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Bibliography on: Microbiome

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ESP: PubMed Auto Bibliography 09 Apr 2020 at 01:46 Created: 


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

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

Citations The Papers (from PubMed®)

RevDate: 2020-04-08

Cevidanes A, Esperón F, Di Cataldo S, et al (2020)

Antimicrobial resistance genes in Andean foxes inhabiting anthropized landscapes in central Chile.

The Science of the total environment, 724:138247 pii:S0048-9697(20)31760-5 [Epub ahead of print].

Antimicrobial resistance (AMR) is considered an emerging public health problem. Greater AMR development rate is associated with "antibiotic-using" environments. Wildlife thriving in anthropized landscapes could be good indicators of the burden of AMR and antibiotic resistance genes (ARGs) in these areas. The aim of this study was to determine the presence and load of ARGs in fecal swabs of wild Andean foxes (Lycalopex culpaeus) from anthropized landscapes of central Chile. DNA was extracted from samples of 72 foxes; 22 ARGs encoding resistance against 8 antibiotic groups were evaluated using qPCR. Eighteen of the 22 ARGs were found and tet(Q) (65.3%; 15/72 of the samples) was the most common gene detected. Almost half of the foxes presented a 'multiresistant microbiome' (i.e. at least three ARG encoding resistance to different groups of antimicrobials). Prevalence of tet(Q) was higher in the cold-humid season than in the warm-dry season, but not for other genes. Up to 15 and 13 ARGs were detected in the fecal samples from two additional foxes that were kept 6 and 11 days, respectively, in a clinical environment (Wildlife Rescue Center) and received antibiotic treatment. Some of the ARGs detected (e.g. mecA and blaCTX-M) in the present study are of particular concern from the public health perspective. Wild foxes seem to be good sentinels for ARG environmental burden in highly anthropized environments of central Chile.

RevDate: 2020-04-08

Yu AI, Zhao L, Eaton KA, et al (2020)

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis.

Cell reports, 31(1):107471.

There is increasing evidence that gut microbiome perturbations, also known as dysbiosis, can influence colorectal cancer development. To understand the mechanisms by which the gut microbiome modulates cancer susceptibility, we examine two wild-type mouse colonies with distinct gut microbial communities that develop significantly different tumor numbers using a mouse model of inflammation-associated tumorigenesis. We demonstrate that adaptive immune cells contribute to the different tumor susceptibilities associated with the two microbial communities. Mice that develop more tumors have increased colon lamina propria CD8+ IFNγ+ T cells before tumorigenesis but reduced CD8+ IFNγ+ T cells in tumors and adjacent tissues compared with mice that develop fewer tumors. Notably, intratumoral T cells in mice that develop more tumors exhibit increased exhaustion. Thus, these studies suggest that microbial dysbiosis can contribute to colon tumor susceptibility by hyperstimulating CD8 T cells to promote chronic inflammation and early T cell exhaustion, which can reduce anti-tumor immunity.

RevDate: 2020-04-08

Haddad EN, Sugino KY, Tucker RM, et al (2020)

Gut enterotypes are stable during Bifidobacterium and Lactobacillus probiotic supplementation.

Journal of food science [Epub ahead of print].

The human gut microbiome has been classified into three distinct enterotypes (Bacteroides, Prevotella, and Ruminococcus). The relationship between probiotics and gut enterotype is not yet clear. Cayenne pepper is effective in vitro as a prebiotic for Bifidobacteria and Lactobacilli, so cayenne ingestion with probiotics may lead to more profound gut microbial shifts. We aimed to determine whether probiotics (with or without cayenne pepper) alter gut bacterial community composition and if these changes are associated with the original gut enterotype of the individual. A total of 27 adult participants provided three fecal samples: prior to probiotic treatment (baseline), post probiotic treatment (probiotic), and post probiotic plus cayenne pepper treatment (probiotic + cayenne). DNA was extracted, amplified, and the V4 region sequenced on the Illumina MiSeq platform using V2 chemistry. Sequence reads were processed in mothur and assigned using the SILVA reference by phylotype. Three enterotypes characterized the study population-Bacteroides (B; n = 6), Prevotella (P; n = 11), and Ruminoccocus (R; n = 10). There was no significant increase in probiotic genera in fecal samples after treatment periods. Alpha diversity scores were significantly lower in B-type but not in P- or R-type individuals after probiotic treatment. For the majority of individuals, their enterotype remained constant regardless of probiotic (and cayenne) treatment. This suggests that baseline gut community characteristics and enterotype classification influence responsiveness to probiotic treatment, but that enterotype is stable across administration of prebiotic and probiotics. PRACTICAL APPLICATION: A person's gut microbial community influences their responsiveness to probiotics and prebiotic ingredients. Consumers must understand that it is difficult to shift their gut microbiota even with simultaneous administration of prebiotic and probiotic. Greater understanding of these phenomena will enable consumers to choose the most efficacious products for their needs.

RevDate: 2020-04-08

Koay YC, Chen YC, Wali JA, et al (2020)

Plasma Levels of TMAO can be Increased with 'Healthy' and 'Unhealthy' Diets and Do Not Correlate with the Extent of Atherosclerosis but with Plaque Instability.

Cardiovascular research pii:5817823 [Epub ahead of print].

AIMS: The microbiome-derived metabolite trimethylamine-N-oxide (TMAO) has attracted major interest and controversy both as a diagnostic biomarker and therapeutic target in atherothrombosis.

METHODS AND RESULTS: Plasma TMAO increased in mice on 'unhealthy' high-choline diets and notably also on 'healthy' high-fibre diets. Interestingly, TMAO was found to be generated by direct oxidation in the gut in addition to oxidation by hepatic flavin-monooxygenases. Unexpectedly, two well-accepted mouse models of atherosclerosis, ApoE-/- and Ldlr-/- mice, which reflect the development of stable atherosclerosis, showed no association of TMAO with the extent of atherosclerosis. This finding was validated in the Framingham Heart Study showing no correlation between plasma TMAO and coronary artery calcium score or carotid intima-media thickness, as measures of atherosclerosis in human subjects. However, in the tandem-stenosis mouse model, which reflects plaque instability as typically seen in patients, TMAO levels correlated with several characteristics of plaque instability, such as markers of inflammation, platelet activation, and intraplaque haemorrhage.

CONCLUSIONS: Dietary-induced changes in the microbiome, of both 'healthy' and 'unhealthy' diets, can cause an increase in the plasma level of TMAO. The gut itself is a site of significant oxidative production of TMAO. Most importantly, our findings reconcile contradictory data on TMAO. There was no direct association of plasma TMAO and the extent of atherosclerosis, both in mice and humans. However, using a mouse model of plaque instability we demonstrated an association of TMAO plasma levels with atherosclerotic plaque instability. The latter confirms TMAO as being a marker of cardiovascular risk.

TRANSLATIONAL PERSPECTIVE: There has been keen interest lately in the microbiome as a novel therapeutic target in the prevention and treatment of cardiovascular diseases. Trimethylamine-N-oxide (TMAO) is a microbiome-derived metabolite that has received a lot of interest as a novel biomarker and potential therapeutic target in atherothrombosis. However, there have been conflicting reports of its association with atherosclerosis and thrombosis, with some even showing an inverse association. In spite of this, in the correct context TMAO appears to be an excellent biomarker of subclinical atherosclerosis that can identify those at short-term and long-term risk of myocardial infarction. Herein, we reveal different dietary-microbiome interactions that help explain the apparent contradictions of TMAO's association with atherothrombosis. This insight is critical for the appropriate use of TMAO as a potential diagnostic and therapeutic target. Furthermore, using a unique murine model, we reveal TMAO to be associated with several features of plaque instability, providing insight into its utility as a marker of cardiovascular risk.

RevDate: 2020-04-08

Pongking T, Haonon O, Dangtakot R, et al (2020)

A combination of monosodium glutamate and high-fat and high-fructose diets increases the risk of kidney injury, gut dysbiosis and host-microbial co-metabolism.

PloS one, 15(4):e0231237 pii:PONE-D-19-27649.

Consumption of either monosodium glutamate (MSG) or high-fat and high-fructose (HFF) diets changes the gut microbiome and hence contributes to development of several diseases. In this study, with an emphasis on kidney injury, hamsters were divided into 4 groups as follows: (1) hamsters fed with standard diet (control); (2) hamsters fed with standard diet and MSG in drinking water (MSG); (3) hamsters fed with high-fat and high-fructose diets (HFF), and (4) animals fed MSG+HFF. After 8 months, the animals were used for the study. Despite showing normal kidney function, hamsters fed with MSG+HFF exhibited signs of kidney damage as demonstrated by the highest expression levels of high-mobility group box-1 and kidney injury molecule-1 in kidney tissues, while slight changes of histopathological features in H&E-stained sections and normal levels of creatinine were observed, indicating possible early stages of kidney injury. Sequencing of the microbial 16S rRNA gene revealed that animals fed with the MSG+HFF diet had a higher ratio of gut Firmicutes/Bacteroidetes along with marked changes in abundance and diversity of gut microbiome compared to hamsters fed with MSG or HFF alone. In addition, 1H Nuclear magnetic resonance spectroscopy showed an elevation of urine p-cresol sulfate levels in the MSG+HFF group. These results indicate that consumption of both MSG and HFF increases the risk of kidney injury, induces gut dysbiosis and an increase in the amount of p-cresol sulfate in hamsters.

RevDate: 2020-04-08

Kaur K, Khatri I, Akhtar A, et al (2020)

Metagenomics analysis reveals features unique to Indian distal gut microbiota.

PloS one, 15(4):e0231197 pii:PONE-D-19-16291.

Various factors including diet, age, geography, culture and socio-economic status have a role in determining the composition of the human gut microbiota. The human gut microbial composition is known to be altered in disease conditions. Considering the important role of the gut microbiome in maintaining homeostasis and overall health, it is important to understand the microbial diversity and the functional metagenome of the healthy gut. Here, we characterized the microbiota of 31 fecal samples from healthy individuals of Indian ethnic tribes from Ladakh, Jaisalmer and Khargone by shotgun metagenomic sequencing. Sequence analysis revealed that Bifidobacterium and Prevotella were the key microbes contributing to the differences among Jaisalmer, Khargone and Ladakh samples at the genus level. Our correlation network study identified carbohydrate-active enzymes and carbohydrate binding proteins that are associated with specific genera in the different Indian geographical regions studied. Network analysis of carbohydrate-active enzymes and genus abundance revealed that the presence of different carbohydrate-active enzymes is driven by differential abundance of genera. The correlation networks were different in the different geographical regions, and these interactions suggest the role of less abundant genera in shaping the gut environment. We compared our data with samples from different countries and found significant differences in taxonomic composition and abundance of carbohydrate-active enzymes in the gut microbiota as compared to the other countries.

RevDate: 2020-04-08

Chopra A, Radhakrishnan R, M Sharma (2020)

Porphyromonas gingivalis and adverse pregnancy outcomes: a review on its intricate pathogenic mechanisms.

Critical reviews in microbiology [Epub ahead of print].

Porphyromonas gingivalis (P. gingivalis), a Gram-negative facultative anaerobe of the oral cavity, is associated with the onset of various adverse pregnancy outcomes. P. gingivalis is linked with the development of preeclampsia, preterm labour, spontaneous abortion, gestational diabetes, foetal growth restriction, and misconception. The unique virulence factors, surface adhesions, enzymes of P. gingivalis can directly injure and alter the morphology, microbiome the foetal and maternal tissues. P. gingivalis can even exaggerate the production of cytokines, free radicals and acute-phase proteins in the uterine compartment that increases the risk of myometrial contraction and onset of preterm labour. Although evidence confirms the presence of P. gingivalis in the amniotic fluid and placenta of women with poor pregnancy outcomes, the intricate molecular mechanisms by which P. gingivalis initiates various antenatal and postnatal maternal and foetal complications are not well explained in the literature. Therefore, the present review aims to comprehensively summarise and highlight the recent and unique molecular pathogenic mechanisms of P. gingivalis associated with adverse pregnancy outcomes.

RevDate: 2020-04-08

Zagrodnik R, Duber A, Lezyk M, et al (2020)

Enrichment vs. bioaugmentation - microbiological production of caproate from mixed carbon sources by mixed bacterial culture and Clostridium kluyveri.

Environmental science & technology [Epub ahead of print].

Chain elongation is a process that produces medium chain fatty acids (MCFAs) such as caproic acid which is one of the promising products of carboxylate platform. This study analyzed the impact of bioaugmentation of heat treated anaerobic digester sludge with C. kluyveri (AS+Ck) on caproic acid production from mixed substrate (lactose, lactate, acetate and ethanol). It was compared with processes initiated with non-augmented heat treated anaerobic digester sludge (AS) and mono-culture of C. kluyveri (Ck). Moreover, stability of the chain elongation process was evaluated by performing repeated batch experiments. All bacterial cultures demonstrated efficient caproate production in the first batch cycle. After 18 days caproate concentration reached 9.06 ± 0.43, 7.86 ± 0.38 and 7.67 ± 0.37 g/L for AS, Ck and AS+Ck cultures, respectively. AS microbiome was enriched towards caproate production in the second cycle and showed the highest caproate concentration of 11.44 ± 0.47 g/L. On the other hand, bioaugmented culture showed the lowest caproate production in the second cycle (4.10 ± 0.30 g/L). Microbiome analysis in both, AS and AS+Ck culture samples, indicated strong enrichment towards the anaerobic order of Clostridia. Strains belonging to genera Sporanaerobacter, Paraclostridium, Haloimpatiens, Clostridium and Bacillus were dominating in the bioreactors.

RevDate: 2020-04-08

Tushuizen ME, Holleboom AG, Koot BGP, et al (2020)

[Non-alcoholic fatty liver disease; a full-bodied epidemic].

Nederlands tijdschrift voor geneeskunde, 164:.

Non-alcoholic fatty liver disease (NAFLD) is the most common cause of fatty liver disease. NAFLD is defined as the presence of fatty liver disease observed in imaging or histopathological examinations when there is no secondary cause such as excessive alcohol use or use of certain medications. NAFLD encompasses a whole spectrum, from simple steatosis to steatohepatitis ('non-alcoholic steatohepatitis', NASH), fibrosis and - ultimately - cirrhosis and hepatocellular carcinoma. Several factors play a role in the complex pathogenesis of NAFLD such as genetic predisposition, overweight, insulin resistance, inflammation, bile salts, gut microbiome and nutrition. Patients with NAFLD have an increased risk of developing type 2 diabetes mellitus, cardiovascular disease and malignancies such as hepatocellular carcinoma. To date, no medicines have been authorised for the treatment of NAFLD. The cornerstone of NAFLD treatment is lifestyle adjustment aimed at weight reduction.

RevDate: 2020-04-08

Demir M, Lang S, Martin A, et al (2020)

Phenotyping non-alcoholic fatty liver disease by the gut microbiota - ready for prime time?.

Journal of gastroenterology and hepatology [Epub ahead of print].

BACKGROUND & AIM: Several studies observed alterations in the gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD). However, analyzed patient populations and methods strongly differ among these studies. The aim of this study was to prove the reproducibility of published results and to provide a detailed overview of all findings in our NAFLD cohort using next generation sequencing methods.

METHODS: The individual taxonomic microbiota composition of fecal samples from 90 NAFLD patients and 21 healthy controls was analyzed using 16S rRNA gene sequencing. Study participants were grouped according to their disease stage and compared regarding their gut microbiota composition. Studies were identified from PubMed listed publications and the results were compared to the findings in our cohort.

RESULTS: Results from 13 identified studies were compared to our data. A decreased abundance of the Bacteroidetes and Ruminococcaceae as well as an increased abundance of Lactobacillaceae and Veillonellaceae and Dorea were the most frequently reported changes among NAFLD patients in 4/13, 5/13, 4/13, 2/13, 3/13 studies, respectively. Even though these alterations in the gut microbiota composition were also observed in our patient cohort, the majority of published differences could not be reproduced, neither in our own nor in other NAFLD cohort studies.

CONCLUSIONS: Despite repeatedly reproduced abundance patterns of specific bacteria, the heterogeneous study results did not reveal a consistent disease specific gut microbiota signature. Further prospective studies with homogenous patient cohorts and standardised methods are necessary to phenotype NAFLD by the gut microbiota.

RevDate: 2020-04-08

Anderson G (2020)

Melatonin and cocaine: role of mitochondria, immunity, and gut microbiome.

Revista brasileira de psiquiatria (Sao Paulo, Brazil : 1999) pii:S1516-44462020005007206 [Epub ahead of print].

RevDate: 2020-04-08

Guard J, Rothrock M, Jones D, et al (2020)

Low Dose Infection of Hens in Lay with Salmonella enterica Serovar Enteritidis from Different Genomic Clades.

Avian diseases, 64(1):7-15.

Salmonella enterica serovar Enteritidis is the leading cause of salmonellosis in people, and modeling of infections in chickens is used to identify intervention strategies. A review of 80 manuscripts encompassing 119 experiments indicated that the mean dose of infection was 108 CFU per bird. Experiments of less than 106 CFU were primarily conducted in immature birds. To address a lack of information on the impact of low dosages on the hen at lay, two experiments were conducted in triplicate. Experiment A addressed issues associated with vaccination; thus, hens were infected intramuscularly at 103, 105, and 107 CFU. For Experiment B, which was focused more on colonization and invasion, hens were infected orally with 5 × 103 CFU with 4 strains from different genomic clades. Samples from liver, spleen, ovarian pedicle, and paired ceca in both experiments were cultured 5, 6, 7, and 8 days postinfection. Eggshell microbiome taxa were assessed in Experiment B. Results indicated that dosages of 103 CFU in both experiments produced enough positive samples to be used within models. The intramuscular route resulted in approximately twice as many positive samples as the oral route. The kinetics of infection appeared to differ between low and high dosages suggestive of a J-curve response. These results could impact risk assessments if the hen at lay has a nonlinear response to infectious dose.

RevDate: 2020-04-08

Voth E, S Khanna (2020)

Fecal microbiota transplantation for treatment of patients with recurrent Clostridioides difficile infection.

Expert review of anti-infective therapy [Epub ahead of print].

Introduction: Recurrent Clostridiodes difficile infection (rCDI) is a growing public health burden, and is associated with poor patient outcomes. Fecal microbiota transplantation (FMT) is a novel therapy with an aim to restore the disrupted microbiota with demonstrated success in management of rCDI and a favorable safety profile.Areas covered: This review includes a comprehensive overview of a search of the literature including epidemiology of rCDI, basics of the gut microbiome, antibiotic therapy for rCDI along with rationale for, safety and efficacy of FMT for rCDI.Expert opinion: Patients exposed to risk factors, such as antimicrobial agents, are at risk for disruption of the gut microbiome resulting in reduction of microbial diversity and dysbiosis. Dysbiotic microbiota predispose to primary and rCDI. Strategies to improve the current and future management of rCDI are under clinical investigation, including narrow spectrum antibiotics, monoclonal antibodies, and FMT, which has shown a high success rate for rCDI. Further investigation is needed to determine optimal standardization of the methodological components of FMT including donor screening, stool preparation, storage and instillation, and patient follow-up. Newer methods of microbiota replacement therapies including enema- and capsule-based therapies are under investigation.

RevDate: 2020-04-08

Goodarzi A, Mozafarpoor S, Bodaghabadi M, et al (2020)

The potential of probiotics for treating acne vulgaris: A review of literature on acne and microbiota.

Dermatologic therapy [Epub ahead of print].

Acne is known as a chronic inflammatory skin disease with sever adverse effects on quality of life in the patients. The increasing resistance to antibiotics has decreased their effectiveness in treating acne. As viable microbial dietary supplements, probiotics provide health benefits through fighting pathogens and maintaining the homeostasis of the gut and skin microbiome. The present article reviewed the potential of probiotics as beneficial microorganisms for treating acne vulgaris. This review of literature was conducted through a bibliographic search of popular databases, including Science Direct, PubMed, Scielo and Medline, using keywords such as probiotics, prebiotics, synbiotics, microbiome, and acne vulgaris to determine potential applications of these beneficial microbiomes in treating acne vulgaris. Acne lesions are associated with increases in proportion of Propionibacterium acnes as a skin commensal bacterium. The environmental studies showed inhibitory effects of probiotics on P. acnes, mediating by antibacterial proteins and bacteriocin-like inhibitory substances, and their immunomodulatory effects onkeratinocytes and epithelial cells. Probiotics were also found to inhibit cytokine IL-8 in epithelial cells and keratinocytes, suggesting immunomodulatory activities. Moreover, glycerol fermentation by Staphylococcus epidermidis was found to be a natural skin defense against acne and an overgrowth inhibitor of P. acnes. As an antimicrobial agent in lotions and cosmetic formulations, Lactococcus sp. can decrease the inflammatory mediators that are produced by P. acnes and cause vasodilation, edema, mast cell degranulation and TNF-alpha release. Oral administration of probiotics was found to constitute an adjuvant therapy to conventional modalities for treating mild-to-moderate acne vulgaris.

RevDate: 2020-04-08

Heinen R, Hannula SE, De Long JR, et al (2020)

Plant community composition steers grassland vegetation via soil legacy effects.

Ecology letters [Epub ahead of print].

Soil legacy effects are commonly highlighted as drivers of plant community dynamics and species co-existence. However, experimental evidence for soil legacy effects of conditioning plant communities on responding plant communities under natural conditions is lacking. We conditioned 192 grassland plots using six different plant communities with different ratios of grasses and forbs and for different durations. Soil microbial legacies were evident for soil fungi, but not for soil bacteria, while soil abiotic parameters did not significantly change in response to conditioning. The soil legacies affected the composition of the succeeding vegetation. Plant communities with different ratios of grasses and forbs left soil legacies that negatively affected succeeding plants of the same functional type. We conclude that fungal-mediated soil legacy effects play a significant role in vegetation assembly of natural plant communities.

RevDate: 2020-04-08

Huan Z, Yao Y, Yu J, et al (2020)

Differences in the gut microbiota between Cercopithecinae and Colobinae in captivity.

Journal of microbiology (Seoul, Korea) pii:10.1007/s12275-020-9493-9 [Epub ahead of print].

The gut microbiome of captive primates can provide a window into their health and disease status. The diversity and composition of gut microbiota are influenced by not only host phylogeny, but also host diet. Old World monkeys (Cercopithecidae) are divided into two subfamilies: Cercopithecinae and Colobinae. The diet and physiological digestive features differ between these two subfamilies. Accordingly, highthroughput sequencing was used to examine gut microbiota differences between these two subfamilies, using data from 29 Cercopithecinae individuals and 19 Colobinae individuals raised in captivity. Through a comparative analysis of operational taxonomic units (OTUs), significant differences in the diversity and composition of gut microbiota were observed between Cercopithecinae and Colobinae. In particular, the gut microbiota of captive Old World monkeys clustered strongly by the two subfamilies. The Colobinae microbial diversity was higher than that of Cercopithecinae. Additionally, Firmicutes, Lactobacillaceae, Veillonellaceae, and Prevotella abundance were higher in Cercopithecinae, while Bacteroidetes, Ruminococcaceae, Christensenellaceae, Bacteroidaceae, and Acidaminococcaceae abundance were higher in Colobinae. PICRUSt analysis revealed that the predicted metagenomes of metabolic pathways associated with proteins, carbohydrates, and amino acids were significantly higher in Colobinae. In the context of host phylogeny, these differences between Cercopithecinae and Colobinae could reflect adaptations associated with their respective diets. This well-organized dataset is a valuable resource for future related research on primates and gut microbiota. Moreover, this study may provide useful insight into animal management practices and primate conservation.

RevDate: 2020-04-08

Harper CE, CJ Hernandez (2020)

Cell biomechanics and mechanobiology in bacteria: Challenges and opportunities.

APL bioengineering, 4(2):021501 pii:1.5135585.

Physical forces play a profound role in the survival and function of all known forms of life. Advances in cell biomechanics and mechanobiology have provided key insights into the physiology of eukaryotic organisms, but much less is known about the roles of physical forces in bacterial physiology. This review is an introduction to bacterial mechanics intended for persons familiar with cells and biomechanics in mammalian cells. Bacteria play a major role in human health, either as pathogens or as beneficial commensal organisms within the microbiome. Although bacteria have long been known to be sensitive to their mechanical environment, understanding the effects of physical forces on bacterial physiology has been limited by their small size (∼1 μm). However, advancements in micro- and nano-scale technologies over the past few years have increasingly made it possible to rigorously examine the mechanical stress and strain within individual bacteria. Here, we review the methods currently used to examine bacteria from a mechanical perspective, including the subcellular structures in bacteria and how they differ from those in mammalian cells, as well as micro- and nanomechanical approaches to studying bacteria, and studies showing the effects of physical forces on bacterial physiology. Recent findings indicate a large range in mechanical properties of bacteria and show that physical forces can have a profound effect on bacterial survival, growth, biofilm formation, and resistance to toxins and antibiotics. Advances in the field of bacterial biomechanics have the potential to lead to novel antibacterial strategies, biotechnology approaches, and applications in synthetic biology.

RevDate: 2020-04-08

McGivney E, Cederholm L, Barth A, et al (2020)

Rapid Physicochemical Changes in Microplastic Induced by Biofilm Formation.

Frontiers in bioengineering and biotechnology, 8:205.

Risk assessment of microplastic (MP) pollution requires understanding biodegradation processes and related changes in polymer properties. In the environment, there are two-way interactions between the MP properties and biofilm communities: (i) microorganisms may prefer some surfaces, and (ii) MP surface properties change during the colonization and weathering. In a 2-week experiment, we studied these interactions using three model plastic beads (polyethylene [PE], polypropylene [PP], and polystyrene [PS]) exposed to ambient bacterioplankton assemblage from the Baltic Sea; the control beads were exposed to bacteria-free water. For each polymer, the physicochemical properties (compression, crystallinity, surface chemistry, hydrophobicity, and surface topography) were compared before and after exposure under controlled laboratory conditions. Furthermore, we characterized the bacterial communities on the MP surfaces using 16S rRNA gene sequencing and correlated community diversity to the physicochemical properties of the MP. Significant changes in PE crystallinity, PP stiffness, and PS maximum compression were observed as a result of exposure to bacteria. Moreover, there were significant correlations between bacterial diversity and some physicochemical characteristics (crystallinity, stiffness, and surface roughness). These changes coincided with variation in the relative abundance of unique OTUs, mostly related to the PE samples having significantly higher contribution of Sphingobium, Novosphingobium, and uncultured Planctomycetaceae compared to the other test materials, whereas PP and PS samples had significantly higher abundance of Sphingobacteriales and Alphaproteobacteria, indicating possible involvement of these taxa in the initial biodegradation steps. Our findings demonstrate measurable signs of MP weathering under short-term exposure to environmentally relevant microbial communities at conditions resembling those in the water column. A systematic approach for the characterization of the biodegrading capacity in different systems will improve the risk assessment of plastic litter in aquatic environments.

RevDate: 2020-04-08

Saunte DML, Gaitanis G, RJ Hay (2020)

Malassezia-Associated Skin Diseases, the Use of Diagnostics and Treatment.

Frontiers in cellular and infection microbiology, 10:112.

Yeasts of the genus, Malassezia, formerly known as Pityrosporum, are lipophilic yeasts, which are a part of the normal skin flora (microbiome). Malassezia colonize the human skin after birth and must therefore, as commensals, be normally tolerated by the human immune system. The Malassezia yeasts also have a pathogenic potential where they can, under appropriate conditions, invade the stratum corneum and interact with the host immune system, both directly but also through chemical mediators. The species distribution on the skin and the pathogenetic potential of the yeast varies between different Malassezia related diseases such as head and neck dermatitis, seborrheic dermatitis, pityriasis versicolor, and Malassezia folliculitis. The diagnostic methods used to confirm the presence of Malassezia yeasts include direct microcopy, culture based methods (often a combination of morphological features of the isolate combined with biochemical test), molecular based methods such as Polymerase Chain Reaction techniques, and Matrix Assisted Laser Desorption/Ionization-Time Of Flight mass spectrometry and the chemical imprint method Raman spectroscopy. Skin diseases caused by Malassezia are usually treated with antifungal therapy and if there are associated inflammatory skin mechanisms this is often supplemented by anti-inflammatory therapy. The aim of this paper is to provide an overview of Malassezia related skin disease, diagnostic methods and treatment options.

RevDate: 2020-04-08

Vendrik KEW, Ooijevaar RE, de Jong PRC, et al (2020)

Fecal Microbiota Transplantation in Neurological Disorders.

Frontiers in cellular and infection microbiology, 10:98.

Background: Several studies suggested an important role of the gut microbiota in the pathophysiology of neurological disorders, implying that alteration of the gut microbiota might serve as a treatment strategy. Fecal microbiota transplantation (FMT) is currently the most effective gut microbiota intervention and an accepted treatment for recurrent Clostridioides difficile infections. To evaluate indications of FMT for patients with neurological disorders, we summarized the available literature on FMT. In addition, we provide suggestions for future directions. Methods: In July 2019, five main databases were searched for studies and case descriptions on FMT in neurological disorders in humans or animal models. In addition, the website was consulted for registered planned and ongoing trials. Results: Of 541 identified studies, 34 were included in the analysis. Clinical trials with FMT have been performed in patients with autism spectrum disorder and showed beneficial effects on neurological symptoms. For multiple sclerosis and Parkinson's disease, several animal studies suggested a positive effect of FMT, supported by some human case reports. For epilepsy, Tourette syndrome, and diabetic neuropathy some studies suggested a beneficial effect of FMT, but evidence was restricted to case reports and limited numbers of animal studies. For stroke, Alzheimer's disease and Guillain-Barré syndrome only studies with animal models were identified. These studies suggested a potential beneficial effect of healthy donor FMT. In contrast, one study with an animal model for stroke showed increased mortality after FMT. For Guillain-Barré only one study was identified. Whether positive findings from animal studies can be confirmed in the treatment of human diseases awaits to be seen. Several trials with FMT as treatment for the above mentioned neurological disorders are planned or ongoing, as well as for amyotrophic lateral sclerosis. Conclusions: Preliminary literature suggests that FMT may be a promising treatment option for several neurological disorders. However, available evidence is still scanty and some contrasting results were observed. A limited number of studies in humans have been performed or are ongoing, while for some disorders only animal experiments have been conducted. Large double-blinded randomized controlled trials are needed to further elucidate the effect of FMT in neurological disorders.

RevDate: 2020-04-08

Arredondo-Hernández R, Schmulson M, Orduña P, et al (2020)

Mucosal Microbiome Profiles Polygenic Irritable Bowel Syndrome in Mestizo Individuals.

Frontiers in cellular and infection microbiology, 10:72.

Irritable bowel syndrome (IBS) is the most frequent functional gastrointestinal disorder, worldwide, with a high prevalence among Mestizo Latin Americans. Because several inflammatory disorders appear to affect this population, a further understanding of host genomic background variants, in conjunction with colonic mucosa dysbiosis, is necessary to determine IBS physiopathology and the effects of environmental pressures. Using a simple polygenic model, host single nucleotide polymorphisms (SNPs) and the taxonomic compositions of microbiota were compared between IBS patients and healthy subjects. As proof of concept, five IBS-Rome III patients and five healthy controls (HCs) were systematically studied. The human and bacterial intestinal metagenome of each subject was taxonomically annotated and screened for previously annotated IBS, ulcerative colitis, and Crohn's disease-associated SNPs or taxon abundance. Dietary data and fecal markers were collected and associated with the intestinal microbiome. However, more than 1,000 variants were found, and at least 76 SNPs differentiated IBS patients from HCs, as did associations with 4 phyla and 10 bacterial genera. In this study, we found elements supporting a polygenic background, with frequent variants, among the Mestizo population, and the colonic mucosal enrichment of Bacteroides, Alteromonas, Neisseria, Streptococcus, and Microbacterium, may serve as a hallmark for IBS.

RevDate: 2020-04-08

Xu J, Peng JJ, Yang W, et al (2020)

Vaginal microbiomes and ovarian cancer: a review.

American journal of cancer research, 10(3):743-756.

The human microbiome, often termed as "the forgotten organ", is an aggregation of microorganisms and their genomes that forms a mutualistic complex with the host. Recent research has shown the symbiotic merits of a microbiome ecosystem and its crucial role in the hosts' physiological functions. Disruption of this symbiotic relationship is prone to cause a broad spectrum of ailments, including cancer. The compositional and environmental factors that tip the scales from beneficial co-existence to the development of malignancy is actively investigated. Herein we review the latest research in knowledge regarding the association between the vaginal microbiomes and oncogenesis, with a particular focus on ovarian carcinoma.

RevDate: 2020-04-08

Comeau D, Novinscak A, Joly DL, et al (2020)

Spatio-Temporal and Cultivar-Dependent Variations in the Cannabis Microbiome.

Frontiers in microbiology, 11:491.

The incipient legalization and commercialization of Cannabis sativa in Canada have promulgated research into characterizing the plant's microbiome as it promotes many facets of plant growth and health. The emblematic production of commercially important secondary metabolites, namely tetrahydrocannabinol (THC), cannabidiol (CBD) and terpenes, has warranted investigating the modulating capacity of these molecules on the plant microbiome. C. sativa cultivars can be classified into chemotypes depending on the relative levels of THC and CBD they produce; their biosynthesis also varies spatially and temporally during the life cycle of the plant. To study the differential microbiome structure and diversity between cultivars in a spatio-temporal manner, we extracted microbial DNA from the rhizosphere, endorhizosphere, and phyllosphere during the entire life cycle of three different chemotypes; CBD Yummy (<1% THC/13% CBD), CBD shark (6% THC/10% CBD) and Hash (14% THC/ < 1% CBD). Illumina marker gene sequencing of bacterial (16S) and fungal (ITS) communities were coupled to the QIIME2, PICRUSt, and LEfSe pipelines for analysis. Our study describes spatio-temporal and cultivar-dependent variations in the fungal and bacterial microbiome of C. sativa, and details strong cultivar-dependent variance in the belowground microbiome. Furthermore, the predicted pathway abundance of the bacterial microbiome is concomitantly subject to spatio-temporal variations; pathways related to lipid, amino acid, glucose and pentose metabolism were noteworthy. These results describe, for the first time, spatio-temporal and cultivar-dependent variations in the microbiome of C. sativa produced under strict commercial settings. Describing the microbiome is the first step in discoveries that could help in engineering a plant growth and health promoting microbiome in future works.

RevDate: 2020-04-08

Sierra MA, Danko DC, Sandoval TA, et al (2020)

The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials.

Frontiers in microbiology, 11:398.

The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in Colombian Paramos using 16S rRNA gene amplicon sequencing and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes varied in diversity indexes and number of OTUs, but were composed predominantly by the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia. In the case of Cora and Cladonia, the microbiomes were distinguished based on the identity of the lichen host. While the majority of the lichen-associated microorganisms were not present in all lichens sampled, sixteen taxa shared among this diverse group of lichens suggest a core lichen microbiome that broadens our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant microbial strains. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.

RevDate: 2020-04-08

Colagiero M, Rosso LC, Catalano D, et al (2020)

Response of Tomato Rhizosphere Bacteria to Root-Knot Nematodes, Fenamiphos and Sampling Time Shows Differential Effects on Low Level Taxa.

Frontiers in microbiology, 11:390.

A factorial taxonomic metabarcoding study was carried out to determine the effect of root-knot nematodes (Meloidogyne incognita, RKN) and the nematocide fenamiphos on the rhizosphere microbiome of tomato. Plants inoculated (or not) with RKN second-stage juveniles (J2), and treated (or not) with the nematocide, were tested in a 6 months greenhouse assay using a RKN-free soil proceeding from an organic crop. Rhizosphere soil was sampled at J2 inoculation, 3 months later (before the second nematocidal treatment), and again after 3 months. At each sampling, the RNAs were extracted and the 16S rRNA V4 regions sequenced with a Next Generation Sequencing (NGS) protocol. Changes in bacteria metagenomic profiles showed an effect of the treatments applied, with different representations of taxa in samples receiving nematodes and fenamiphos, at the two sampling times. In general, a tendence was observed toward an increase number of OTUs at 6 months, in all treatments. β-Proteobacteria were the most abundant class, for all treatments and times. When compared to soil before transplanting, the presence of tomato roots increased frequency of Actinobacteria and Thermoleophilia, reducing abundance of Solibacteres. At lowest taxonomic levels the samples clustered in groups congruent with the treatments applied, with OTUs differentially represented in relation to RKN and/or fenamiphos applications. Bacillus, Corynebacterium, Streptococcus, and Staphylococcus were more represented at 6 months in samples inoculated with RKN. The nematodes with the nematocide application increased the emergence of rare OTUs or reduced/enhanced the abundance of other taxa, from different lineages.

RevDate: 2020-04-08

Zhou H, Sun L, Zhang S, et al (2020)

Evaluating the Causal Role of Gut Microbiota in Type 1 Diabetes and Its Possible Pathogenic Mechanisms.

Frontiers in endocrinology, 11:125.

Type 1 diabetes (T1D) is a multifactorial autoimmune disease mediated by genetic, epigenetic, and environmental factors. In recent years, the emergence of high-throughput sequencing has allowed us to investigate the role of gut microbiota in the development of T1D. Significant changes in the composition of gut microbiome, also termed dysbiosis, have been found in subjects with clinical or preclinical T1D. However, whether the dysbiosis is a cause or an effect of the disease remains unclear. Currently, increasing evidence has supported a causal link between intestine microflora and T1D development. The current review will focus on recent research regarding the associations between intestine microbiome and T1D progression with an intention to evaluate the causality. We will also discuss the possible mechanisms by which imbalanced gut microbiota leads to the development of T1D.

RevDate: 2020-04-08

Oh M, L Zhang (2020)

DeepMicro: deep representation learning for disease prediction based on microbiome data.

Scientific reports, 10(1):6026 pii:10.1038/s41598-020-63159-5.

Human microbiota plays a key role in human health and growing evidence supports the potential use of microbiome as a predictor of various diseases. However, the high-dimensionality of microbiome data, often in the order of hundreds of thousands, yet low sample sizes, poses great challenge for machine learning-based prediction algorithms. This imbalance induces the data to be highly sparse, preventing from learning a better prediction model. Also, there has been little work on deep learning applications to microbiome data with a rigorous evaluation scheme. To address these challenges, we propose DeepMicro, a deep representation learning framework allowing for an effective representation of microbiome profiles. DeepMicro successfully transforms high-dimensional microbiome data into a robust low-dimensional representation using various autoencoders and applies machine learning classification algorithms on the learned representation. In disease prediction, DeepMicro outperforms the current best approaches based on the strain-level marker profile in five different datasets. In addition, by significantly reducing the dimensionality of the marker profile, DeepMicro accelerates the model training and hyperparameter optimization procedure with 8X-30X speedup over the basic approach. DeepMicro is freely available at

RevDate: 2020-04-08

Tan W, Wang J, Bai W, et al (2020)

Soil bacterial diversity correlates with precipitation and soil pH in long-term maize cropping systems.

Scientific reports, 10(1):6012 pii:10.1038/s41598-020-62919-7.

Unraveling the key drivers of bacterial community assembly in agricultural soils is pivotal for soil nutrient management and crop productivity. Presently, the drivers of microbial community structure remain unexplored in maize cropping systems under complex and variable environmental scenarios across large spatial scales. In this study, we conducted high-throughput 16S rRNA gene sequencing and network analysis to identify the major environmental factors driving bacterial community diversity and co-occurrence patterns in 21 maize field soils across China. The results show that mean annual precipitation and soil pH are the major environmental factors that shape soil bacterial communities in maize soils. The similarities of bacterial communities significantly decreased with increasing geographic distance between different sites. The differences in spatial turnover rates across bacterial phyla indicate the distinct dispersal capabilities of bacterial groups, and some abundant phyla exhibited high dispersal capabilities. Aeromicrobium, Friedmanniella, Saccharothrix, Lamia, Rhodococcus, Skermanella, and Pedobacter were identified as keystone taxa. Based on the node-level and network-level topological features, members of the core microbiome were more frequently found in the center of the ecosystem network compared with other taxa. This study highlights the major environmental factors driving bacterial community assembly in agro-ecosystems and the central ecological role of the core microbiome in maintaining the web of complex bacterial interactions.

RevDate: 2020-04-08

Soltys K, Stuchlikova M, Hlavaty T, et al (2020)

Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.

Scientific reports, 10(1):6024 pii:10.1038/s41598-020-62811-4.

Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.

RevDate: 2020-04-08

Jacobs KM, Price TK, Thomas-White K, et al (2020)

Cultivable Bacteria in Urine of Women With Interstitial Cystitis: (Not) What We Expected.

Female pelvic medicine & reconstructive surgery [Epub ahead of print].

OBJECTIVE: Multiple studies show cultivatable bacteria in urine of most women. The existence of these bacteria challenges interstitial cystitis (IC)/painful bladder syndrome (PBS) diagnosis, which presumes a sterile bladder. The aims of this study were (1) to compare the female bladder microbiomes in women with IC/PBS and unaffected controls and (2) to correlate baseline bladder microbiome composition with symptoms.

METHODS: This cross-sectional study enrolled 49 IC/PBS and 40 controls. All provided catheterized urine samples and completed validated questionnaires. A subset of the IC/PBS cohort provided voided and catheterized urine samples. All samples from both cohorts were assessed by the expanded quantitative urine culture (EQUC) protocol; a subset was assessed by 16S rRNA gene sequencing.

RESULTS: Of the IC/PBS cohort, 49.0% (24/49) were EQUC positive; in these EQUC-positive samples, the most common urotypes were Lactobacillus (45.8%) and Streptococcus (33.3%). Of the controls, 40.0% were EQUC positive; of these EQUC-positive samples, the most common urotype was Lactobacillus (50.0%). The urotype distribution was significantly different (P < 0.05), as 16% of the IC/PBS cohort, but 0% of controls, were Streptococcus urotype (P < 0.01). Symptom-free IC/PBS participants were less likely to be EQUC positive (12.5%) than IC/PBS participants with moderate or severe symptoms (68.8% and 46.2%) and the control cohort (60%; P < 0.05).

CONCLUSION: Lactobacillus was the most common urotype. However, the presence of Lactobacillus did not differ between cohorts, and it did not impact IC/PBS symptom severity. Bacteria were not isolated from most participants with active IC/PBS symptoms. These findings suggest that bacteria may not be an etiology for IC/PBS.

RevDate: 2020-04-08

Zhao M, Jiang Z, Cai H, et al (2020)

Modulation of the Gut Microbiota during High-Dose Glycerol Monolaurate-Mediated Amelioration of Obesity in Mice Fed a High-Fat Diet.

mBio, 11(2): pii:mBio.00190-20.

Obesity and associated metabolic disorders are worldwide public health issues. The gut microbiota plays a key role in the pathophysiology of diet-induced obesity. Glycerol monolaurate (GML) is a widely consumed food emulsifier with antibacterial properties. Here, we explore the anti-obesity effect of GML (1,600 mg/kg of body weight) in high-fat diet (HFD)-fed mice. HFD-fed mice were treated with 1,600 mg/kg GML. Integrated microbiome, metabolome, and transcriptome analyses were used to systematically investigate the metabolic effects of GML, and antibiotic treatment was used to assess the effects of GML on the gut microbiota. Our data indicated that GML significantly reduced body weight and visceral fat deposition, improved hyperlipidemia and hepatic lipid metabolism, and ameliorated glucose homeostasis and inflammation in HFD-fed mice. Importantly, GML modulated HFD-induced gut microbiota dysbiosis and selectively increased the abundance of Bifidobacterium pseudolongum Antibiotic treatment abolished all the GML-mediated metabolic improvements. A multiomics (microbiome, metabolome, and transcriptome) association study showed that GML significantly modulated glycerophospholipid metabolism, and the abundance of Bifidobacterium pseudolongum strongly correlated with the metabolites and genes that participated in glycerophospholipid metabolism. Our results indicated that GML may be provided for obesity prevention by targeting the gut microbiota and regulating glycerophospholipid metabolism.

RevDate: 2020-04-08

Tettamanti Boshier FA, Srinivasan S, Lopez A, et al (2020)

Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome.

mSystems, 5(2): pii:5/2/e00777-19.

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentrations of individual bacterial species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We sought to determine the accuracy of an inferred measure of bacterial concentration using total bacterial load and relative abundance. We analyzed 1,320 samples from 20 women with a history of frequent bacterial vaginosis who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, P < 2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacteria associated with larger errors. A total of 92% of the >0.5-log10 errors occurred when the relative abundance was <10%. Many errors occurred during early bacterial expansion from or late contraction to low abundance. When the relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR in the vaginal microbiome. However, targeted qPCR is required to capture bacteria at low relative abundance and is preferable for characterizing growth and decay kinetics of single species.IMPORTANCE Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species' relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species' concentrations, as measured by taxon-specific qPCR assays. Overall, the inferred bacterial concentrations were a reasonable proxy of species-specific qPCR values, particularly when bacteria are present at a higher relative abundance. This approach offers an opportunity to assess the concentrations of bacterial species and how they change in a community over time without developing individual qPCR assays for each taxon.

RevDate: 2020-04-08

Quinn TP, I Erb (2020)

Interpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance Selection.

mSystems, 5(2): pii:5/2/e00230-19.

Since the turn of the century, technological advances have made it possible to obtain the molecular profile of any tissue in a cost-effective manner. Among these advances are sophisticated high-throughput assays that measure the relative abundances of microorganisms, RNA molecules, and metabolites. While these data are most often collected to gain new insights into biological systems, they can also be used as biomarkers to create clinically useful diagnostic classifiers. How best to classify high-dimensional -omics data remains an area of active research. However, few explicitly model the relative nature of these data and instead rely on cumbersome normalizations. This report (i) emphasizes the relative nature of health biomarkers, (ii) discusses the literature surrounding the classification of relative data, and (iii) benchmarks how different transformations perform for regularized logistic regression across multiple biomarker types. We show how an interpretable set of log contrasts, called balances, can prepare data for classification. We propose a simple procedure, called discriminative balance analysis, to select groups of 2 and 3 bacteria that can together discriminate between experimental conditions. Discriminative balance analysis is a fast, accurate, and interpretable alternative to data normalization.IMPORTANCE High-throughput sequencing provides an easy and cost-effective way to measure the relative abundance of bacteria in any environmental or biological sample. When these samples come from humans, the microbiome signatures can act as biomarkers for disease prediction. However, because bacterial abundance is measured as a composition, the data have unique properties that make conventional analyses inappropriate. To overcome this, analysts often use cumbersome normalizations. This article proposes an alternative method that identifies pairs and trios of bacteria whose stoichiometric presence can differentiate between diseased and nondiseased samples. By using interpretable log contrasts called balances, we developed an entirely normalization-free classification procedure that reduces the feature space and improves the interpretability, without sacrificing classifier performance.

RevDate: 2020-04-08

Lee S, Goodson M, Vang W, et al (2020)

2'-fucosyllactose Supplementation Improves Gut-Brain Signaling and Diet-Induced Obese Phenotype and Changes the Gut Microbiota in High Fat-Fed Mice.

Nutrients, 12(4): pii:nu12041003.

Obesity is characterized by fat accumulation, chronic inflammation and impaired satiety signaling, which may be due in part to gut microbial dysbiosis. Manipulations of the gut microbiota and its metabolites are attractive targets for obesity treatment. The predominant oligosaccharide found in human milk, acts as a prebiotic with beneficial effects on the host. However, little is known about the beneficial effects of 2'-FL in obesity. The aim of this study was to determine the beneficial effects of 2'-FL supplementation on the microbiota-gut-brain axis and the diet-induced obese phenotype in high fat (HF)-fed mice. Male C57/BL6 mice (n = 6/group; six weeks old) were counter-balanced into six weight-matched groups and fed either a low-fat (LF; 10% kcal as fat), HF (45% kcal as fat) or HF diet with 2'-FL (HF_2'-FL) at 1, 2, 5 and 10% (w/v) in drinking water for six weeks. General phenotypes (body weight, energy intake, fat and lean mass), cecal microbiome and metabolites, gut-brain signaling, intestinal permeability and inflammatory and lipid profiles were assessed. Only 10% 2'-FL, but not 1, 2 or 5%, decreased HF diet-induced increases in energy intake, fat mass and body weight gain. A supplementation of 10% 2'-FL changed the composition of cecal microbiota and metabolites compared to LF- and HF-fed mice with an increase in Parabacteroides abundance and lactate and pyruvate, respectively, whose metabolic effects corresponded to our study findings. In particular, 10% 2'-FL significantly reversed the HF diet-induced impairment of cholecystokinin-induced inhibition of food intake. Gene expressions of interleukin (IL)-1β, IL-6, and macrophage chemoattractant protein-1 in the cecum were significantly downregulated by 10% 2'-FL compared to the HF group. Furthermore, 10% 2'-FL suppressed HF diet-induced upregulation of hepatic peroxisome proliferator-activated receptor gamma, a transcription factor for adipogenesis, at the gene level. In conclusion, 10% 2'-FL led to compositional changes in gut microbiota and metabolites associated with improvements in metabolic profiles and gut-brain signaling in HF-fed mice. These findings support the use of 2'-FL for modulating the hyperphagic response to HF diets and improving the microbiota-gut-brain axis.

RevDate: 2020-04-08

Ivanov DO, Evsyukova II, Mazzoccoli G, et al (2020)

The Role of Prenatal Melatonin in the Regulation of Childhood Obesity.

Biology, 9(4): pii:biology9040072.

There is a growing awareness that pregnancy can set the foundations for an array of diverse medical conditions in the offspring, including obesity. A wide assortment of factors, including genetic, epigenetic, lifestyle, and diet can influence foetal outcomes. This article reviews the role of melatonin in the prenatal modulation of offspring obesity. A growing number of studies show that many prenatal risk factors for poor foetal metabolic outcomes, including gestational diabetes and night-shift work, are associated with a decrease in pineal gland-derived melatonin and associated alterations in the circadian rhythm. An important aspect of circadian melatonin's effects is mediated via the circadian gene, BMAL1, including in the regulation of mitochondrial metabolism and the mitochondrial melatoninergic pathway. Alterations in the regulation of mitochondrial metabolic shifts between glycolysis and oxidative phosphorylation in immune and glia cells seem crucial to a host of human medical conditions, including in the development of obesity and the association of obesity with the risk of other medical conditions. The gut microbiome is another important hub in the pathoetiology and pathophysiology of many medical conditions, with negative consequences mediated by a decrease in the short-chain fatty acid, butyrate. The effects of butyrate are partly mediated via an increase in the melatoninergic pathway, indicating interactions of the gut microbiome with melatonin. Some of the effects of melatonin seem mediated via the alpha 7 nicotinic receptor, whilst both melatonin and butyrate may regulate obesity through the opioidergic system. Oxytocin, a recently recognized inhibitor of obesity, may also be acting via the opioidergic system. The early developmental regulation of these processes and factors by melatonin are crucial to the development of obesity and many diverse comorbidities.

RevDate: 2020-04-08

Andrianova NV, Popkov VA, Klimenko NS, et al (2020)

Microbiome-Metabolome Signature of Acute Kidney Injury.

Metabolites, 10(4): pii:metabo10040142.

Intestinal microbiota play a considerable role in the host's organism, broadly affecting its organs and tissues. The kidney can also be the target of the microbiome and its metabolites (especially short-chain fatty acids), which can influence renal tissue, both by direct action and through modulation of the immune response. This impact is crucial, especially during kidney injury, because the modulation of inflammation or reparative processes could affect the severity of the resulting damage or recovery of kidney function. In this study, we compared the composition of rat gut microbiota with its outcome, in experimental acute ischemic kidney injury and named the bacterial taxa that play putatively negative or positive roles in the progression of ischemic kidney injury. We investigated the link between serum creatinine, urea, and a number of metabolites (acylcarnitines and amino acids), and the relative abundance of various bacterial taxa in rat feces. Our analysis revealed an increase in levels of 32 acylcarnitines in serum, after renal ischemia/reperfusion and correlation with creatinine and urea, while levels of three amino acids (tyrosine, tryptophan, and proline) had decreased. We detected associations between bacterial abundance and metabolite levels, using a compositionality-aware approach-Rothia and Staphylococcus levels were positively associated with creatinine and urea levels, respectively. Our findings indicate that the gut microbial community contains specific members whose presence might ameliorate or, on the contrary, aggravate ischemic kidney injury. These bacterial taxa could present perspective targets for therapeutical interventions in kidney pathologies, including acute kidney injury.

RevDate: 2020-04-07

Tempero M (2020)

Health and the Gut Microbiome: Who Knew?.

Journal of the National Comprehensive Cancer Network : JNCCN, 18(4):365.

RevDate: 2020-04-07

Seldin M, Yang X, AJ Lusis (2019)

Systems genetics applications in metabolism research.

Nature metabolism, 1(11):1038-1050.

The common forms of metabolic diseases are highly complex, involving hundreds of genes, environmental and lifestyle factors, age-related changes, sex differences and gut-microbiome interactions. Systems genetics is a population-based approach to address this complexity. In contrast to commonly used 'reductionist' approaches, such as gain or loss of function, that examine one element at a time, systems genetics uses high-throughput 'omics' technologies to quantitatively assess the many molecular differences among individuals in a population and then to relate these to physiologic functions or disease states. Unlike genome-wide association studies, systems genetics seeks to go beyond the identification of disease-causing genes to understand higher-order interactions at the molecular level. The purpose of this review is to introduce the systems genetics applications in the areas of metabolic and cardiovascular disease. Here, we explain how large clinical and omics-level data and databases from both human and animal populations are available to help researchers place genes in the context of pathways and networks and formulate hypotheses that can then be experimentally examined. We provide lists of such databases and examples of the integration of reductionist and systems genetics data. Among the important applications emerging is the development of improved nutritional and pharmacological strategies to address the rise of metabolic diseases.

RevDate: 2020-04-07

Kwan SY, Jiao J, Qi J, et al (2020)

Bile Acid Changes Associated With Liver Fibrosis and Steatosis in the Mexican-American Population of South Texas.

Hepatology communications, 4(4):555-568 pii:HEP41490.

Biomarkers to predict risk of liver fibrosis in subjects with nonalcoholic fatty liver disease, a common risk factor for hepatocellular carcinoma, would allow for early preventive interventions. We sought to characterize bile acid profiles associated with liver fibrosis in subjects from the community-based Cameron County Hispanic Cohort, a population in South Texas with high rates of nonalcoholic fatty liver disease, liver fibrosis and hepatocellular carcinoma. Plasma bile acid levels were measured in 390 subjects. These subjects were screened with liver elastography, detecting significant liver fibrosis in 58 subjects and steatosis in 186 subjects. Unsupervised clustering of the bile acid profiles revealed five clusters that differed by liver fibrosis, liver steatosis, liver injury, age and gender, identifying these parameters as major determinants of circulating bile acid changes. Total bile acid levels were significantly higher in subjects with fibrosis, with chenodeoxycholic acid displaying the greatest increase among individual bile acids. The primary conjugated bile acids, glycocholic and glycochenodeoxycholic acids, displayed the strongest association with fibrosis by logistic regression. High lithocholic acid levels were strongly associated with advanced fibrosis. In contrast, deoxycholic acid and total unconjugated secondary bile acids were positively associated with steatosis, whereas relative glycoursodeoxycholic acid abundance was negatively associated. Milk and yogurt intake notably contributed to fibrosis-associated bile acid changes. In addition, multiple families within the Firmicutes phylum, Prevotellaceae, and Bacteroides species in stool significantly correlated with fibrosis-associated and steatosis-associated bile acid parameters, suggesting that the gut microbiome contributes to bile acid changes in the context of liver disease. Conclusion: Circulating bile acid levels were markedly but differently changed in liver fibrosis and steatosis in a high-risk Mexican-American population.

RevDate: 2020-04-07

Parthasarathy G, Revelo X, H Malhi (2020)

Pathogenesis of Nonalcoholic Steatohepatitis: An Overview.

Hepatology communications, 4(4):478-492 pii:HEP41479.

Nonalcoholic fatty liver disease (NAFLD) is a heterogeneous group of liver diseases characterized by the accumulation of fat in the liver. The heterogeneity of NAFLD is reflected in a clinical and histologic spectrum where some patients develop isolated steatosis of the liver, termed nonalcoholic fatty liver, whereas others develop hepatocyte injury, ballooning, inflammation, and consequent fibrosis, termed nonalcoholic steatohepatitis (NASH). Systemic insulin resistance is a major driver of hepatic steatosis in NAFLD. Lipotoxicity of accumulated lipids along with activation of the innate immune system are major drivers of NASH. Lipid-induced sublethal and lethal stress culminates in the activation of inflammatory processes, such as the release of proinflammatory extracellular vesicles and cell death. Innate and adaptive immune mechanisms involving macrophages, dendritic cells, and lymphocytes are central drivers of inflammation that recognize damage- and pathogen-associated molecular patterns and contribute to the progression of the inflammatory cascade. While the activation of the innate immune system and the recruitment of proinflammatory monocytes into the liver in NASH are well known, the exact signals that lead to this remain less well defined. Further, the contribution of other immune cell types, such as neutrophils and B cells, is an area of intense research. Many host factors, such as the microbiome and gut-liver axis, modify individual susceptibility to NASH. In this review, we discuss lipotoxicity, inflammation, and the contribution of interorgan crosstalk in NASH pathogenesis.

RevDate: 2020-04-07

Libisch B, Keresztény T, Kerényi Z, et al (2020)

Metagenomic Analysis of Acquired Antibiotic Resistance Determinants in the Gut Microbiota of Wild Boars (Sus Scrofa) - Preliminary Results.

Journal of veterinary research, 64(1):111-118 pii:jvetres-2020-0015.

Introduction: Land application of manure that contains antibiotics and resistant bacteria may facilitate the establishment of an environmental reservoir of antibiotic-resistant microbes, promoting their dissemination into agricultural and natural habitats. The main objective of this study was to search for acquired antibiotic resistance determinants in the gut microbiota of wild boar populations living in natural habitats.

Material and Methods: Gastrointestinal samples of free-living wild boars were collected in the Zemplén Mountains in Hungary and were characterised by culture-based, metagenomic, and molecular microbiological methods. Bioinformatic analysis of the faecal microbiome of a hunted wild boar from Japan was used for comparative studies. Also, shotgun metagenomic sequencing data of two untreated sewage wastewater samples from North Pest (Hungary) from 2016 were analysed by bioinformatic methods. Minimum spanning tree diagrams for seven-gene MLST profiles of 104 E. coli strains isolated in Europe from wild boars and domestic pigs were generated in Enterobase.

Results: In the ileum of a diarrhoeic boar, a dominant E. coli O112ab:H2 strain with intermediate resistance to gentamicin, tobramycin, and amikacin was identified, displaying sequence type ST388 and harbouring the EAST1 toxin astA gene. Metagenomic analyses of the colon and rectum digesta revealed the presence of the tetQ, tetW, tetO, and mefA antibiotic resistance genes that were also detected in the gut microbiome of four other wild boars from the mountains. Furthermore, the tetQ and cfxA genes were identified in the faecal microbiome of a hunted wild boar from Japan.

Conclusion: The gastrointestinal microbiota of the free-living wild boars examined in this study carried acquired antibiotic resistance determinants that are highly prevalent among domestic livestock populations.

RevDate: 2020-04-07

Fulcher JA, Li F, Cook RR, et al (2019)

Rectal Microbiome Alterations Associated With Oral Human Immunodeficiency Virus Pre-Exposure Prophylaxis.

Open forum infectious diseases, 6(11):ofz463 pii:ofz463.

Background: Oral daily tenofovir (TFV) disoproxil fumarate/emtricitabine (TDF/FTC) for human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) is highly effective for HIVprevention, yet long-term effects are not fully understood. We investigated the effects of PrEP on the rectal microbiome in a cohort of men who have sex with men (MSM).

Methods: This cross-sectional analysis included HIV-negative MSM either on PrEP (n = 37) or not (n = 37) selected from an ongoing cohort using propensity score matching. Rectal swabs were used to examine microbiome composition using 16S ribosomal ribonucleic acid gene sequencing, and associations between PrEP use and microbiota abundance were examined. Hair specimens were used to quantify TFV and FTC exposure over the past 6 weeks on a subset of participants (n = 15).

Results: Pre-exposure prophylaxis use was associated with a significant increase in Streptococcus abundance (adjusted P = .015). Similar associations were identified using least absolute shrinkage and selection operator (LASSO) regression, confirming the increase in Streptococcus and also showing increased Mitsuokella, Fusobacterium, and decreased Escherichia/Shigella. Increased Fusobacterium was significantly associated with increasing TFV exposure.

Conclusions: Oral TDF/FTC for PrEP is associated with rectal microbiome changes compared to well matched controls, specifically increased Streptococcus and Fusobacterium abundance. This study highlights the need for future investigations of the role of microbiome changes on HIV susceptibility and effectiveness of PrEP.

RevDate: 2020-04-07

Damiani G, Bragazzi NL, McCormick TS, et al (2020)

Gut microbiota and nutrient interactions with skin in psoriasis: A comprehensive review of animal and human studies.

World journal of clinical cases, 8(6):1002-1012.

The intestinal tract (i.e., the gut), is where the body's nutrients are absorbed, and is simultaneously inhabited by numerous microbes. An increasing body of literature suggests a crucial role for the gut microbiome in modulating systemic inflammatory disease. Psoriasis is a chronic systemic inflammatory disease and its pathogenesis is related to the interaction between genetic susceptibility, immune response and environmental triggers. The omics era has allowed physicians to assess different aspects of psoriasis pathogenesis such as the microbiome, infectome, and autoinfectome. Furthermore, diet appears to play an important role in modulating disease activity, perhaps by influencing gut microbes. Given these observations, we aimed to summarize the current knowledge regarding skin-microbiome-gut-nutrients and psoriasis.

RevDate: 2020-04-07

Fernández de Ullivarri M, Arbulu S, Garcia-Gutierrez E, et al (2020)

Antifungal Peptides as Therapeutic Agents.

Frontiers in cellular and infection microbiology, 10:105.

Fungi have been used since ancient times in food and beverage-making processes and, more recently, have been harnessed for the production of antibiotics and in processes of relevance to the bioeconomy. Moreover, they are starting to gain attention as a key component of the human microbiome. However, fungi are also responsible for human infections. The incidence of community-acquired and nosocomial fungal infections has increased considerably in recent decades. Antibiotic resistance development, the increasing number of immunodeficiency- and/or immunosuppression-related diseases and limited therapeutic options available are triggering the search for novel alternatives. These new antifungals should be less toxic for the host, with targeted or broader antimicrobial spectra (for diseases of known and unknown etiology, respectively) and modes of actions that limit the potential for the emergence of resistance among pathogenic fungi. Given these criteria, antimicrobial peptides with antifungal properties, i.e., antifungal peptides (AFPs), have emerged as powerful candidates due to their efficacy and high selectivity. In this review, we provide an overview of the bioactivity and classification of AFPs (natural and synthetic) as well as their mode of action and advantages over current antifungal drugs. Additionally, natural, heterologous and synthetic production of AFPs with a view to greater levels of exploitation is discussed. Finally, we evaluate the current and potential applications of these peptides, along with the future challenges relating to antifungal treatments.

RevDate: 2020-04-07

Askarova S, Umbayev B, Masoud AR, et al (2020)

The Links Between the Gut Microbiome, Aging, Modern Lifestyle and Alzheimer's Disease.

Frontiers in cellular and infection microbiology, 10:104.

Gut microbiome is a community of microorganisms in the gastrointestinal tract. These bacteria have a tremendous impact on the human physiology in healthy individuals and during an illness. Intestinal microbiome can influence one's health either directly by secreting biologically active substances such as vitamins, essential amino acids, lipids et cetera or indirectly by modulating metabolic processes and the immune system. In recent years considerable information has been accumulated on the relationship between gut microbiome and brain functions. Moreover, significant quantitative and qualitative changes of gut microbiome have been reported in patients with Alzheimer's disease. On the other hand, gut microbiome is highly sensitive to negative external lifestyle aspects, such as diet, sleep deprivation, circadian rhythm disturbance, chronic noise, and sedentary behavior, which are also considered as important risk factors for the development of sporadic Alzheimer's disease. In this regard, this review is focused on analyzing the links between gut microbiome, modern lifestyle, aging, and Alzheimer's disease.

RevDate: 2020-04-07

Rodríguez-Ruano SM, Juhaňáková E, Vávra J, et al (2020)

Methodological Insight Into Mosquito Microbiome Studies.

Frontiers in cellular and infection microbiology, 10:86.

Symbiotic bacteria affect competence for pathogen transmission in insect vectors, including mosquitoes. However, knowledge on mosquito-microbiome-pathogen interactions remains limited, largely due to methodological reasons. The current, cost-effective practice of sample pooling used in mosquito surveillance and epidemiology prevents correlation of individual traits (i.e., microbiome profile) and infection status. Moreover, many mosquito studies employ laboratory-reared colonies that do not necessarily reflect the natural microbiome composition and variation in wild populations. As a consequence, epidemiological and microbiome studies in mosquitoes are to some extent uncoupled, and the interactions among pathogens, microbiomes, and natural mosquito populations remain poorly understood. This study focuses on the effect the pooling practice poses on mosquito microbiome profiles, and tests different approaches to find an optimized low-cost methodology for extensive sampling while allowing for accurate, individual-level microbiome studies. We tested the effect of pooling by comparing wild-caught, individually processed mosquitoes with pooled samples. With individual mosquitoes, we also tested two methodological aspects that directly affect the cost and feasibility of broad-scale molecular studies: sample preservation and tissue dissection. Pooling affected both alpha- and beta-diversity measures of the microbiome, highlighting the importance of using individual samples when possible. Both RNA and DNA yields were higher when using inexpensive reagents such as NAP (nucleic acid preservation) buffer or absolute ethanol, without freezing for short-term storage. Microbiome alpha- and beta-diversity did not show overall significant differences between the tested treatments compared to the controls (freshly extracted samples or dissected guts). However, the use of standardized protocols is highly recommended to avoid methodological bias in the data.

RevDate: 2020-04-07

Suzuki S, T Yamada (2020)

Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication.

PeerJ, 8:e8722 pii:8722.

Background: With the development of DNA sequencing technology, static omics profiling in microbial communities, such as taxonomic and functional gene composition determination, has become possible. Additionally, the recently proposed in situ growth rate estimation method allows the applicable range of current comparative metagenomics to be extended to dynamic profiling. However, with this method, the applicable target range is presently limited. Furthermore, the characteristics of coverage depth during replication have not been sufficiently investigated.

Results: We developed a probabilistic model that mimics coverage depth dynamics. This statistical model explains the bias that occurs in the coverage depth due to DNA replication and errors that arise from coverage depth observation. Although our method requires a complete genome sequence, it involves a stable to low coverage depth (>0.01×). We also evaluated the estimation using real whole-genome sequence datasets and reproduced the growth dynamics observed in previous studies. By utilizing a circular distribution in the model, our method facilitates the quantification of unmeasured coverage depth features, including peakedness, skewness, and degree of density, around the replication origin. When we applied the model to time-series culture samples, the skewness parameter, which indicates the asymmetry, was stable over time; however, the peakedness and degree of density parameters, which indicate the concentration level at the replication origin, changed dynamically. Furthermore, we demonstrated the activity measurement of multiple replication origins in a single chromosome.

Conclusions: We devised a novel framework for quantifying coverage depth dynamics. Our study is expected to serve as a basis for replication activity estimation from a broader perspective using the statistical model.

RevDate: 2020-04-07

Ding K, Hua F, W Ding (2020)

Gut Microbiome and Osteoporosis.

Aging and disease, 11(2):438-447 pii:ad-11-2-438.

Gut microbiome refers to the microbes that live in human digestive tract and are symbiotic with the human body. They participate in the regulation of various physiological and pathological processes of the human body and are associated with various diseases. The pathological process of osteoporosis is affected by gut microbes. The molecular mechanisms of osteoporosis mainly include: 1) Intestinal barrier and nutrient absorption (involving SCFAs). 2) Immunoregulation (Th-17 and T-reg cells balance). 3) Regulation of intestinal-brain axis (involving 5-HT). Gut microbes can increase bone mass and improve osteoporosis by inhibiting osteoclast proliferation and differentiation, inducing apoptosis, reducing bone resorption, or promoting osteoblast proliferation and maturation. However, the therapeutic effect of gut microbes on osteoporosis remains to be further proven. At present, some of the findings on the impact of gut microbes on osteoporosis has been applied in clinical, including early diagnosis and intervention of osteoporosis and adjuvant therapy. In this article, we reviewed the molecular mechanisms underlying the regulatory effect of gut microbes on osteoporosis and the clinical practice of using gut microbes to improve bone health.

RevDate: 2020-04-07

St Surin-Lord S, J Miller (2020)

Topical Treatment of Truncal Acne with Tretinoin Lotion 0.05% and Azelaic Acid Foam.

Case reports in dermatological medicine, 2020:5217567.

Truncal acne is present in approximately half of all patients with facial acne but is also occasionally seen in isolation. Important considerations when selecting treatment options for adult female acne, whether on the face, back, chest, or shoulders, include patient compliance, treatment response time, tolerability of the treatment, and psychosocial impact of the disease. Oral antibiotics are widely prescribed for truncal acne due to the challenges of applying topical therapy to such an extensive body surface area. In cases of severe inflammatory and nodular acne vulgaris, this may be a reasonable consideration; however, oral antibiotics should only be used for short durations. Overprescription contributes to microbial resistance and may cause disruption of the gastrointestinal microbiome. In many cases of mild, moderate, or even severe truncal acne, combinations of topical therapies may be valid alternatives. The introduction of foam formulations with enhanced percutaneous absorption and tretinoin lotion formulations that incorporate moisturizing/hydrating agents challenges the previously held idea that effective and tolerable treatment of truncal acne requires oral treatment. This case series describes four female African-American patients with truncal acne successfully treated with a combination of tretinoin lotion 0.05% and azelaic acid 15% foam.

RevDate: 2020-04-07

Rodriguez RM, Hernandez BY, Menor M, et al (2020)

The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing.

Computational and structural biotechnology journal, 18:631-641 pii:S2001-0370(19)30413-1.

Identification of microbial composition directly from tumor tissue permits studying the relationship between microbial changes and cancer pathogenesis. We interrogated bacterial presence in tumor and adjacent normal tissue strictly in pairs utilizing human whole exome sequencing to generate microbial profiles. Profiles were generated for 813 cases from stomach, liver, colon, rectal, lung, head & neck, cervical and bladder TCGA cohorts. Core microbiota examination revealed twelve taxa to be common across the nine cancer types at all classification levels. Paired analyses demonstrated significant differences in bacterial shifts between tumor and adjacent normal tissue across stomach, colon, lung squamous cell, and head & neck cohorts, whereas little or no differences were evident in liver, rectal, lung adenocarcinoma, cervical and bladder cancer cohorts in adjusted models. Helicobacter pylori in stomach and Bacteroides vulgatus in colon were found to be significantly higher in adjacent normal compared to tumor tissue after false discovery rate correction. Computational results were validated with tissue from an independent population by species-specific qPCR showing similar patterns of co-occurrence among Fusobacterium nucleatum and Selenomonas sputigena in gastric samples. This study demonstrates the ability to identify bacteria differential composition derived from human tissue whole exome sequences. Taken together our results suggest the microbial profiles shift with advanced disease and that the microbial composition of the adjacent tissue can be indicative of cancer stage disease progression.

RevDate: 2020-04-07

Hazzouri KM, Flowers JM, Nelson D, et al (2020)

Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era.

Frontiers in plant science, 11:293.

Date palm (Phoenix dactylifera L.) is a socio-economically important crop in the Middle East and North Africa and a major contributor to food security in arid regions of the world. P. dactylifera is both drought and salt tolerant, but recent water shortages and increases in groundwater and soil salinity have threatened the continued productivity of the crop. Recent studies of date palm have begun to elucidate the physiological mechanisms of abiotic stress tolerance and the genes and biochemical pathways that control the response to these stresses. Here we review recent studies on tolerance of date palm to salinity and drought stress, the role of the soil and root microbiomes in abiotic stress tolerance, and highlight recent findings of omic-type studies. We present a perspective on future research of abiotic stress in date palm that includes improving existing genome resources, application of genetic mapping to determine the genetic basis of variation in tolerances among cultivars, and adoption of gene-editing technologies to the study of abiotic stress in date palms. Development of necessary resources and application of the proposed methods will provide a foundation for future breeders and genetic engineers aiming to develop more stress-tolerant cultivars of date palm.

RevDate: 2020-04-07

Fabian BK, Tetu SG, IT Paulsen (2020)

Application of Transposon Insertion Sequencing to Agricultural Science.

Frontiers in plant science, 11:291.

Many plant-associated bacteria have the ability to positively affect plant growth and there is growing interest in utilizing such bacteria in agricultural settings to reduce reliance on pesticides and fertilizers. However, our capacity to utilize microbes in this way is currently limited due to patchy understanding of bacterial-plant interactions at a molecular level. Traditional methods of studying molecular interactions have sought to characterize the function of one gene at a time, but the slow pace of this work means the functions of the vast majority of bacterial genes remain unknown or poorly understood. New approaches to improve and speed up investigations into the functions of bacterial genes in agricultural systems will facilitate efforts to optimize microbial communities and develop microbe-based products. Techniques enabling high-throughput gene functional analysis, such as transposon insertion sequencing analyses, have great potential to be widely applied to determine key aspects of plant-bacterial interactions. Transposon insertion sequencing combines saturation transposon mutagenesis and high-throughput sequencing to simultaneously investigate the function of all the non-essential genes in a bacterial genome. This technique can be used for both in vitro and in vivo studies to identify genes involved in microbe-plant interactions, stress tolerance and pathogen virulence. The information provided by such investigations will rapidly accelerate the rate of bacterial gene functional determination and provide insights into the genes and pathways that underlie biotic interactions, metabolism, and survival of agriculturally relevant bacteria. This knowledge could be used to select the most appropriate plant growth promoting bacteria for a specific set of conditions, formulating crop inoculants, or developing crop protection products. This review provides an overview of transposon insertion sequencing, outlines how this approach has been applied to study plant-associated bacteria, and proposes new applications of these techniques for the benefit of agriculture.

RevDate: 2020-04-07

Okamura Y, Morimoto N, Ikeda D, et al (2020)

Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka (Oryzias latipes).

Frontiers in immunology, 11:425.

In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the gastrointestinal tract (GI), the induction of antimicrobial peptide (AMP) production via Paneth cells is a fundamental role of IL-17A and F in maintaining homeostasis of the GI microbiome and health. Although mammalian IL-17A and F homologs (referred to as IL-17A/F1-3) have been identified in several fish species, their function in the intestine is poorly understood. Additionally, the fish intestine lacks Paneth cells, and its GI structure is very different from that of mammals. Therefore, the GI microbiome modulatory mechanism via IL-17A/F genes has not been fully elucidated. In this study, Japanese medaka (Oryzias latipes) were used as a teleost model, and IL-17A/F1-knockout (IL-17A/F1-KO) medaka were established using the CRISPR/Cas9 genome editing technique. Furthermore, two IL-17A/F1-deficient medaka strains were generated, including one strain containing a 7-bp deletion (-7) and another with an 11-bp addition (+11). After establishing F2 homozygous KO medaka, transcriptome analysis (RNA-seq) was conducted to elucidate IL-17A/F1-dependent gene induction in the intestine. Results of RNA-seq and real-time PCR (qPCR) demonstrated down-regulation of immune-related genes, including interleukin-1β (IL-1β), complement 1q subunit C (C1qc), transferrin a (Tfa), and G-type lysozyme (LyzG), in IL-17A/F1-KO medaka. Interestingly, protein and lipid digestive enzyme genes, including phospholipase A2, group IB (pla2g1b), and elastase-1-like (CELA1), were also downregulated in the intestines of IL-17A/F1-KO medaka. Furthermore, to reveal the influence of these downregulated genes on the gut microbiome in IL-17A/F1-KO, 16S rRNA-based metagenomic sequencing analysis was conducted to analyze the microbiome constitution. Under a non-exposed state, the intestinal microbiome of IL-17A/F1-KO medaka differed at the phylum level from wild-type, with significantly higher levels of Verrucomicrobia and Planctomycetes. Additionally, at the operational taxonomic unit (OTU) level of the human and fish pathogens, the Enterobacteriaceae Plesiomonas shigelloides was the dominant species in IL-17A/F1-KO medaka. These findings suggest that IL-17A/F1 is involved in the maintenance of a healthy gut microbiome.

RevDate: 2020-04-07

Park H, Cho D, Huang E, et al (2020)

Amelioration of Alcohol Induced Gastric Ulcers Through the Administration of Lactobacillus plantarum APSulloc 331261 Isolated From Green Tea.

Frontiers in microbiology, 11:420.

Gastric inflammation is an indication of gastric ulcers and possible other underlying gastric malignancies. Epidemiological studies have revealed that several Asian countries, including South Korea, suffer from a high incidence of gastric diseases derived from high levels of stress, alcoholic consumption, pyloric infection and usage of non-steroidal anti-inflammatory drugs (NSAIDs). Clinical treatments of gastric ulcers are generally limited to proton pump inhibitors that neutralize the stomach acid, and the application of antibiotics for Helicobacter pylori eradication, both of which are known to have a negative effect on the gut microbiota. The potential of probiotics for alleviating gastrointestinal diseases such as intestinal bowel syndrome and intestinal bowel disease receives increasing scientific interest. Probiotics may support the amelioration of disease-related symptoms through modulation of the gut microbiota without causing dysbiosis. In this study the potential of Lactobacillus plantarum APSulloc 331261 (GTB1TM), isolated from green tea, was investigated for alleviating gastric inflammation in an alcohol induced gastric ulcer murine model (positive control). Treatment with the test strain significantly influenced the expression of pro-inflammatory and anti-inflammatory biomarkers, interleukin 6 (IL6) and interleukin 10 (IL10), of which the former was down- and the latter up-regulated when the alcohol induced mice were treated with the test strain. This positive effect was also indicated by less severe gastric morphological changes and the histological score of the gastric tissues. A significant increase in the abundance of Akkermansia within the GTB1TM treated group compared to the positive control group also correlated with a decrease in the ratio of acetate over propionate. The increased levels of propionate in the GTB1TM group appear to result from the impact of the test strain on the microbial population and the resulting metabolic activities. Moreover, there was a significant increase in beta-diversity in the group that received GTB1TM over that of the alcohol induced control group.

RevDate: 2020-04-07

Macke E, Callens M, Massol F, et al (2020)

Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities.

Frontiers in microbiology, 11:380.

In spite of the growing interest in the role of the gut microbiome (GM) in host physiology and health, the mechanisms governing its assembly and its effects on the environment are poorly understood. In this article, we show that the host genotype and the GM of Daphnia influence the community structure of the surrounding bacterioplankton (BPK). When Daphnia genotypes were placed in an identical environment, both the GM and BPK showed a genotype and diet-dependent taxonomic composition. Overall, the GM strongly differed from the BPK in taxonomic composition and was characterized by a lower α-diversity, suggesting a selective rejecting of bacteria from the regional species pool. In a microbiome transplant experiment, the assembly of both the GM and BPK was strongly affected by the host genotype and the inoculum to which germ-free Daphnia were exposed. The combination of these results suggests a strong interaction between the host genotype, its GM and free-living microbial communities. Currently, it is generally assumed that an animal's diet has a strong effect on the animal's GM, but only a negligible (if any) effect on the surrounding environment. However, our results indicate that the diet/microbiome inocula have a small effect on the gut community and a large effect on the community in the surrounding environment. This structuring genotype × microbiome × environment effect is an essential prerequisite that could indicate that microbiomes play an important role in eco-evolutionary processes.

RevDate: 2020-04-07

McDonald RC, Watts JEM, HJ Schreier (2020)

Corrigendum: Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus.

Frontiers in microbiology, 11:331.

[This corrects the article DOI: 10.3389/fmicb.2019.02687.].

RevDate: 2020-04-07

Li Y, Faden HS, L Zhu (2020)

The Response of the Gut Microbiota to Dietary Changes in the First Two Years of Life.

Frontiers in pharmacology, 11:334.

The infant gut microbiota undergoes significant changes in the first two years of life in response to changes in the diet. The discontinuation of the milk-based diet of the first year and the introduction of solid foods in the second year of life results in a decline in bifidobacterium, a shift from infant strains of bifidobacterium to adult strains which preferentially metabolize oligosaccharides derived from plants rather than from milk, a surge in short chain fatty acids such as acetic, propionic and butyric acid from newly acquired commensal clostridium, and the transformation of primary bile acids into secondary bile acids by a limited number of newly acquired and highly specialized Clostridium spp. By 3 years of age, diet and gut microbiota closely resemble those of adults. Gut bacteria required for the production of SCFAs and secondary BAs are potential targets for the intervention of microbiome-related diseases.

RevDate: 2020-04-07

Zeng Z, Mukherjee A, Varghese AP, et al (2020)

Roles of G protein-coupled receptors in inflammatory bowel disease.

World journal of gastroenterology, 26(12):1242-1261.

Inflammatory bowel disease (IBD) is a complex disease with multiple pathogenic factors. Although the pathogenesis of IBD is still unclear, a current hypothesis suggests that genetic susceptibility, environmental factors, a dysfunctional immune system, the microbiome, and the interactions of these factors substantially contribute to the occurrence and development of IBD. Although existing and emerging drugs have been proven to be effective in treating IBD, none can cure IBD permanently. G protein-coupled receptors (GPCRs) are critical signaling molecules implicated in the immune response, cell proliferation, inflammation regulation and intestinal barrier maintenance. Breakthroughs in the understanding of the structures and functions of GPCRs have provided a driving force for exploring the roles of GPCRs in the pathogenesis of diseases, thereby leading to the development of GPCR-targeted medication. To date, a number of GPCRs have been shown to be associated with IBD, significantly advancing the drug discovery process for IBD. The associations between GPCRs and disease activity, disease severity, and disease phenotypes have also paved new avenues for the precise management of patients with IBD. In this review, we mainly focus on the roles of the most studied proton-sensing GPCRs, cannabinoid receptors, and estrogen-related GPCRs in the pathogenesis of IBD and their potential clinical values in IBD and some other diseases.

RevDate: 2020-04-07

Yu B, Yu B, L Yu (2020)

Commentary: Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome.

Indian journal of microbiology, 60(2):259-261.

Human beings have co-evolved with the microorganisms in our environment for millions of years, and have developed into a symbiosis in a mutually beneficial/defensive way. Human beings have significant multifaceted relationships with the diverse microbial community. Apart from the important protective role of microbial community exposure in development of early immunity, millions of inimitable bacterial genes of the diverse microbial community are the indispensable source of essential nutrients like essential amino acids and essential fatty acids for human body. The essential nutrition from microbiome is harvested through xenophagy. As an immune effector, xenophagy will capture any microorganisms that touch the epithelial cells of our gastrointestinal tract, degrade them and turn them into nutrients for the use of our body.

RevDate: 2020-04-07

Ekanayake A, Madegedara D, Chandrasekharan V, et al (2020)

Respiratory Bacterial Microbiota and Individual Bacterial Variability in Lung Cancer and Bronchiectasis Patients.

Indian journal of microbiology, 60(2):196-205.

Respiratory bacterial microbiota plays a key role in human health. Lung cancer microbiome is a significant yet an understudied area while bronchiectasis microbiome is often studied. We assessed the bacterial microbiota in the upper and lower respiratory tract of the patients with lung cancer and bronchiectasis against a healthy group and their variations in individuality. 16S rRNA gene based metagenomic sequencing was used to detect entire bacterial community along with conventional aerobic bacterial culturing. In comparison to healthy, increased bacterial diversity was observed in diseased population. Abundance of more than 1% was considered and bacteria were identified in 97% similarity. Only lung cancer patients exhibited bacteria specific to the disease: Corynebacterium tuberculostearicum and Keratinibaculum paraultunense. However, Enterococcus faecalis and Delftia tsuruhatensis were also observed limited to lung cancer and bronchiectasis respectively, in less than 1% but supported with bacterial culturing. In conclusion the disease condition and intra-group variability should be considered in future with larger cohorts to understand individual patient variability highlighting the social habits and gender of the individual.

RevDate: 2020-04-07

Dafale NA, Srivastava S, HJ Purohit (2020)

Zoonosis: An Emerging Link to Antibiotic Resistance Under "One Health Approach".

Indian journal of microbiology, 60(2):139-152.

Current scenario in communicable diseases has generated new era that identifies the "One health" approach to understand the sharing and management of etiological agents with its impact on ecosystem. Under this context the relevance of zoonotic diseases generates major concern. The indiscriminate and higher use of antibiotics in animal husbandry creates substantial pressure on the gut microbiome for development of resistance due to shorter generation time and high density. Thus, gut works as a bioreactor for the breeding of ARBs in this scenario and are continuously released in different niches. These ARBs transfer resistance genes among native flora through horizontal gene transfer events, vectors and quorum sensing. About 60% of infectious diseases in human are caused by zoonotic pathogens have potential to carry ARGs which could be transmitted to humans. The well documented zoonotic diseases are anthrax cause by Bacillus anthracis, bovine tuberculosis by Mycobacterium tuberculosis, brucellosis by Brucella abortus, and hemorrhagic colitis by Escherichia coli. Similarly, most of the antibiotics are not completely metabolized and released in unmetabolized forms which enters the food chain and affect various ecological niches through bioaccumulation. The persistence period of antibiotics ranges from < 1 to 3466 days in environment. The consequences of misusing the antibiotic in livestock and their fate in various ecological niches have been discussed in this review. Further the light sheds on antibiotics persistence and it biodegradation through different abiotic and biotic approaches in environment. The knowledge on personnel hygiene and strong surveillance system for zoonotic disease including ARBs transmission, prevention and control measures should be established to regulate the spread of AMR in the environment and subsequently to the human being through a food web.

RevDate: 2020-04-07

Adamovsky O, Buerger A, Vespalcova H, et al (2020)

Evaluation of microbiome-host relationships in the zebrafish gastrointestinal system reveals adaptive immunity is a target of bis(2-ethylhexyl) phthalate (DEHP) exposure.

Environmental science & technology [Epub ahead of print].

To improve physical characteristics of plastics such as flexibility and durability, producers enrich materials with phthalates such as di-2-(ethylhexyl) phthalate (DEHP). DEHP is a high production volume chemical associated with metabolic and immune disruption in animals and humans. To reveal mechanisms implicated in phthalate-related disruption in the gastrointestinal system, male and female zebrafish were fed DEHP (3 ppm) daily for two months. At the transcriptome level, DEHP significantly upregulated gene networks in the intestine associated with helper T cells (Th1, Th2 and Th17) specific pathways. The activation of gene networks associated with adaptive immunity were linked to the suppression of networks for tight junction, gap junctional intercellular communication, and transmembrane transporters, all of which are precursors for impaired gut integrity and performance. On a class level, DEHP exposure increased Bacteroidia and Gammaproteobacteria and decreased Verrucomicrobiae in both the male and female gastrointestinal system. Further, in males there was a relative increase in Fusobacteriia, Betaproteobacteria and a relative decrease in Saccharibacteria. Predictive algorithms revealed the functional shift in the microbiome community, and the metabolites they produce, act to modulate intestinal adaptive immunity. This finding suggests that the gut microbiota may contribute to the adverse effects of DEHP on the host by altering metabolites sensed by both intestinal and immune Th cells. Our results suggest that the microbiome-gut-immune axis can be modified by DEHP and emphasizes the value of multi-omics approaches to study microbiome-host interactions following chemical perturbations.

RevDate: 2020-04-07

Qu Q, Zhang Z, Peijnenburg WJGM, et al (2020)

Rhizosphere microbiome assemble and its impact on plant growth.

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

Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome, as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays. Keywords: Plant, Rhizosphere microbiome, Growth-promotion, Disease-resistance, Synthetic microbial community.

RevDate: 2020-04-07

McGovern BH, Ford CB, Henn MR, et al (2020)

SER-109, an Investigational Microbiome Drug to Reduce Recurrence after Clostridioides difficile infection: Lessons Learned from a Phase 2 Trial.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:5817059 [Epub ahead of print].

BACKGROUND: Recurrent C. difficile infection (rCDI) is associated with loss of microbial diversity and microbe-derived secondary bile acids, which inhibit C. difficile germination and growth. SER-109, an investigational microbiome drug of donor-derived, purified spores, reduced recurrence in a dose-ranging, open-label Phase (Ph)1 study in subjects with multiply rCDI.

METHODS: In a Ph2 double-blind trial, subjects with clinical resolution on standard-of-care antibiotics were stratified by age (< or ≥65 years) and randomized 2:1 to single-dose SER-109 or placebo. Subjects were diagnosed at study entry by PCR or toxin testing. Safety, C. difficile-positive diarrhea through week 8, SER-109 engraftment and bile acid changes were assessed.

RESULTS: 89 subjects were enrolled; 67% were female; 80.9% diagnosed by PCR. rCDI rates were lower in the SER-109 arm than placebo (44.1% versus 53.3%, respectively) but did not meet statistical significance. In a pre-planned analysis, rates were reduced among subjects ≥65 years (45.2% versus 80%, respectively; RR:1.77, 95% CI:1.11-2.81) while the <65 group showed no benefit. Early engraftment of SER-109 was associated with non-recurrence (p <0.05) and increased secondary bile acid concentrations (p<0.0001). Whole metagenomic sequencing from this study and our prior Ph1 study revealed previously unappreciated dose-dependent engraftment kinetics and confirmed an association between early engraftment and nonrecurrence. Engraftment kinetics suggest that Ph2 dosing was suboptimal. Adverse events were generally mild-to-moderate in severity.

CONCLUSIONS: Early SER-109 engraftment was associated with reduced CDI recurrence and favorable safety was observed. A higher dose of SER-109 and requirements for toxin testing were implemented in the current Ph3 trial.

RevDate: 2020-04-07

Vaelli PM, Theis KR, Williams JE, et al (2020)

The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts.

eLife, 9: pii:53898.

Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block voltage-gated sodium (Nav) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure cultures of isolated bacterial symbionts from toxic newts. We then screened bacterial culture media for TTX using LC-MS/MS and identified TTX-producing bacterial strains from four genera, including Aeromonas, Pseudomonas, Shewanella, and Sphingopyxis. Additionally, we sequenced the Nav channel gene family in toxic newts and found that newts expressed Nav channels with modified TTX binding sites, conferring extreme physiological resistance to TTX. This study highlights the complex interactions among adaptive physiology, animal-bacterial symbiosis, and ecological context.

RevDate: 2020-04-07

Larrick J, AR Mendelsohn (2020)

Supplementation with brush border enzyme alkaline phosphatase slows aging.

Rejuvenation research [Epub ahead of print].

Diminished integrity of the intestinal epithelial barrier with advanced age is believed to contribute to aging-associated dysfunction and pathologies in animals. In mammals, diminished gut integrity contributes to inflammaging, the increase in inflammatory processes observed in old age. Recent work suggests that expression of intestinal alkaline phosphatase (IAP) plays a key role in maintaining gut integrity. IAP expression decreases with increasing age in mice and humans. Absence of IAP leads to liver inflammation and shortened lifespans in mice lacking the IAP gene. In normal mice, exogenous supplemental IAP reverses age-induced barrier dysfunction, improves aging-associated metabolic dysfunction, prevents microbiome dysbiosis (imbalance), and extends lifespan. Consistent with a IAP playing a conserved role in maintaining gut integrity, increased dietary IAP increases aging-diminished physical performance in flies. IAP helps maintain gut integrity in part by supporting the expression of tight junction proteins that maintain the intestinal epithelial barrier and by inactivating bacterial pro-inflammatory factors such as lipopolysaccharides (LPS) by dephosphorylation. Recombinant IAP is in late clinical trials for sepsis-associated acute kidney injury suggesting it may soon become available as a therapeutic. Taken together these reports support the idea that directly increasing IAP levels by supplemental recombinant IAP or by indirectly increasing IAP levels using dietary means to induce endogenous IAP may slow the development of aging-associated pathologies.

RevDate: 2020-04-07

Nisenbaum M, Corti-Monzón G, Villegas-Plazas M, et al (2020)

Enrichment and key features of a robust and consistent indigenous marine-cognate microbial consortium growing on oily bilge wastewaters.

Biodegradation pii:10.1007/s10532-020-09896-w [Epub ahead of print].

Oily bilge wastewater (OBW) is a hazardous hydrocarbon-waste generated by ships worldwide. In this research, we enriched, characterized and study the hydrocarbon biodegradation potential of a microbial consortium from the bilges of maritime ships. The consortium cZ presented a biodegradation efficiency of 66.65% for total petroleum hydrocarbons, 72.33% for aromatics and 97.76% removal of n-alkanes. This consortium showed the ability to grow in OBWs of diverse origin and concentration. A 67-fold increase in biomass was achieved using a Sequential Batch Reactor with OBW as the only carbon and energy source. The bacterial community composition of the enriched OBW bacterial consortium at the final stable stage was characterized by 16S amplicon Illumina sequencing showing that 25 out of 915 of the emerged predominant bacterial types detected summed up for 84% of total composition. Out of the 140 taxa detected, 13 alone accumulated 94.9% of the reads and were classified as Marinobacter, Alcanivorax, Parvibaculum, Flavobacteriaceae, Gammaproteobacteria PYR10d3, Novispirillum and Xanthomonadaceae among the most predominant, followed by Thalassospira, Shewanella, Rhodospirillaceae, Gammaprotobacteria, Rhodobacteriaceae and Achromobacter. The microbial community from OBW bioreactor enrichments is intrinsically diverse with clear selection of predominant types and remarkably exhibiting consistent and efficient biodegradation achieved without any nutrient or surfactant addition. Due to there is very little information available in the OBW biodegradation field, this work contributes to the body of knowledge surrounding the treatment improvement of this toxic waste and its potential application in wastewater management.

RevDate: 2020-04-07

Chang , Sharma L, CS Dela Cruz (2020)

Harnessing Murine Microbiome Models to Study Human Lung Microbiome.

Chest, 157(4):776-778.

RevDate: 2020-04-07

Ye X, Li Z, Luo X, et al (2020)

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community.

Microbiome, 8(1):49 pii:10.1186/s40168-020-00824-x.

BACKGROUND: Myxobacteria are micropredators in the soil ecosystem with the capacity to move and feed cooperatively. Some myxobacterial strains have been used to control soil-borne fungal phytopathogens. However, interactions among myxobacteria, plant pathogens, and the soil microbiome are largely unexplored. In this study, we aimed to investigate the behaviors of the myxobacterium Corallococcus sp. strain EGB in the soil and its effect on the soil microbiome after inoculation for controlling cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum (FOC).

RESULTS: A greenhouse and a 2-year field experiment demonstrated that the solid-state fermented strain EGB significantly reduced the cucumber Fusarium wilt by 79.6% (greenhouse), 66.0% (2015, field), and 53.9% (2016, field). Strain EGB adapted to the soil environment well and decreased the abundance of soil-borne FOC efficiently. Spatiotemporal analysis of the soil microbial community showed that strain EGB migrated towards the roots and root exudates of the cucumber plants via chemotaxis. Cooccurrence network analysis of the soil microbiome indicated a decreased modularity and community number but an increased connection number per node after the application of strain EGB. Several predatory bacteria, such as Lysobacter, Microvirga, and Cupriavidus, appearing as hubs or indicators, showed intensive connections with other bacteria.

CONCLUSION: The predatory myxobacterium Corallococcus sp. strain EGB controlled cucumber Fusarium wilt by migrating to the plant root and regulating the soil microbial community. This strain has the potential to be developed as a novel biological control agent of soil-borne Fusarium wilt. Video abstract.

RevDate: 2020-04-07

Zhou Y, Coventry DR, Gupta VVSR, et al (2020)

The preceding root system drives the composition and function of the rhizosphere microbiome.

Genome biology, 21(1):89 pii:10.1186/s13059-020-01999-0.

BACKGROUND: The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production.

RESULTS: This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched.

CONCLUSIONS: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.

RevDate: 2020-04-07

Gerges-Knafl D, Peter P, Zimprich A, et al (2020)

The urinary microbiome shows different bacterial genera in renal transplant recipients and non-transplant patients at time of acute kidney injury - a pilot study.

BMC nephrology, 21(1):117 pii:10.1186/s12882-020-01773-1.

BACKGROUND: In the past urine was considered sterile. Through the introduction of next generation sequencing, it has become clear that a urinary microbiome exists. Acute kidney injury (AKI) represents a major threat to kidney transplant recipients. Remarkable changes in the urinary metabolome occur during AKI, which may influence the urinary microbiome. To our knowledge, this is the first study that examines the urinary microbiome in renal transplant recipients (RTX) and non-transplant recipients (nRTX) at time of AKI.

METHODS: In this cross-sectional pilot-study the urinary microbiome of 21 RTX and 9 nRTX with AKI was examined. Clean catch morning urine samples were obtained from all patients on the first day of AKI diagnosis. AKI was defined according to KDIGO guidelines. Urinary microbiota and the urinary metabolome during AKI were assessed in one patient. 16S rRNA sequencing was performed. Sequences were processed using UPARSE-pipeline for operational taxonomic units (OTU) and taxon finding.

RESULTS: We successfully extracted and sequenced bacterial DNA from 100% of the urine samples. All 30 patients revealed at least 106,138 reads. 319 OTU and 211 different genera were identified. The microbiotic diversity richness in the RTX group was no different from the nRTX group. Eighteen genera were solely present in nRTX and 7 in RTX.

CONCLUSIONS: The urinary microbiome at time of AKI showed different bacterial genera in RTX compared to nRTX. The nRTX group exhibited no different diversity to the RTX group. Irrespective of the status of a previous renal transplantation, the urinary microbiome comprised > 210 different genera. An intraindividual change in microbiota diversity and richness was observed in one study patient during recovery from AKI.

RevDate: 2020-04-07

Spence JD (2020)

Impaired Renal Function and Cerebrovascular Disease.

RevDate: 2020-04-07

Skonieczna-Żydecka K, Janda K, Kaczmarczyk M, et al (2020)

The Effect of Probiotics on Symptoms, Gut Microbiota and Inflammatory Markers in Infantile Colic: A Systematic Review, Meta-Analysis and Meta-Regression of Randomized Controlled Trials.

Journal of clinical medicine, 9(4): pii:jcm9040999.

Immaturity in digestive-tract motor function and altered intestinal microbiome may play roles in pathogenesis of infantile colic. We assessed the impact of probiotic therapy on crying duration day, in newborns experiencing colic attacks. The PubMed, Embase, Cinnahl, Web of Science databases, and a clinical trials registry ( were searched from inception until 12/02/2020. Random-effects meta-analyses were used to derive standardized mean differences/differences in means and risk ratios. We included 16 studies, which involved 1319 newborns aged up to 6 months. Lactobacillus reuteri strain DSM17938 was administered predominantly (n = 10). Probiotic intervention reduced the duration of crying (standardized mean difference = -2.012, 95% confidence interval: -2.763 to -1.261, z = -5.25, p < 0.0001). The probability of at least a 50% reduction in crying duration was at least 1.98 times higher in the intervention group than in controls (Z = 4.80, p < 0.0001). The effects of the intervention were not significantly affected by the risk of bias assessment, percentage of breastfed infants, and duration of the study. In 11 studies, data concerning gut microbiota composition and function and/or immunological markers were given. Probiotics significantly shortened the crying duration, but a causal relationship between the modulatory effect of probiotics on microbiota and the immune system has not been confirmed.

RevDate: 2020-04-06

Pohl HG, Groah SL, Pérez-Losada M, et al (2020)

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

International neurourology journal, 24(1):41-51.

PURPOSE: Compared to the microbiome of other body sites, the urinary microbiome remains poorly understood. Although noninvasive voided urine specimens are convenient, contamination by urethral microbiota may confound understanding of the bladder microbiome. Herein we compared the voiding- versus catheterization-associated urine microbiome of healthy men and women.

METHODS: An asymptomatic, healthy cohort of 6 women and 14 men underwent midstream urine collection, followed by sterile catheterization of the bladder after bladder refilling. Urine samples underwent urine dipstick testing and conventional microscopy and urine cultures. Samples also underwent Illumina MiSeq-based 16S ribosomal RNA gene amplification and sequencing.

RESULTS: All organisms identified by urine culture were also identified by 16S amplification; however, next-generation sequencing (NGS) also detected bacteria not identified by cultivation. Lactobacillus and Streptococcus were the most abundant species. Abundances of the 9 predominant bacterial genera differed between the urethra and bladder. Voided and catheterized microbiomes share all dominant (>1%) genera and Operational Taxonomic Units but in similar or different proportions. Hence, urethra and bladder microbiomes do not differ in taxonomic composition, but rather in taxonomic structure. Women had higher abundance of Lactobacillus and Prevotella than men.

CONCLUSION: Our findings lend credence to the hypothesis that Lactobacilli are important members of the healthy urine microbiome. Our data also suggest that the microbiomes of the urethra and bladder differ from one another. In conclusion, urine collection method results in different 16S-based NGS data, likely due to the sensitivity of NGS methods enabling detection of urethral bacteria present in voided but not catheterized urine specimens.

RevDate: 2020-04-06

Kim SY, DY Yi (2020)

Components of human breast milk: from macronutrient to microbiome and microRNA.

Clinical and experimental pediatrics pii:cep.2020.00059 [Epub ahead of print].

Human breast milk (HBM) is essential for the infant's growth and development right after birth and is an irreplaceable source of nutrition for early human survival. Various infant formulas have many similarities to HBM in many components, but there is no perfect substitute for HBM. Recently, various breast milk components and their roles have been studied according to the development of various analysis techniques. As is already well known, HBM contains about 87-88% water, and 124 g/L solid components as macronutrients, including about 7% (60-70 g/L) carbohydrates, 1% (8-10 g/L) protein, and 3.8% (35-40 g/L) fat. The composition may vary depending on the environmental factors, including maternal diet. Colostrum is low in fat but high in protein and relatively rich in immune-protective components. Although HBM contains enough vitamins to ensure normal growth of the infant, vitamins D and K may be insufficient, and the infant may require their supplementation. Growth factors in HBM also serve as various bioactive proteins and peptides on the intestinal tract, vasculature, nervous system, and endocrine system. In the past, HBM of a healthy mother was thought to be sterile. However, several subsequent studies have confirmed the presence of rich and diverse microbial communities in HBM. Some studies suggested that the genera Staphylococcus and Streptococcus may be universally predominant in HBM, but the origin of microbiota still remains controversial. Lastly, milk is the one of most abundant body fluid of microRNAs, which are known to play a role in various functions, such as immunoprotection and developmental programming, through delivering from HBM and absorption by intestinal epithelial cells. In conclusion, HBM is the most important source of nutrition for infants and includes microbiomes and miRNAs for growth, development, and immunity.

RevDate: 2020-04-06

Mukherjee A, Singh BK, JP Verma (2020)

Harnessing chickpea (Cicer arietinum L.) seed endophytes for enhancing plant growth attributes and bio-controlling against Fusarium sp.

Microbiological research, 237:126469 pii:S0944-5013(20)30199-3 [Epub ahead of print].

A seed microbiome is likely to have important impacts on plant fitness and productivity but functional potentials of seed microbiome remain poorly understood. It is also suggested that bio-inoculants developed from or compatible with seed microbiome are more likely to produce desired outcomes of sustainable increase in agriculture productivity but few empirical evidences are available. The aim of this study was to identify culturable endophytes of the germinating and dry seeds of chickpea (Cicer arietinum L.), and their functional attributes. We isolated 29 bacterial strains from chickpea seeds (8 strains from dry and 21 strains from germinating seeds). Phylogenetic analysis based on 16S rDNA showed that the seed endophytic bacteria belong to Enterobacter sp., Bacillus sp., Pseudomonas sp., Staphylococcus sp., Pantoea sp. and Mixta sp. Isolates produced significant amount of Indole-3-acetic acid (IAA) (Enterobacter hormaechei BHUJPCS-15; 58.91 μg/ml), solubilised phosphate (Bacillus subtilis BHUJPCS-24; 999.85 μg/ml) and potassium, ammonia (Bacillus subtilis BHUJPCS-12; 148.73 μg/ml), and also inhibited the growth of chickpea pathogen (Pseudomonas aeruginosa BHUJPCS-7 against Fusarium oxysporum f.sp. ciceris) under laboratory conditions. Several seed endophytes induced significant increase in plant growth and increased tolerance of chickpea plants to the pathogen (Fusarium oxysporum f.sp. ciceris) when tested in vitro. Re-introduction of these isolates, resulted in significant increase in plant length, biomass and chlorophyll contents and bio-controlling activity against Fusarium oxysporum f.sp. ciceris. These results provide a direct evidence for the presence of beneficial seed microbiome and suggest these isolates could be further developed into potential bio-inoculants for improving diseases management and sustainable increase in agriculture productivity.

RevDate: 2020-04-06

Bendiks ZA, Knudsen KEB, Keenan MJ, et al (2020)

Conserved and variable responses of the gut microbiome to resistant starch type 2.

Nutrition research (New York, N.Y.), 77:12-28 pii:S0271-5317(19)31117-0 [Epub ahead of print].

Resistant starch type 2 (RS2), a dietary fiber comprised solely of glucose, has been extensively studied in clinical trials and animal models for its capacity to improve metabolic and systemic health. Because the health modulatory effects of RS2 and other dietary fibers are thought to occur through modification of the gut microbiome, those studies frequently include assessments of RS2-mediated changes to intestinal microbial composition and function. In this review, we identify the conserved responses of the gut microbiome among 13 human and 35 animal RS2 intervention studies. Consistent outcomes of RS2 interventions include reductions in bacterial α-diversity; increased production of lumenal short-chain fatty acids; and enrichment of Ruminococcus bromii, Bifidobacterium adolescentis, and other gut taxa. Different taxa are usually responsive in animal models, and many RS2-mediated changes to the gut microbiome vary within and between studies. The root causes for this variation are examined with regard to methodological and analytical differences, host genetics and age, species differences (eg, human, animal), health status, intervention dose and duration, and baseline microbial composition. The significant variation found for this single dietary compound highlights the challenges in targeting the gut microbiome to improve health with dietary interventions. This knowledge on RS2 also provides opportunities to improve the design of nutrition studies targeting the gut microbiome and to ultimately identify the precise mechanisms via which dietary fiber benefits human health.

RevDate: 2020-04-06

Biagi E, Caroselli E, Barone M, et al (2020)

Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO2 vents.

The Science of the total environment, 724:138048 pii:S0048-9697(20)31561-8 [Epub ahead of print].

Coral microbiomes, the complex microbial communities associated with the different anatomic compartments of the coral, provide important functions for the host's survival, such as nutrient cycling at the host's surface, prevention of pathogens colonization, and promotion of nutrient uptake. Microbiomes are generally referred to as plastic entities, able to adapt their composition and functionality in response to environmental change, with a possible impact on coral acclimatization to phenomena related to climate change, such as ocean acidification. Ocean sites characterized by natural gradients of pCO2 provide models for investigating the ability of marine organisms to acclimatize to decreasing seawater pH. Here we compared the microbiome of the temperate, shallow water, non-symbiotic solitary coral Astroides calycularis that naturally lives at a volcanic CO2 vent in Ischia Island (Naples, Italy), with that of corals living in non-acidified sites at the same island. Bacterial DNA associated with the different anatomic compartments (mucus, tissue and skeleton) of A. calycularis was differentially extracted and a total of 68 samples were analyzed by 16S rRNA gene sequencing. In terms of phylogenetic composition, the microbiomes associated with the different coral anatomic compartments were different from each other and from the microbial communities of the surrounding seawater. Of all the anatomic compartments, the mucus-associated microbiome differed the most between the control and acidified sites. The differences detected in the microbial communities associated to the three anatomic compartments included a general increase in subdominant bacterial groups, some of which are known to be involved in different stages of the nitrogen cycle, such as potential nitrogen fixing bacteria and bacteria able to degrade organic nitrogen. Our data therefore suggests a potential increase of nitrogen fixation and recycling in A. calycularis living close to the CO2 vent system.

RevDate: 2020-04-06

Pickert G, Wirtz S, Matzner J, et al (2020)

Wheat Consumption Aggravates Colitis in Mice via Amylase Trypsin Inhibitor-mediated Dysbiosis.

Gastroenterology pii:S0016-5085(20)30447-9 [Epub ahead of print].

BACKGROUND & AIMS: Wheat has become the world´s major staple and its consumption correlates with prevalence of non-communicable disorders such as inflammatory bowel diseases. Amylase trypsin inhibitors (ATIs), a component of wheat, activate the intestine's innate immune response via toll-like receptor 4 (TLR4). We investigated the effects of wheat and ATIs on severity of colitis and fecal microbiota in mice.

METHODS: C57BL/6 wildtype and Tlr4-/- mice were fed wheat- or ATI-containing diets or a wheat-free (control) diet and then given dextran sodium sulfate to induce colitis; we also studied Il10-/- mice, which develop spontaneous colitis. Changes in fecal bacteria were assessed by taxa-specific quantitative PCR and 16S ribosomal RNA metagenomic sequencing. Feces were collected from mice on wheat-containing, ATI-containing, control diets and transplanted to intestines of mice with and without colitis on control or on ATI-containing diets. Intestinal tissues were collected and analyzed by histology, immunohistochemistry and flow cytometry. Bacteria with reported immunomodulatory effects were incubated with ATIs and analyzed in radial diffusion assays.

RESULTS: The wheat- or ATI-containing diets equally increased inflammation in intestinal tissues of C57BL/6 mice with colitis, compared with mice on control diets. The ATI-containing diet promoted expansion of taxa associated with development of colitis comparable to the wheat-containing diet. ATIs inhibited proliferation of specific human commensal bacteria in radial diffusion assays. Transplantation of microbiota from feces of mice fed the wheat- or ATI-containing diets to intestines of mice on control diets increased the severity of colitis in these mice. The ATI-containing diet did not increase the severity of colitis in Tlr4-/- mice.

CONCLUSIONS: Consumption of wheat or wheat-ATIs increases intestinal inflammation in mice with colitis, via TLR4, and alters their fecal microbiota. Wheat-based, ATI-containing diets therefore activate TLR4 signaling and promote intestinal dysbiosis.

RevDate: 2020-04-06

Kappel BA, De Angelis L, Heiser M, et al (2020)

Cross-omics analysis revealed gut microbiome-related metabolic pathways underlying atherosclerosis development after antibiotics treatment.

Molecular metabolism pii:S2212-8778(20)30049-1 [Epub ahead of print].

OBJECTIVE: The metabolic influence of gut microbiota plays a pivotal role in the pathogenesis of cardiometabolic diseases. Antibiotics affect intestinal bacterial diversity, and long-term usage has been identified as an independent risk factor for atherosclerosis-driven events. The aim of this study was to explore the interaction between gut dysbiosis by antibiotics and metabolic pathways with the impact on atherosclerosis development.

METHODS: We combined oral antibiotics with different diets in an Apolipoprotein E-knockout mouse model linking gut microbiota to atherosclerotic lesion development via an integrative cross-omics approach including serum metabolomics and cecal 16S rRNA targeted metagenomic sequencing. We further investigated patients with carotid atherosclerosis compared to control subjects with comparable cardiovascular risk.

RESULTS: Here, we show that increased atherosclerosis by antibiotics was connected to a loss of intestinal diversity and alterations of microbial metabolic functional capacity with a major impact on the host serum metabolome. Pathways were modulated by antibiotics and connected to atherosclerosis, which included diminished tryptophan and disturbed lipid metabolism. These pathways were related to the reduction of certain members of Bacteroidetes and Clostridia by antibiotics in the gut. Patients with atherosclerosis presented a similar metabolic signature as those induced by antibiotics in our mouse model.

CONCLUSION: Taken together, this work provides insights into the complex interaction between intestinal microbiota and host metabolism. Our data highlight that detrimental effects of antibiotics on the gut flora are connected to a pro-atherogenic metabolic phenotype beyond classical risk factors.

RevDate: 2020-04-06

Tam A, Filho FSL, Ra SW, et al (2020)

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome.

PloS one, 15(4):e0230932 pii:PONE-D-19-34202.

RATIONALE: Chronic smoke exposure is associated with weight loss in patients with Chronic Obstructive Pulmonary Disease (COPD). However, the biological contribution of chronic smoking and sex on the cecal microbiome has not been previously investigated.

METHODS: Adult male, female and ovariectomized mice were exposed to air (control group) or smoke for six months using a standard nose-only smoke exposure system. DNA was extracted from the cecal content using the QIAGEN QIAamp® DNA Mini Kit. Droplet digital PCR was used to generate total 16S bacterial counts, followed by Illumina MiSeq® analysis to determine microbial community composition. The sequencing data were resolved into Amplicon Sequence Variants and analyzed with the use of QIIME2®. Alpha diversity measures (Richness, Shannon Index, Evenness and Faith's Phylogenetic Diversity) and beta diversity (based on Bray-Curtis distances) were assessed and compared according to smoke exposure and sex.

RESULTS: The microbial community was different between male and female mice, while ovariectomy made the cecal microbiome similar to that of male mice. Chronic smoke exposure led to significant changes in the cecal microbial community in both male and female mice. The organism, Alistipes, was the most consistent bacteria identified at the genus level in the cecal content that was reduced with chronic cigarette exposure and its expression was positively related to the whole-body weight of these mice.

CONCLUSION: Chronic smoke exposure is associated with changes in the cecal content microbiome; these changes may play a role in the weight changes that are observed in cigarette smokers.

RevDate: 2020-04-06

Munoz-Ucros J, Panke-Buisse K, J Robe (2020)

Bacterial community composition of vermicompost-treated tomato rhizospheres.

PloS one, 15(4):e0230577 pii:PONE-D-19-29736.

Vermicompost application has been shown to promote plant growth, alter the rhizosphere microbiome, and suppress plant pathogens. These beneficial properties are often attributed to the activity of vermicompost-associated microorganisms. However, little is known about the microbial shifts that occur in the rhizosphere after vermicompost application. To better understand the impact of vermicompost treatments on the assembly of rhizosphere bacterial communities, 16S rDNA communities of vermicompost and rhizospheres of each peat- and soil-grown tomatoes were profiled after conventional fertigation, irrigation without additional nutrients, and addition of three different vermicompost-extracts. The full dataset consisted of 412 identified genera, of which 317 remained following stringent quality filtration. Tomato rhizosphere microbiome responses to treatments were complex and unique between peat and soil growth substrates. Direct colonization of vermicompost-origin taxa into rhizospheres was limited, with genera Photobacterium and Luteimonas colonizing peat rhizospheres, genera Truepera, Phenylobacterium, and Lysinibacillus colonizing soil rhizospheres, and genus Pelagibius appearing in both soil and peat rhizospheres. Further patterns of differential abundance and presence/absence between treatments highlight vermicompost-mediated effects on rhizosphere microbiome assembly as an interplay of rhizosphere medium, direct colonization of vermicompost-origin taxa and vermicompost-induced shifts in the rhizosphere microbial community. This exploratory analysis is intended to provide an initial look at 16S community composition of vermicompost and the effects of vermicompost treatment on the rhizosphere microbiome assembly to highlight interactions of potential merit for subsequent investigations.

RevDate: 2020-04-06

Lockwood MB, SJ Green (2020)

Clinical care is evolving: The microbiome for advanced practice nurses.

Journal of the American Association of Nurse Practitioners, 32(4):290-292.

Over the course of four billion years, humans have developed an intimate relationship with the more than 37 trillion microbes that inhabit our bodies. This relationship runs the gamut from symbiosis to pathogenesis. The number of microbial cells is roughly equivalent to that of mammalian cells in the body. However, due to substantial microbial diversity in host-associated communities, the genetic content of the microbiome is roughly 150 times greater than that of the human genome. Microbial genes encode for proteins capable of producing a wide variety of molecules essential for our health and survival. Many factors such as mode of birth, diet, chlorination of water, and medications significantly affect the richness and diversity of the microbiome. Advanced practice nurses have important roles to play as clinicians, scientists, educators, and patient advocates as our understanding of the microbiome's effects on health becomes better articulated. An understanding of how the microbiome can affect an individual's health or the efficacy of treatment will soon be essential in the clinical setting, and nurses should be encouraged to educate themselves on the relationship between our microbial partners, the environment, and human health.

RevDate: 2020-04-06

Rahmati M, N Macklon (2020)

Testing the endometrium: is there enough evidence to justify clinical use?.

Current opinion in obstetrics & gynecology [Epub ahead of print].

PURPOSE OF REVIEW: Embryo implantation remains the limiting factor in assisted reproduction outcomes. To date research has mainly focused on improving embryo quality, numbers and selection as the route to improve treatment results. However, with success rates plateauing, interest in the possibility of modulating the endometrial factor is increasing, and a number of biomarkers are now available that offer the possibility of assessing endometrial function.

RECENT FINDINGS: In this review, we review recent evidence for the efficacy of a number of these biomarkers, with emphasis on those that aim to enable improvement in embryo/endometrial developmental synchrony endometrium and that offer an assessment of the degree of immune activation of the endometrium. The emerging field of reproductive tract microbiome analysis is also considered. Finally, nascent biomarkers of materno-foetal dialogue, including noncoding RNAs, microvesicles and endometrial glycans are discussed.

SUMMARY: Tests of potential clinical value are emerging, but further validation studies are required. The usage of innovative endometrial biomarkers provides the possibility of targeted therapies rather than the blind empirical approaches to face embryo implantation failure. It also enables the possibility of randomized controlled trials of interventions targeting the individual cause rather empirical treatments of undiagnosed recurrent implantation failure.

RevDate: 2020-04-06

Valdés-Ferrer S, Benkendorff A, R Sankowski (2020)

Persistent inflammatory states and their implications in brain disease.

Current opinion in neurology [Epub ahead of print].

PURPOSE OF REVIEW: Apart from mental, motor and sensory functions, the human central nervous system (CNS) regulates a plethora of homeostatic (autonomic and hormonal) bodily functions. These functions are dependent on specialized neuronal networks. To ensure connectivity of these networks, they are continuously refined and supported by glial cells that outnumber neurons by, according to some accounts, an order of magnitude. Among glial cells, microglia - the brain resident macrophages - plays a crucial role in maintaining neuronal networks. However, in their concomitant role as brain immune cells microglia also engage in inflammatory signaling that may disrupt neuronal networks. Here, we review novel insights for molecular pathways involved in the protective functions of microglia and other immune cells in response to systemic signals and stimuli.

RECENT FINDINGS: Recent evidence suggests that aging and systemic disease push individual microglia toward proinflammatory phenotypes compromising the connectivity of neuronal networks, resulting in neuropsychiatric disease. Furthermore, cells (self as well as the microbiome) outside the CNS have been shown to affect neuronal function.

SUMMARY: These recent findings have critical implications for mental health, particularly of an aging population, in particular for the development of novel immunomodulatory therapies for brain disease.

RevDate: 2020-04-06

Shah A, Macdonald GA, Morrison M, et al (2020)

Targeting the Gut Microbiome as a Treatment for Primary Sclerosing Cholangitis: A Conceptional Framework.

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

Primary sclerosing cholangitis (PSC) is a rare, immune-mediated, chronic cholestatic liver disease associated with a unique phenotype of inflammatory bowel disease that frequently manifests as pancolitis with right-sided predominance. Available data suggest a bidirectional interplay of the gut-liver axis with critical roles for the gastrointestinal microbiome and circulating bile acids (BAs) in the pathophysiology of PSC. BAs shape the gut microbiome, whereas gut microbes have the potential to alter BAs, and there are emerging data that alterations of BAs and the microbiome are not simply a consequence but the cause of PSC. Clustering of PSC in families may suggest that PSC occurs in genetically susceptible individuals. After exposure to an environmental trigger (e.g., microbial byproducts or BAs), an aberrant or exaggerated cholangiocyte-induced immune cascade occurs, ultimately leading to bile duct damage and progressive fibrosis. The pathophysiology can be conceptualized as a triad of (1) gut dysbiosis, (2) altered BA metabolism, and (3) immune-mediated biliary injury. Immune activation seems to be central to the disease process, but immunosuppression does not improve clinical outcomes or alter the natural history of PSC. Currently, orthoptic liver transplantation is the only established life-saving treatment, whereas antimicrobial therapy or fecal transplantation is an emerging therapeutic option for PSC. The beneficial effects of these microbiome-based therapies are likely mediated by a shift of the gut microbiome with favorable effects on BA metabolism. In the future, personalized approaches will allow to better target the interdependence between microbiome, immune function, and BA metabolism and potentially cure patients with PSC.

RevDate: 2020-04-06

Mennini M, Fierro V, Di Nardo G, et al (2020)

Microbiota in non-IgE-mediated food allergy.

Current opinion in allergy and clinical immunology [Epub ahead of print].

PURPOSE OF REVIEW: To perform a nonsystematic review of the literature on the microbiota in the different types of non-IgE-mediated food allergy.

RECENT FINDINGS: The commonest non-IgE-mediated disorders managed by allergists include: eosinophilic esophagitis, food protein-induced enteropathy, food protein-induced enterocolitis syndrome, and food protein-induced allergic proctocolitis. The review of the literature describes how at phylum level we observe an increase of Proteobacteria in eosinophilic esophagitis esophageal microbiota and in food protein-induced enterocolitis syndrome, and food protein-induced allergic proctocolitis gut microbiota, while we observe an increase of Bacteroidetes in healthy controls. Several studies endorse the concept that a bloom of Proteobacteria in the gut reflects dysbiosis or an unstable gut microbial community structure. In several studies, the type of diet, the use of probiotics and in a single experience the use of fecal microbiota transplantation has produced significant variations of the microbiota.

SUMMARY: Genetic factors alone cannot account for the rapid rise in food allergy prevalence and the microbiome might be contributing to allergy risk. Our review showed that common features of the pathological microbiota among different types of non-IgE-mediated food allergy can be identified. These evidences suggest a possible role of the microbiota in the pathogenesis and non-IgE-mediated food allergies and the need to understand the effects of its modulation on the disorders themselves.

RevDate: 2020-04-06

Byrd DA, Sinha R, Hoffman KL, et al (2020)

Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing.

mSphere, 5(1): pii:5/1/e00827-19.

Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies.IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.

RevDate: 2020-04-06

Miyake S, Ding Y, Soh M, et al (2020)

Cultivation and description of Duncaniella dubosii sp. nov., Duncaniella freteri sp. nov. and emended description of the species Duncaniella muris.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

Three bacterial strains, C9, H5 and TLL-A3, were isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of 16S rRNA genes indicated that the strains belonged to the Muribaculaceae, and shared 91.6-99.9 % sequence identity with the recently described Duncaniella muris DSM 103720T. Genome-sequencing of the isolates was performed to compare average nucleotide identities (ANI) between strains. The ANI analysis revealed that all isolates shared highest ANI with D. muris DSM 103720T, with strain C9 being most similar (ANI: 98.0 %) followed by strains H5 (ANI: 76.4 %) and TLL-A3 (ANI: 74.4 %). Likewise, digital DNA-DNA hybridization (dDDH) indicated high similarity of strain C9 (dDDH: 86.6 %) to D. muris DSM 103720T, but strains H5 and TLL-A3 showed lower similarity (dDDH <35 %) to either of the three type species of the Muribaculaceae (Muribaculum intestinale DSM 28989T, Paramuribaculum intestinale DSM 100749T, D. muris DSM 103720T). MK-10 and MK-11 were abundant in all three isolates, but concentrations varied between species. Based on genotypic, phylogenetic and phenotypic differences, the strains TLL-A3 and H5 are considered to represent novel species of the genus Duncaniella, for which the names Duncaniella freteri sp. nov., and Duncaniella dubosii sp. nov., are proposed. The respective type strains are TLL-A3T (=DSM 108168T=KCTC 15769T), and H5T (=DSM 107170T=KCTC 15734T). Strain C9 reveals limited sequence dissimilarity and minor differences in morphological properties with Duncaniella muris DSM 103720T and is therefore proposed to belong to the same species. The respective strain is C9 (=DSM 107165=KCTC 15733).

RevDate: 2020-04-06

Ivaska LE, Hanif T, Ahmad F, et al (2020)

Tonsillar microbial diversity, abundance and interrelations in atopic and non-atopic individuals.

RevDate: 2020-04-06

de Wert LA, Rensen SS, Soons Z, et al (2020)

The cutaneous microbiome in hospitalized patients with pressure ulcers.

Scientific reports, 10(1):5963 pii:10.1038/s41598-020-62918-8.

This study investigated whether there are differences in the composition of the cutaneous microbiome of the unaffected skin between patients with pressure ulcers compared with those without pressure ulcers. The cutaneous microbiome of the unaffected skin of 15 patients with sacral pressure ulcers compared to 15 patients without pressure ulcers was analysed. It demonstrated that the inter-individual variation in skin microbiota of patients with pressure ulcers was significantly higher (P = 0.01). The abundance of 23 species was significantly different with Staphylococcus aureus and unclassified Enterococcus the most abundant species in patients with pressure ulcers. Random Forest models showed that eight species were associated with pressure ulcers occurrence in 81% of the patients. A subset of four species gave the strongest interaction. The presence of unclassified Enterococcus had the highest association with pressure ulcer occurrence. This study is the first to demonstrate that the cutaneous microbiome is altered in patients with pressure ulcers.

RevDate: 2020-04-06

Quin C, DL Gibson (2020)

Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants.

Gut microbes [Epub ahead of print].

Colonization of the gastrointestinal tract with microorganisms during infancy represents a critical control point for shaping life-long immune-mediated disease susceptibility. Abnormal colonization or an imbalance of microbes, termed dysbiosis, is implicated in several diseases. Consequently, recent research has aimed at understanding ways to manipulate a dysbiotic microbiome during infancy to resemble a normal, healthy microbiome. However, one of the fundamental issues in microbiome research is characterizing what a "normal" infant microbiome is based on geography, ethnicity and cultural variations. This review provides a comprehensive account of what is currently known about the infant microbiome from a global context. In general, this review shows that the influence of cultural variations in feeding practices, delivery modes and hygiene are the biggest contributors to microbial variability. Despite geography or race, all humans have similar microbial succession during infancy.

RevDate: 2020-04-06

Shapiro RM, JH Antin (2020)

Therapeutic options for steroid-refractory acute and chronic GVHD: an evolving landscape.

Expert review of hematology [Epub ahead of print].

Introduction: The traditional therapeutic modalities to manage SR-acute GVHD have focused on the inhibition of the alloreactive T-cell response, while in the setting of SR-chronic GVHD the focus has been on a combination of T-cell and B-cell targeting strategies. However, new therapeutic modalities have shown promise. The purpose of this review is to summarize the current treatment landscape of SR-acute and chronic GVHD.Areas covered: A systematic search of MEDLINE, EMBASE, and databases for published articles, abstracts, and clinical trials pertaining to available therapeutic modalities for SR-acute and SR-chronic GVHD was conducted. Also highlighted is a number of ongoing clinical trials in both SR-acute and SR-chronic GVHD with strategies targeting the JAK-1/2 pathway, the Treg:Tcon ratio, the immunomodulation mediated by mesenchymal stem cells, and the gut microbiome, among others. Expert opinion: Ruxolitinib has emerged as the preferred therapeutic modality for SR-acute GVHD, with alpha-1-antitrypsin and extracorporeal photophoresis (ECP) being reasonable alternatives. Ruxolitinib and Ibrutinib are among the preferred options for SR-chronic GVHD, with ECP being a viable alternative particularly if the skin is involved. A number of novel therapeutic modalities, including those enhancing the activity of regulatory T-cells have shown great promise in early phase trials of SR-chronic GVHD.

RevDate: 2020-04-06

Wauters L, Burns G, Ceulemans M, et al (2020)

Duodenal inflammation: an emerging target for functional dyspepsia?.

Expert opinion on therapeutic targets [Epub ahead of print].

Introduction: Functional dyspepsia (FD) is one of the most common functional gastrointestinal disorders and is classified into postprandial distress and epigastric pain syndrome. Despite the recognition of duodenal inflammation as a potential trigger of symptoms, only limited anti-inflammatory therapies exist.Areas covered: This narrative review summarizes the recent advances in the pathophysiology and treatment of FD; it identifies potential therapeutic targets and gaps in the field. An electronic literature search was conducted in Pubmed up to 31st of December 2019.Expert opinion: There is compelling evidence for the role of duodenal inflammation and the eosinophil-mast cell axis in the pathogenesis of dyspeptic symptoms. Traditional prokinetic drugs and neuromodulators target gastric dysmotility and visceral hypersensitivity, but are hampered by limited efficacy and side effects. Independent of acid suppression, the anti-inflammatory action of proton pump inhibitors, which remain the first-line therapy in FD, may also explain their therapeutic effect. Other existing and newly established anti-inflammatory drugs should be investigated while trials including probiotics and selective antibiotics should examine the host microbiome and immune activation. Targeted treatments for potential causes of duodenal pathology such as impaired permeability and dysbiosis, are likely to emerge in the future.

RevDate: 2020-04-06

Morales-Marroquin E, Hanson B, Greathouse L, et al (2020)

Comparison of methodological approaches to human gut microbiota changes in response to metabolic and bariatric surgery: A systematic review.

Obesity reviews : an official journal of the International Association for the Study of Obesity [Epub ahead of print].

Substantial differences in the response of gut microbial composition to metabolic and bariatric surgery have been reported. Therefore, the goal of the present review is to evaluate if methodological differences could be driving this lack of consistency. A search was conducted using PUBMED, Web of Science, Science Direct and COCHRANE using the following inclusion criteria: human studies written in English with a baseline sampling point, using gut microbiota as an outcome and either Roux-n-Y gastric bypass or sleeve gastrectomy. Sixteen articles were selected (total 221 participants). Roux-n-Y gastric bypass caused more alterations in gut microbial composition in comparison with sleeve gastrectomy. Substantial variability was found in study designs, data collection and analyses across studies. Increases in several families and genera from the phylum Proteobacteria and Bacteroidetes, the family Streptococcaceae, the species Akkermansia muciniphila and Streptococcus salivarius and a decrease in the phylum Firmicutes and the family Bifidobacteriaceae were reported. There is a need for standardization not only of microbial analysis but also of study designs when analysing the effect of bariatric surgery on the human gut microbiome. In addition, outcomes from different surgical procedures should not be combined as they produce distinctive effects on gut microbial composition.

RevDate: 2020-04-06

Zhang M, Zou X, Zhao D, et al (2020)

Pork Meat Proteins Alter Gut Microbiota and Lipid Metabolism Genes in the Colon of Adaptive Immune-deficient Mice.

Molecular nutrition & food research [Epub ahead of print].

SCOPE: Excessive consumption of processed meat has been linked to an increasing risk of gut diseases. We investigated how pork meat proteins affect colon homeostasis between normal and immune-compromised mice.

METHODS AND RESULTS: Immune-deficient mice (Rag1-/-) and wild-type mice were fed a diet that contained 20% casein or protein isolated from cooked pork or dry-cured pork for 3 months. Rag1-/- mice showed greater variations in transcriptome responses and higher microbial diversity than wild-type mice after consumption of the pork meat protein diets. Intake of pork meat protein diets also increased body weight and induced colonic oxidative stress, low-grade inflammation and gene expression involved in immune function and cell cycle and migration. Key genes like Hmox1, Ppara, and Pparg were highly upregulated by pork meat protein. These changes were associated with decreased abundances of Blautia, Bifidobacterium and Alistipes and increased abundances of Akkermansia muciniphila and Ruminococcaceae.

CONCLUSION: Pork meat proteins affect colon health in both wild-type and Rag1-/- mice by altering the microbiome profile under the complex interaction with adaptive immunity. Our findings give a new insight into the understanding of meat intake, immunity and gut health. This article is protected by copyright. All rights reserved.

RevDate: 2020-04-06

Brandwein M, Fuks G, Israel A, et al (2020)

Skin Microbiome Compositional Changes in Atopic Dermatitis Accompany Dead Sea Climatotherapy.

Photochemistry and photobiology, 96(2):450.

RevDate: 2020-04-05

Risely A (2020)

Applying the core microbiome to understand host-microbe systems.

The Journal of animal ecology [Epub ahead of print].

1.The host-associated core microbiome was originally coined to refer to common groups of microbes or genes that were likely to be particularly important for host biological function. However, the term has evolved to encompass variable definitions across studies, often identifying key microbes with respect to their spatial distribution, temporal stability, or ecological influence, as well as their contribution to host function and fitness. 2.A major barrier to reaching a consensus over how to define the core microbiome and its relevance to biological, ecological and evolutionary theory is a lack of precise terminology and associated definitions, as well the persistent association of the core microbiome with host function. Common, temporal, and ecological core microbiomes can together generate insights into ecological processes that act independently of host function, whilst functional and host-adapted cores distinguish between facultative and near-obligate symbionts that differ in their effects on host fitness. 3.This commentary summarizes five broad definitions of the core microbiome that have been applied across the literature, highlighting their strengths and limitations for advancing our understanding of host-microbe systems, noting where they are likely to overlap, and discussing their potential relevance to host function and fitness. 4.No one definition of the core microbiome is likely to capture the range of key microbes across a host population. Applied together, they have the potential to reveal different layers of microbial organisation from which we can begin to understand the ecological and evolutionary processes that govern host-microbe interactions.

RevDate: 2020-04-05

Huang S, Kleerebezem R, Rabaey K, et al (2020)

Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10551-w [Epub ahead of print].

Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day-1, with a concurrent production of n-butyrate of 7.9 mM day-1. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.

RevDate: 2020-04-05

Utro F, Haiminen N, Siragusa E, et al (2020)

Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes.

iScience, 23(4):100988 pii:S2589-0042(20)30172-3 [Epub ahead of print].

Increasingly available microbial reference data allow interpreting the composition and function of previously uncharacterized microbial communities in detail, via high-throughput sequencing analysis. However, efficient methods for read classification are required when the best database matches for short sequence reads are often shared among multiple reference sequences. Here, we take advantage of the fact that microbial sequences can be annotated relative to established tree structures, and we develop a highly scalable read classifier, PRROMenade, by enhancing the generalized Burrows-Wheeler transform with a labeling step to directly assign reads to the corresponding lowest taxonomic unit in an annotation tree. PRROMenade solves the multi-matching problem while allowing fast variable-size sequence classification for phylogenetic or functional annotation. Our simulations with 5% added differences from reference indicated only 1.5% error rate for PRROMenade functional classification. On metatranscriptomic data PRROMenade highlighted biologically relevant functional pathways related to diet-induced changes in the human gut microbiome.


ESP Quick Facts

ESP Origins

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

ESP Support

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

ESP Rationale

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

ESP Goal

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

ESP Usage

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

ESP Content

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

ESP Help

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

ESP Plans

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

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

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

Digital Books

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


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


Biographical information about many key scientists.

Selected Bibliographies

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

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