Intestinal inflammation was scored by histology. Significantly higher intestinal inflammation was observed in challenge groups compared with the control. However, there were no significant differences in intestinal inflammation scores between groups coinfected with both Eimeria spp. and Salmonella Typhimurium and birds infected with Salmonella alone, and Eimeria coinfection did not increase Salmonella prevalence or abundance. Contrary to mouse studies, tetrathionate reductase did not enhance Salmonella Typhimurium cecal colonization or systemic spread in chickens. SPI-1 and SPI-2 played a significant role in Salmonella dissemination and cecal colonization in chickens, respectively.

RevDate: 2020-01-09

Flores-Rodriguez C, B Min (2019)

Enrichment of specific microbial communities by optimum applied voltages for enhanced methane production by microbial electrosynthesis in anaerobic digestion.

Bioresource technology, 300:122624 pii:S0960-8524(19)31854-1 [Epub ahead of print].

This study investigates the distribution of microbiome in microbial electrosynthesis systems at different applied voltages (0.5, 1.0, and 1.5 V) for methane production. Results revealed that more favorable conditions for methane production were observed with 1.0 V applied voltage. In Venn plots, the bioelectrodes at 1.0 V had higher numbers of unique operational taxonomic units compared to those at 0.5 and 1.5 V. Hierarchical cluster, non-metric multidimensional scaling, and principal component ordinate analyses revealed that the biocathode at 1.0 V clustered separately from the rest of the biofilms mainly because of the quantitative differences in the microbial distribution. Taxonomically, exoelectrogens (Geobacter spp.) dominated the bioanode at 1.0 V, while the syntrophic assemblages of hydrogen-producing bacteria (i.e., Bacteroidetes and Firmicutes) and hydrogen-consuming methanogens (i.e., Methanobacterium sp.) existed in the biocathode. These results suggest that the optimum applied voltage enriched specific microbial communities on the anode and cathode for enhanced methane production.

RevDate: 2020-01-09

Choi M, Chaudhary R, Lee M, et al (2019)

Enhanced selective enrichment of partial nitritation and anammox bacteria in a novel two-stage continuous flow system using flat-type poly (vinylalcohol) cryogel films.

Bioresource technology, 300:122546 pii:S0960-8524(19)31776-6 [Epub ahead of print].

To improve stability of nitrogen removal in partial nitritation (PN)-anammox process, flat-type cryogel films using poly (vinylalcohol) named as FT-CPVAF were applied in continuous reactors. Stable PN operation was maintained with short acclimation of 8 days and ammonium oxidation rate of 1.68 ± 0.12 kg N m-3 d-1 comparatively higher than previous studies. The nitrogen removal, initially inhibited by an oxygen shock, was immediately reactivated with short lag-period by immobilization of anammox bacteria in FT-CPVAF. A novel two-stage PN-anammox process was operated in a continuous flow using FT-CPVAF for treatment of ammonium-rich synthetic wastewater (influent 315 mg NH4+-N L-1) showing 89.6 ± 0.76% of nitrogen removal at short hydraulic retention time (7.7 h). The use of FT-CPVAF enhanced selective enrichment of AOB and anammox bacter ia confirmed by high-throughput sequencing of i.e., relative abundances of Nitrosomonas europaea C-31 (37.14% in PN reactor) and 'Candidatus Jettenia caeni' (34.36% in anammox reactor).


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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