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Bibliography on: Microbiome

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ESP: PubMed Auto Bibliography 05 Jun 2020 at 01:45 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: 2020-06-04

Cabrol L, Thalasso F, Gandois L, et al (2020)

Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes.

The Science of the total environment, 736:139588 pii:S0048-9697(20)33105-3 [Epub ahead of print].

Arctic lakes emit methane (CH4) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH4 oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH4 mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH4 concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH4 was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH4 cycling in these Siberian Arctic lakes by mitigating the majority of produced CH4 before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH4 cycle in lakes, a crucial component of the global CH4 cycle.

RevDate: 2020-06-04

Zhang YG, Lu R, Wu S, et al (2020)

Vitamin D receptor protects against dysbiosis and tumorigenesis via the JAK/STAT pathway in intestine.

Cellular and molecular gastroenterology and hepatology pii:S2352-345X(20)30086-2 [Epub ahead of print].

BACKGROUND: Vitamin D exerts regulatory roles via vitamin D receptor (VDR) in mucosal immunity, host defense, and inflammation involving host factors and microbiome. Human Vdr gene variation shapes the microbiome and VDR deletion leads to dysbiosis. Low VDR expression and diminished vitamin D/VDR signaling are observed in colon cancer. Nevertheless, how intestinal epithelial VDR is involved in tumorigenesis through gut microbiota remains unknown. We hypothesized that intestinal VDR protects mice against dysbiosis via modulating the JAK/STAT pathway in tumorigenesis. To test our hypothesis, we used an azoxymethane/Dextran Sulfate Sodium-induced cancer model in intestinal VDR conditional knockout (VDRΔIEC) mice, cell cultures, stem-cell derived colonoids, and human colon cancer samples.

RESULTS: VDRΔIEC mice have higher numbers of tumors with location shifted from distal to proximal colon. Fecal microbiota analysis showed that VDR deletion leads to bacterial profile shift from normal to susceptible carcinogenesis. We found enhanced bacterial staining in mouse and human tumors. Microbial metabolites from VDRΔIEC mice showed elevated secondary bile acids, consistent with the observations in human CRC. We further identified that VDR protein bound to the Jak2 promoter, suggesting that VDR transcriptionally regulated Jak2. The JAK/STAT pathway is critical in intestinal and microbial homeostasis. Fecal samples from VDRΔIEC mice activate the STAT3 signaling in human and mouse organoids. Lack of VDR led to hyperfunction of Jak2 in respond to intestinal dysbiosis. A JAK/STAT inhibitor abolished the microbiome-induced activation of STAT3.

CONCLUSION: We provide insights into the mechanism of VDR dysfunction leading to dysbiosis and tumorigenesis. It indicates a new target - microbiome and VDR for prevention of cancer.

RevDate: 2020-06-04

Narla S, Price KN, Sachdeva M, et al (2020)

Proceeding report of the fourth Symposium on Hidradenitis Suppurativa Advances (SHSA) 2019.

Journal of the American Academy of Dermatology pii:S0190-9622(20)30989-0 [Epub ahead of print].

The 4th Annual Symposium on Hidradenitis Suppurativa (SHSA) took place on 1-3 November 2019 at the Westin Book Cadillac Hotel in Detroit, Michigan, U.S.A. This symposium was a joint meeting of the United States Hidradenitis Suppurativa Foundation (HSF) and the Canadian Hidradenitis Suppurativa Foundation (CHSF). This cross- disciplinary meeting with experts from around the world was an opportunity to discuss the most recent advances in the study of hidradenitis suppurativa (HS) pathogenesis, clinical trials, classification, scoring systems, complementary/ alternative medical treatments (CAM), diet, pain management, surgical and laser treatment, and ultrasound assessment. A special pre-conference workshop was held on the use of neodymium-doped yttrium aluminum garnet (Nd:YAG) laser hair reduction, sinus tract deroofing, carbon dioxide (CO2) laser excision with ultrasound mapping and tumescent anesthesia for the treatment of HS. The focused workshops on establishing an HS clinic, setting up an HS support group, Hidradenitis Suppurativa PRospective Observational REgistry and bioSpecimen RepoSitory (HS PROGRESS), and wound care were held during the meeting. A special program called HS Ambassadors was established for patients who may have questions about the conference presentations and in addition, a meet and greet for patients and HS Ambassadors was arranged. To facilitate networking between those early in their career and clinical and research experts, a mentoring reception was held.

RevDate: 2020-06-04

Ozkan J, Coroneo M, Sandbach J, et al (2020)

Bacterial contamination of intravitreal needles by the ocular surface microbiome.

The ocular surface pii:S1542-0124(20)30088-4 [Epub ahead of print].

PURPOSE: The ocular surface microbiota are recognised as one of causative microorganisms in post-procedural endophthalmitis but in many cases the vitreous tap is culture negative. This study investigated bacterial contamination of intravitreal (IVT) needles using multiple approaches covering culturing, 16S rRNA gene sequencing, fluorescent in situ hybridisation (FISH) and scanning electron microscopy (SEM).

METHODS: IVT needles were obtained immediately after injection from patients undergoing treatment for predominantly age-related macular degeneration. Eighteen needles were analysed by culturing on chocolate blood agar. In addition, 40 needles were analysed by extracting DNA and paired-end sequencing of the 16S rRNA gene. Sequences were quality filtered (USEARCH), taxonomically classified (SILVA) and contaminant filtered (DECONTAM). Nine needles were analysed by either FISH using the bacterial probe EUB338 or SEM.

RESULTS: Using culturing, three bacteria were identified from 5 of 18 needles (28%) - Kocuria kristinae, Staphylococcus hominis and Sphingomonas paucimobilis. The negative control needles showed no growth. Following rigorous data filtering, bacterial community analysis using 16S rRNA gene sequencing showed the presence of predominantly Corynebacterium but also Pseudomonas, Acinetobacter, Sphingomonas, Staphylococcus and Bacillus on the needles. Cocci-shaped cells in a tetrad formation were observed using FISH, while SEM images showed cocci-shaped bacteria in pairs and irregular tetrads.

CONCLUSIONS: The study showed evidence for a large diversity of bacteria on IVT needles and visually confirmed their adherence. The diversity was similar to that found on the ocular surface and in conjunctival tissue. This suggests the risk of exogenous endophthalmitis remains even with sterilization of the conjunctival surface.

RevDate: 2020-06-04

Hayes CL, Peters BJ, JA Foster (2020)

Microbes and mental health: Can the microbiome help explain clinical heterogeneity in psychiatry?.

Frontiers in neuroendocrinology pii:S0091-3022(20)30040-6 [Epub ahead of print].

Trillions of microbes cover the surfaces of our bodies and inhabit our gastrointestinal tract. In the past decade, research efforts examining the role of the microbiome in mental health have moved to the forefront of neuroscience and psychiatry. Based on a foundation of animal studies demonstrating the vital role for microbiota-brain communication in brain development, behavior, and brain function over the life span, clinical studies have started to consider the microbiome in psychiatric disorders. The composition, diversity and function of commensal microbes is influenced by genetic, lifestyle, and environmental factors. This review provides an overview of the factors contributing to individual differences in the microbiome, reviews recent work in psychiatric disorders, and considers what is needed to advance a better understanding of how the microbiome impacts mental health which may help us understand the heterogeneity observed in clinical psychiatric populations.

RevDate: 2020-06-04

Gu S, Chen Y, Wu Z, et al (2020)

Alterations of the Gut Microbiota in Patients with COVID-19 or H1N1 Influenza.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:5851452 [Epub ahead of print].

BACKGROUND: Coronavirus disease 2019 (COVID-19) is an emerging serious global health problem. Gastrointestinal symptoms are common in COVID-19 patients, and SARS-CoV-2 RNA has been detected in stool specimens. However, the relationship between the gut microbiome and disease remains to be established.

METHODS: We conducted a cross-sectional study of 30 COVID-19 patients, 24 influenza A (H1N1) patients, and 30 matched healthy controls (HC) to identify differences in the gut microbiota by 16S ribosomal RNA (rRNA) gene V3-V4 region sequencing.

RESULTS: Compared with HC, COVID-19 patients had significantly reduced bacterial diversity, a significantly higher relative abundance of opportunistic pathogens, such as Streptococcus, Rothia, Veillonella and Actinomyces, and a lower relative abundance of beneficial symbionts. Five biomarkers showed high accuracy for distinguishing COVID-19 patients from HC with an area under the curve (AUC) up to 0.89. Patients with H1N1 displayed lower diversity and different overall microbial composition compared with COVID-19 patients. Seven biomarkers were selected to distinguish the two cohorts with an AUC of 0.94.

CONCLUSION: The gut microbial signature of patients with COVID-19 was different from that of H1N1 patients and HC. Our study suggests the potential value of the gut microbiota as a diagnostic biomarker and therapeutic target for COVID-19, but further validation is needed.

RevDate: 2020-06-04

Lin D, Kouzy R, Abi Jaoude J, et al (2020)

Microbiome factors in HPV-driven carcinogenesis and cancers.

PLoS pathogens, 16(6):e1008524 pii:PPATHOGENS-D-19-02038.

RevDate: 2020-06-04

McCabe RA, Receveur JP, Houtz JL, et al (2020)

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors.

PloS one, 15(6):e0234050 pii:PONE-D-20-00922.

Louse flies (Diptera: Hippoboscidae) are obligate ectoparasites that often cause behavioral, pathogenic, and evolutionary effects on their hosts. Interactions between ectoparasites and avian hosts, especially migrating taxa, may influence avian pathogen spread in tropical and temperate ecosystems and affect long-term survival, fitness and reproductive success. The purpose of this study was to characterize the vector-associated microbiome of ectoparasitic louse flies feeding on migrating raptors over the fall migration period. Surveys for louse flies occurred during fall migration (2015-2016) at a banding station in Pennsylvania, United States; flies were collected from seven species of migrating raptors, and we sequenced their microbial (bacteria and archaea) composition using high-throughput targeted amplicon sequencing of the 16S rRNA gene (V4 region). All louse flies collected belonged to the same species, Icosta americana. Our analysis revealed no difference in bacterial communities of louse flies retrieved from different avian host species. The louse fly microbiome was dominated by a primary endosymbiont, suggesting that louse flies maintain a core microbial structure despite receiving blood meals from different host species. Thus, our findings highlight the importance of characterizing both beneficial and potentially pathogenic endosymbionts when interpreting how vector-associated microbiomes may impact insect vectors and their avian hosts.

RevDate: 2020-06-04

Li J, Van Der Pol W, Eraslan M, et al (2020)

Comparison of the gut microbiome composition among individuals with acute or long-standing spinal cord injury vs. able-bodied controls.

The journal of spinal cord medicine [Epub ahead of print].

Objective: Compare the gut microbiome composition among individuals with acute spinal cord injury (A-SCI), long-standing SCI (L-SCI), vs. able-bodied (AB) controls.Design: Cross-sectional study.Setting: The University of Alabama at Birmingham.Participants: Seven adults with A-SCI (36 ± 12 years, 2F/5M, C4-T10, and American Spinal Injury Association Impairment Scale [AIS] A-D), 25 with L-SCI (46 ± 13 years, 6F/19M, C4-L1, and AIS A-D), and 25 AB controls (42 ± 13 years, 9F/16M).Methods: Stool samples were collected after a median of 7 days and 18 years after injury in the A-SCI and L-SCI groups, respectively. Gut microbiome composition was analyzed using the 16S rRNA sequencing technique and QIIME software. The abundances of bacteria communities among groups were compared using the Kruskal-Wallis test adjusted for age.Results: Several alpha diversity indices were different among groups (Chao1, Observed species, and Phylogenetic Diversity), but not others (Shannon and Simpson). Beta diversity differed among each pair of groups (P < 0.05). A number of microbial communities were differentially abundant among the groups (P < 0.05).Conclusion: Our results revealed differences in the gut microbiome composition among groups. Compared to the AB controls, the SCI groups demonstrated microbiome profiles that shared features linked to metabolic syndrome, inflammation-related bowel disorders, depressive disorders, or antibiotics use, whereas the L-SCI group's microbiome included features linked to reduced physical activity compared to the A-SCI and AB controls. Our results provided preliminary data and a scientific foundation for future studies investigating the impact of the gut microbiome composition on long-term health in individuals with SCI.

RevDate: 2020-06-04

Wang CZ, Wan JY, Wan J, et al (2020)

Human intestinal microbiota derived metabolism signature from a North American native botanical Oplopanax horridus with UPLC/Q-TOF-MS analysis.

Biomedical chromatography : BMC [Epub ahead of print].

Oplopanax horridus, distributed in North America, is an herbal medicine traditionally used by Pacific indigenous peoples for various medical conditions. After oral ingestion, constituents in O. horridus extract (OhE) could be converted to their metabolites by enteric microbiome before absorption. In this study, in order to mimic gut environment, the OhE was biotransformed by using the enteric microbiome of healthy human subjects. For accurate and reliable data collection with optimized approaches in sample preparation and analytical conditions, ultra-performance liquid chromatography and quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS) were used to characterize parent constituents and their metabolites. In the extract, 20 parent compounds were identified including polyynes, sesquiterpenes, monoterpeondids, phenylpropanoids, and phenolic acids. After the biotransformation, a total of 78 metabolites were identified, of which 37 of them belong to polyynes metabolites. The common biotransformation pathways are hydroxylation, acetylization, methylation, and demethylation. Based on the pathway distributions, the metabolism signature of OhE has been explored. The metabolism pathways of OhE compounds are dependent on their structural classifications and hydrophilic/hydrophobic properties. In summary, with comprehensive analysis, we systematically investigated human microbiome-derived OhE metabolites. The enteric microbial metabolism signature provides novel information for future effective use of Oplopanax horridus.

RevDate: 2020-06-04

Claar DC, McDevitt-Irwin JM, Garren M, et al (2020)

Increased diversity and concordant shifts in community structure of coral-associated Symbiodiniaceae and bacteria subjected to chronic human disturbance.

Molecular ecology [Epub ahead of print].

Coral-associated bacteria and endosymbiotic algae (Symbiodiniaceae spp.) are both vitally important for the biological function of corals. Yet little is known about their co-occurrence within corals, how their diversity varies across coral species, or how they are impacted by anthropogenic disturbances. Here, we sampled coral colonies (n = 472) from seven species, encompassing a range of life history traits, across a gradient of chronic human disturbance (n = 11 sites on Kiritimati (Christmas) atoll) in the central equatorial Pacific, and quantified the sequence assemblages and community structure of their associated Symbiodiniaceae and bacterial communities. Although Symbiodiniaceae alpha diversity did not vary with chronic human disturbance, disturbance was consistently associated with higher bacterial Shannon diversity and richness, with bacterial richness by sample almost doubling from sites with low to very high disturbance. Chronic disturbance was also associated with altered microbial beta diversity for Symbiodiniaceae and bacteria, including changes in community structure for both and increased variation (dispersion) of the Symbiodiniaceae communities. We also found concordance between Symbiodiniaceae and bacterial community structure, when all corals were considered together, and individually for two massive species, Hydnophora microconos and Porites lobata, implying that symbionts and bacteria respond similarly to human disturbance in these species. Finally, we found that the dominant Symbiodiniaceae ancestral lineage in a coral colony was associated with differential abundances of several distinct bacterial taxa. These results suggest that increased beta diversity of Symbiodiniaceae and bacterial communities may be a reliable indicator of stress in the coral microbiome, and that there may be concordant responses to chronic disturbance between these communities at the whole-ecosystem scale.

RevDate: 2020-06-04

Villa P, Cipolla C, D'Ippolito S, et al (2020)

The interplay between immune system and microbiota in gynecological diseases: a narrative review.

European review for medical and pharmacological sciences, 24(10):5676-5690.

OBJECTIVE: The vaginal microbiome is a dynamic environment, depending on the results of a complex interplay between microbiota and the host. In physiological conditions, Lactobacillus species are the most represented, regulating glycogen metabolism in order to maintain normal pH. Vaginal flora has been divided into five subtypes. Pattern recognition receptors are present on both squamous epithelial cells lining the vagina and columnar cells lining the upper female genital tract. They respond directly to bacterial product expressed by vaginal microbiome. The vagina contains different immune related cells and receptors which can recognize and react with the microbial environment. Altered microbiota and altered interplay between microbiota and immune system underlie several gynecologic diseases.

MATERIALS AND METHODS: In this review, literature data related to vaginal microbiota, vaginal inflammation, immune system and menopause, preterm labor and miscarriage, were summarized. Relevant publications were retrieved from: PubMed, Medline, Scopus and Web of Science.

RESULTS: The vaginal microbiome and the relationship with immune system has been analyzed in different gynecologic conditions. Menopause is associated to estrogen loss which causes vaginal atrophy, reduced abundance of Lactobacilli and increased amount of other bacterial species. Estrogens influence vaginal immunity through known and unknown mechanisms. In bacterial vaginosis (BV), due to many bacterial species, there has been found an inhibition of the chemotaxis and cytokine secretion. A decreased concentration of Lactobacilli seems to be playing a role in preterm labor as well as the increased levels of pro-inflammatory cytokines. Finally, the disequilibrium in the Th1/Th2 immune adaptive response, with a shift from Th2 to Th1, appears to be playing a role in miscarriage.

CONCLUSIONS: The interplay between microbiota and the host closely involves the immune system. In particular, the vaginal microbiota is classically characterized by Lactobacilli even if vaginal microbiome of asymptomatic woman of reproductive age includes multiple aerobic and facultative or obligate anaerobic species. The role of microbiota and immune system in determining gynecological and obstetric events has been studied throughout recent years reaching new advancements. Therefore, additional studies are needed to better comprehend the complexity of the issue.

RevDate: 2020-06-04

Rasmussen TS, Koefoed AK, Jakobsen RR, et al (2020)

Bacteriophage-mediated manipulation of the gut microbiome - promises and presents limitations.

FEMS microbiology reviews pii:5851274 [Epub ahead of print].

Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.

RevDate: 2020-06-04

Chinna Meyyappan A, R Milev (2020)

The Safety, Efficacy, and Tolerability of Microbial Ecosystem Therapeutic-2 in People With Major Depression and/or Generalized Anxiety Disorder: Protocol for a Phase 1, Open-Label Study.

JMIR research protocols, 9(6):e17223 pii:v9i6e17223.

BACKGROUND: The bidirectional signaling between the gut microbiota and the brain, known as the gut-brain axis, is being heavily explored in current neuropsychiatric research. Analyses of the human gut microbiota have shown considerable individual variability in bacterial content, which is hypothesized to influence brain function, and potentially mood and anxiety symptoms, through gut-brain axis communication. Preclinical and clinical research examining these effects suggests that fecal microbiota transplant (FMT) may aid in improving the severity of depression and anxiety symptoms by recolonizing the gastrointestinal (GI) tract with healthy bacteria. The microbial ecosystem therapeutic (ie, microbial ecosystem therapeutic-2 [MET-2]) used in this study is an alternative treatment to FMT, which comprises 40 different strains of gut bacteria from a healthy donor.

OBJECTIVE: The primary objective of this study is to assess subjective changes in mood and anxiety symptoms before, during, and after administration of MET-2. The secondary objectives of this study are to assess the changes in metabolic functioning and the level of repopulation of healthy gut bacteria, the safety and tolerability of MET-2, and the effects of early stress on biomarkers of depression/anxiety and the response to treatment.

METHODS: Adults experiencing depressive or anxiety symptoms will be recruited from the Kingston area. These participants will orally consume an encapsulated MET-2 once daily-containing 40 strains of purified and laboratory-grown bacteria from a single healthy donor-for 8 weeks, followed by a 2-week treatment-free follow-up period. Participants will undergo a series of clinical assessments measuring mood, anxiety, and GI symptoms using validated clinical scales and questionnaires. Molecular data will be collected from blood and fecal samples to assess metabolic changes, neurotransmitter levels, inflammatory markers, and the level of engraftment of the fecal samples that may predict outcomes in depression or anxiety.

RESULTS: Given the association between the gut bacteria and the risk factors of depression, we expect to observe an improvement in the severity of depressive and anxiety symptoms following treatment, and we expect that this improvement is mediated by the recolonization of the GI tract with healthy bacteria. The recruitment for this study has been completed, and the data obtained are currently being analyzed.

CONCLUSIONS: This is the first time MET-2 is being tested in psychiatric indications, specifically depression and anxiety. As such, this may be the first study to show the potential effects of microbial therapy in alleviating psychiatric symptoms as well as its safety and tolerability.


RevDate: 2020-06-04

Gascon M, Harrall KK, Beavers AW, et al (2020)

Feasibility of collection and analysis of microbiome data in a longitudinal randomized trial of community gardening.

Future microbiology [Epub ahead of print].

Aim: We explored the feasibility of collecting and analyzing human microbiome data in a longitudinal randomized controlled trial of community gardening. Methods & materials: Participants were randomly assigned to gardening (N = 8) or control (N = 8). Participants provided stool, mouth, hand and forehead microbiome samples at six timepoints. Analyses combined mixed models with Qiita output. Results: Participant satisfaction was high, with 75% of participants completing evaluations. While no microbial effects were statistically significant due to small sample size, the analysis pipeline utility was tested. Conclusion: Longitudinal collection and analysis of microbiome data in a community gardening randomized controlled trial is feasible. The analysis pipeline will be useful in larger studies for assessment of the pathway between microbiota, gardening and health outcomes.

RevDate: 2020-06-04

Kuczma MP, Szurek EA, Cebula A, et al (2020)

Commensal epitopes drive differentiation of colonic Tregs.

Science advances, 6(16):eaaz3186 pii:aaz3186.

The gut microbiome is the largest source of intrinsic non-self-antigens that are continuously sensed by the immune system but typically do not elicit lymphocyte responses. CD4+ T cells are critical to sustain uninterrupted tolerance to microbial antigens and to prevent intestinal inflammation. However, clinical interventions targeting commensal bacteria-specific CD4+ T cells are rare, because only a very limited number of commensal-derived epitopes have been identified. Here, we used a new approach to study epitopes and identify T cell receptors expressed by CD4+Foxp3+ (Treg) cells specific for commensal-derived antigens. Using this approach, we found that antigens from Akkermansia muciniphila reprogram naïve CD4+ T cells to the Treg lineage, expand preexisting microbe specific Tregs, and limit wasting disease in the CD4+ T cell transfer model of colitis. These data suggest that the administration of specific commensal epitopes may help to widen the repertoire of specific Tregs that control intestinal inflammation.

RevDate: 2020-06-04

Kanuparthy A, Challa T, Meegada S, et al (2020)

Staphylococcus warneri: Skin Commensal and a Rare Cause of Urinary Tract Infection.

Cureus, 12(5):e8337.

Coagulase negative Staphylococci often grow in cultures and form one of the most abundant flora among skin microbiome. It is important and challenging to identify and treat clinically significant infections caused by these organisms. Prosthetic devices, catheters and conditions causing immunocompromised states are the risk factors for such infections. We describe a case of clinically significant and symptomatic urinary tract infection (UTI) in a 65-year-old man with liver cirrhosis caused by Staphylococcus warneri which forms <1% of Staphylococcal skin flora. He was treated successfully with fluoroquinolone antibiotic based on culture results. It is important to understand potential of this organism to cause serious infections which warrant culture-directed antibiotic therapy.

RevDate: 2020-06-04

Zununi Vahed S, Mostafavi S, Hosseiniyan Khatibi SM, et al (2020)

Vascular Calcification: An Important Understanding in Nephrology.

Vascular health and risk management, 16:167-180 pii:242685.

Vascular calcification (VC) is a life-threatening state in chronic kidney disease (CKD). High cardiovascular mortality and morbidity of CKD cases may root from medial VC promoted by hyperphosphatemia. Vascular calcification is an active, highly regulated, and complex biological process that is mediated by genetics, epigenetics, dysregulated form of matrix mineral metabolism, hormones, and the activation of cellular signaling pathways. Moreover, gut microbiome as a source of uremic toxins (eg, phosphate, advanced glycation end products and indoxyl-sulfate) can be regarded as a potential contributor to VC in CKD. Here, an update on different cellular and molecular processes involved in VC in CKD is discussed to elucidate the probable therapeutic pathways in the future.

RevDate: 2020-06-03

Sun T, Miao J, Saleem M, et al (2020)

Bacterial compatibility and immobilization with biochar improved tebuconazole degradation, soil microbiome composition and functioning.

Journal of hazardous materials, 398:122941 pii:S0304-3894(20)30930-4 [Epub ahead of print].

Tebuconazole is a widely used fungicide that may impair soil health. Presently, limited information is available on the bioremediation of tebuconazole-contaminated soil using biochar as a carrier for bacteria. In this study, we firstly isolated a tebuconazole-degrading strain and identified it as Alcaligenes faecalis WZ-2. Then, we used wheat straw-derived biochar as carrier to capture strain WZ-2 to assemble microorganism-immobilized composite. Finally, we investigated the effects of strain WZ-2 and biochar-immobilized WZ-2 on tebuconazole biodegradation, microbial enzyme activities and community composition in the contaminated soil. Results showed that, as compared to control, the strain WZ-2 and biochar-immobilized WZ-2 accelerated the degradation of tebuconazole, while reducing the half-life of tebuconazole from 40.8 to 18.7 and 13.3 days in soil, respectively. However, biochar alone than control slightly retarded the degradation of tebuconazole in soil. Though tebuconazole (10 mg/kg) negatively affected the soil enzyme activities (urease, dehydrogenase, and invertase) and microbiome community structure, the biochar-immobilized WZ-2 not only accelerated the degradation of tebuconazole but also restored native soil microbial enzyme activities and microbiome community composition. Our results suggest that a compatible combination of bacteria with biochar is an attractive and efficient approach for remediation of pesticide-contaminated soil and improvement of soil biological health.

RevDate: 2020-06-03

Ishimaru H, Okamoto N, Fujimura M, et al (2020)

IgE sensitivity to Malassezia pachydermatis and mite allergens in dogs with atopic dermatitis.

Veterinary immunology and immunopathology, 226:110070 pii:S0165-2427(20)30096-9 [Epub ahead of print].

In this study, dogs with atopic dermatitis were separated into non-food-induced atopic dermatitis (NFIAD) group (n = 15) and food-induced atopic dermatitis (FIAD) group (n = 37) based on an elimination diet test. IgE reactivity for crude Malassezia pachydermatis (M. pachydermatis) and house dust mites (HDM) allergen extracts was investigated in the two groups using fluorometric enzyme-linked immunosorbent assay (ELISA) and intradermal skin test (IDST). Nine (60%) of the 15 dogs in NFIAD group and 6 (16%) of the 37 dogs in FIAD group showed specific IgE for M. pachydermatis (Mann-Whitney U-test, P < 0.01). By immunoblotting analysis, the pooled serum samples from dogs with IgE for M. pachydermatis showed IgE reactivity for 50 kDa protein of M. pachydermatis. Twelve (80%) of the 15 dogs in NFIAD group and 8 (22%) of the 37 dogs in FIAD group showed specific IgE for HDM (Mann-Whitney U-test, P < 0.01). In addition, the dogs in NFIAD group significantly show a positive IDST to M. pachydermatis and HDM extracts compared with the dogs in FIAD group. The results suggest that dogs with NFIAD are at increased risk of becoming sensitized to the normal commensal organism M. pachydermatis compared with dogs with FIAD, perhaps co-sensitization occurred due to an HDM protease antigen's, Der f 1 and/or Der p 1, proteolytic activity related epidermal skin barrier defects. Treatment to limit skin colonization may thus be especially important in NFIAD.

RevDate: 2020-06-03

Dess NK, Chapman CD, O College (2020)

"Us vs. Them" Pair Housing: Effects on Body Weight, Open Field Behavior, and Gut Microbiota in Rats Selectively Bred on a Taste Phenotype.

Physiology & behavior pii:S0031-9384(20)30289-4 [Epub ahead of print].

Taste is increasingly recognized as being related to reward, risk, and social processes beyond the ingestive domain. Occidental High (HiS) and Low (LoS) Saccharin Consuming rats have been selectively bred for more than 25 years to study those relationships. The present study examined LoS and HiS rats' sensitivity to a social partner's lineage. The role of gut microbiome transfer between lines was also explored as a possible mediating mechanism. Rats were pair-housed with a rat from either their own line (same-line condition) or the other line (other-line condition); weight gain, saccharin intake, acoustic startle, and open field behavior were measured. Results show for the first time that the lines express different behavioral strategies in a novel open field. In addition, weight gain and open field measures indicate that other-line housing was stressful. Saccharin intake, however, was unaffected by housing condition. A previous finding that the lines possess different gut microbiota was replicated. Although microbial transfer occurred between social partners, no clear evidence was obtained that housing-condition effects on weight gain or behavior were mediated by microbial transfer. Overall, these findings add to the characterization of non-gustatory correlates of a taste phenotype and suggest that rats differing strikingly on the taste phenotype and/or its correlates may be socially incompatible.

RevDate: 2020-06-03

Sorbara MT, Littmann ER, Fontana E, et al (2020)

Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity.

Cell host & microbe pii:S1931-3128(20)30287-0 [Epub ahead of print].

Bacteria belonging to the Lachnospiraceae family are abundant, obligate anaerobic members of the microbiota in healthy humans. Lachnospiraceae impact their hosts by producing short-chain fatty acids, converting primary to secondary bile acids, and facilitating colonization resistance against intestinal pathogens. To increase our understanding of genomic and functional diversity between members of this family, we cultured 273 Lachnospiraceae isolates representing 11 genera and 27 species from human donors and performed whole-genome sequencing assembly and annotation. This analysis revealed substantial inter- and intra-species diversity in pathways that likely influence an isolate's ability to impact host health. These differences are likely to impact colonization resistance through lantibiotic expression or intestinal acidification, influence host mucosal immune cells and enterocytes via butyrate production, or contribute to synergism within a consortium by heterogenous polysaccharide metabolism. Identification of these specific functions could facilitate development of probiotic bacterial consortia that drive and/or restore in vivo microbiome functions.

RevDate: 2020-06-03

Christoff AP, Sereia AFR, Cruz GNF, et al (2020)

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces.

PloS one, 15(6):e0234127 pii:PONE-D-20-08031.

Several studies have shown the ubiquitous presence of bacteria in hospital surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contribute to a major public health issue by increasing patient morbidity and mortality during or after hospital stay. Bacterial high-throughput amplicon gene sequencing along with identification of AMR genes, as well as whole genome sequencing (WGS), are biotechnological tools that allow multiple-sample screening for a diversity of bacteria. In this paper, we used these methods to perform a one-year cross sectional profiling of bacteria and AMR genes in adult and neonatal intensive care units (ICU and NICU) in a Brazilian public, tertiary hospital. Our results showed high abundances of HAI-related bacteria such as S. epidermidis, S. aureus, K. pneumoniae, A. baumannii complex, E. coli, E. faecalis, and P. aeruginosa in patients and hospital surfaces. Most abundant AMR genes detected throughout ICU and NICU were mecA, blaCTX-M-1 group, blaSHV-like, and blaKPC-like. We found that NICU environment and patients were more widely contaminated with pathogenic bacteria than ICU. Patient samples, despite the higher bacterial load, have lower bacterial diversity than environmental samples in both units. Finally, we also identified contamination hotspots in the hospital environment showing constant frequencies of bacterial and AMR contamination throughout the year. Whole genome sequencing (WGS), 16S rRNA oligotypes, and AMR identification allowed a high-resolution characterization of the hospital microbiome profile.

RevDate: 2020-06-03

Rodrigues DR, Briggs W, Duff A, et al (2020)

Cecal microbiome composition and metabolic function in probiotic treated broilers.

PloS one, 15(6):e0225921 pii:PONE-D-19-31622.

Probiotics have become increasingly popular in the poultry industry as a promising nutritional intervention to promote the modulation of intestinal microbial communities and their metabolic activities as a means of improving health and performance. This study aimed to determine the influence of different probiotic formulations on the taxonomic and metabolic profiling of cecal microbial communities, as well as to define associations between cecal microbiota and growth parameters in 21 and 42-day-old broilers. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-forming Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Dietary inclusion of SYNBIO, YEAST, SINGLE2, and SINGLE3 into the diets supported a significant stimulation of BW and BWG by 7 days of age. Besides, SYNBIO reduced the overall mortality rate by 42d (p<0.05). No significant variation was observed among different probiotic-based formulations for cecal microbiota composition. However, there was a treatment-specific effect on the metabolic profiles, with a particular beneficial metabolic adaptation by the microbiota when supplemented by SYNBIO and SINGLE2. Furthermore, the population of Lactobacillales was identified to be strongly associated with lower Enterobacteriales colonization, higher BW means, and lower mortality rate of growing broilers. Overall, the results emphasize that probiotic supplementation may enhance the microbial energy metabolism in the ceca of young broilers.

RevDate: 2020-06-03

Vida A, Bodrogi BL, Balogh B, et al (2020)

Taxamat: Automated biodiversity data management tool - Implications for microbiome studies.

Physiology international, 107(1):12-17.

Working with biodiversity data is a computationally intensive process. Numerous applications and services provide options to deal with sequencing and taxonomy data. Professional statistics software are also available to analyze these type of data. However, in-between the two processes there is a huge need to curate biodiversity sample files. Curation involves creating summed abundance values for chosen taxonomy ranks, excluding certain taxa from analysis, and finally merging and downsampling data files. Very few tools, if any, offer a solution to this problem, thus we present Taxamat, a simple data management application that allows for curation of biodiversity data files before they can be imported to other statistics software. Taxamat is a downloadable application for automated curation of biodiversity data featuring taxonomic classification, taxon filtering, sample merging, and downsampling. Input and output files are compatible with most widely used programs. Taxamat is available on the web at either as a single executable or as an installable package for Microsoft Windows platforms.

RevDate: 2020-06-03

Koppel K, Tang H, Javed I, et al (2020)

Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots.

Nanoscale [Epub ahead of print].

Type 2 diabetes (T2D) and Alzheimer's disease (AD) represent two most prevalent amyloid diseases with a significant global burden. Pathologically, T2D and AD are characterized by the presence of amyloid plaques consisting primarily of toxic human islet amyloid polypeptide (IAPP) and amyloid beta (Aβ). It has been recently revealed that the gut microbiome plays key functions in the pathological progression of neurological disorders through the production of bacterial endotoxins, such as lipopolysaccharide (LPS). In this study, we examined the catalytic effects of LPS on IAPP and Aβ amyloidoses, and further demonstrated their mitigation with zero-dimensional carbon quantum dots (CQDs). Whereas LPS displayed preferred binding with the N-terminus of IAPP and the central hydrophobic core and C-terminus of Aβ, CQDs exhibited propensities for the amyloidogenic and C-terminus regions of IAPP and the N-terminus of Aβ, accordingly. The inhibitory effect of CQDs was verified by an embryonic zebrafish model exposed to the peptides and LPS, where impaired embryonic hatching was rescued and production of reactive oxygen species in the organism was suppressed by the nanomaterial. This study revealed a robust synergy between LPS and amyloid peptides in toxicity induction, and implicated CQDs as a potential therapeutic against the pathologies of T2D and AD.

RevDate: 2020-06-03

Jiang L, B Schnabl (2020)

Gut Microbiota in Liver Disease: What Do We Know and What Do We Not Know?.

Physiology (Bethesda, Md.), 35(4):261-274.

The gut and the liver have a bidirectional communication via the biliary system and the portal vein. The intestinal microbiota and microbial products play an important role for modulating liver diseases such as alcohol-associated liver disease, non-alcoholic fatty liver disease and steatohepatitis, and cholestatic liver diseases. Here, we review the role of the gut microbiota and its products for the pathogenesis and therapy of chronic liver diseases.

RevDate: 2020-06-03

Poll BG, Cheema MU, JL Pluznick (2020)

Gut Microbial Metabolites and Blood Pressure Regulation: Focus on SCFAs and TMAO.

Physiology (Bethesda, Md.), 35(4):275-284.

Shifts in the gut microbiome play a key role in blood pressure regulation, and changes in the production of gut microbial metabolites are likely to be a key mechanism. Known gut microbial metabolites include short-chain fatty acids, which can signal via G-protein-coupled receptors, and trimethylamine-N oxide. In this review, we provide an overview of gut microbial metabolites documented thus far to play a role in blood pressure regulation.

RevDate: 2020-06-03

Lu H, He L, Xu J, et al (2020)

Well-maintained patients with a history of periodontitis still harbor a more disbiotic microbiome than health.

Journal of periodontology [Epub ahead of print].

BACKGROUND: It remains unclear whether well-maintained subjects, with periodontitis in the past, effectively treated, and maintained for a long time, have the same subgingival microbiome as healthy subjects. Therefore, the objective of this study was to investigate the characteristics of the subgingival microbiome in well-maintained patients with a history of periodontitis compared with healthy subjects.

MATERIALS AND METHODS: We recruited in 17 well-maintained individuals (no evidence of clinical inflammation and progress of periodontitis) and 21 healthy individuals. Periodontal clinical parameters, consisting of missing teeth, plaque index (PLI), periodontal depth (PD), and bleeding index (BI) was recorded and analyzed. The pooled subgingival samples from mesiobuccal sites of two maxillary first molars were collected. the V3-V4 region of the 16S rDNA from 38 subgingival samples was sequenced and analyzed. Alpha diversity, microbial composition, types of bacteria, functional pathways between well-maintained group and health group were compared using Mann-Whitney U test. Spearman correlation was used in analyzing the symbiotic relationship among taxa. A classification model was constructed to distinguish two ecological types.

RESULTS: The maintained individuals demonstrated a different microbiome from healthy subjects, with higher diversity, more disordered structure, more pathogenic microbiota, and more host-destructive metabolism pathways. The genera Actinomyces, Streptococcus, Leptotrichia, Capnocytophaga, Lautropia, and Fusobacterium were predominant components with relative abundance more than 5% in the subgingival microbiome in well-maintained patients. The classification model by microbiota got a remarkable accuracy of 83.33%.

CONCLUSIONS: Individuals with well-maintained periodontitis showed a more dysbiotic microbial community with pathogenic bacteria and disordered interactive relationship than healthy individuals. Therefore, close monitoring and scheduling maintenance treatment are necessary for them to maintain a healthy periodontal condition. This article is protected by copyright. All rights reserved.

RevDate: 2020-06-03

Lefèvre E, Gardner CM, CK Gunsch (2020)

A novel PCR clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization.

FEMS microbiology ecology pii:5850752 [Epub ahead of print].

Due to the sequence homology between the bacterial 16S rRNA gene, and plant chloroplast and mitochondrial DNA, the taxonomic characterization of plant microbiome using amplicon-based high throughput sequencing often results in the overwhelming presence of plant-affiliated reads, preventing the thorough description of plant-associated microbial communities. In this work we developed a PCR blocking primer assay targeting the taxonomically informative V5-V6 region of the 16S rRNA gene in order to reduce plant DNA co-amplification, and increase diversity coverage of associated prokaryotic communities. Evaluation of our assay on the characterization of the prokaryotic endophytic communities of Zea mays, Pinus taeda, and Spartina alternifora leaves led to significantly reducing the proportion of plant reads, yielded 20 times more prokaryotic reads, and tripled the number of detected OTUs compared to a commonly used V5-V6 PCR protocol. To expand the application of our PCR clamping assay across a wider taxonomic spectrum of plant hosts, we additionally provide an alignment of chloroplast and mitochondrial DNA sequences encompassing more than 200 terrestrial plant families as a supporting tool for customizing our blocking primers.

RevDate: 2020-06-03

Dugyala S, Ptacek TS, Simon JM, et al (2020)

Putative modulation of the gut microbiome by probiotics enhances preference for novelty in a preliminary double-blind placebo-controlled study in ferrets.

Animal microbiome, 2:.

Background: Increasing evidence suggests a causal relationship between the gut microbiome and psychiatric illnesses. In particular, autism spectrum disorder is associated with gastrointestinal symptoms and alterations in the gut microbiome. Administration of probiotics is a commonly used strategy by caregivers of people with neurodevelopmental illness. However, evidence for successful improvement in gut microbiome and (behavioral) symptoms has been lacking.

Results: Here, we use a novel ferret model of maternal immune activation to show that high-dose probiotic administration in a placebo-controlled study design causes changes in the gut microbiome in the form of a transient increase in the administered bacterial species. In contrast, we found no differences in baseline microbiome composition or changes induced by probiotic administration between animals exposed in utero to maternal immune activation and control animals. However, the relative presence of several bacterial species correlated with an increased preference for novelty (object and conspecific). Intriguingly, several of the hits in this screen are species that have previously emerged in the literature as being associated with autism and anxiety.

Conclusions: Together, our results suggest that high-dose probiotic interventions may be beneficial for the adjunct treatment of psychiatric illnesses. Placebo-controlled clinical trials in humans are urgently needed.

RevDate: 2020-06-03

Haeger A, Costa AS, Romanzetti S, et al (2020)

Effect of a multicomponent exercise intervention on brain metabolism: A randomized controlled trial on Alzheimer's pathology (Dementia-MOVE).

Alzheimer's & dementia (New York, N. Y.), 6(1):e12032 pii:TRC212032.

Background: Physical activity has shown a positive impact on aging and neurodegeneration and represents a possible treatment option in cognitive decline. However, its underlying mechanisms and influences on brain pathology remain unclear. Dementia-MOVE (Multi-Objective Validation of Exercise) is a randomized-controlled pilot trial, including 50 patients with amnestic cognitive impairment associated with Alzheimer's pathology, aiming to analyze the effect of physical activity and fitness on disease progression.

Methods: Dementia-MOVE is divided into two arms, of either an intervention comprising physical activity, for at least twice a week, combined with a psychoeducational program, or a sole psychoeducational program. Physical activity intervention includes a supervised and unsupervised multimodal concept combining resistance, endurance, coordinative, and aerobic training. The primary outcome is the change of brain metabolism due to physical interventional treatment. Besides metabolic magnetic resonance imaging (MRI) including sodium and phosphorus imaging, resting state functional MRI, T1-, T2-weighted and fluid-attenuated inversion recovery (FLAIR), as well as diffusion-weighted imaging (DWI) of the brain and whole-body fat MRI are performed before and after intervention, and will be compared in their sensitivity for the detection of intervention effects. We further assess cognitive performance, neuropsychiatric symptoms, quality of life, fitness, and sleep via questionnaires/interviews and/or fitness trackers, as well as microbiome, under the aspect of Alzheimer's pathology.

Discussion: The aim of Dementia-MOVE is to investigate the effect of a multimodal exercise program on Alzheimer's pathology under different aspects of the disease. In this context, one of the main aims is the comparison of different MRI methods regarding their responsiveness for the detection of alterations induced by physical activity. As an underlying goal, new treatment and diagnostic options, as well as the exploration of fitness effects on brain structure and metabolism within a whole-body perspective of Alzheimer's disease are envisaged.

RevDate: 2020-06-03

Dowden RA, McGuinness LR, Wisniewski PJ, et al (2020)

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system.

Scientific reports, 10(1):8984 pii:10.1038/s41598-020-65740-4.

The mammalian gut microbiome can potentially impact host health and disease state. It is known that the mouse-genome, eating-behavior, and exercise-status promotes higher taxonomic rank-level alterations (e.g. family to phyla-level) of the gut microbiota. Here, host genotype or activity status was investigated to determine if selection of individual bacterial species or strains could be discerned within the murine digestive system. For this study, the fecal bacterial community of adenylyl cyclase 5 knock-out (AC5KO, n = 7) mice or their wild-type (WT, n = 10) littermates under exercise or sedentary conditions were profiled by sequencing rRNA operons. AC5KO mice were chosen since this genotype displays enhanced longevity/exercise capacity and protects against cardiovascular/metabolic disease. Profiling of rRNA operons using the Oxford MinION yielded 65,706 2-D sequences (after size selection of 3.7-5.7 kb) which were screened against an NCBI 16S rRNA gene database. These sequences were binned into 1,566 different best BLAST hits (BBHs) and counted for each mouse sample. Non-metric multidimensional scaling (NMDS) of the gut microbial community demonstrated clustering by physical activity (p = 0.001) but not by host genotype. Additionally, sequence similarity and phylogenetic analysis demonstrated that different bacterial species (closely related to Muribaculum intestinale and Parasutterella excrementihominis) inhabit AC5KO or WT mice depending on activity status. Other bacterial species of the gut microbiota did not follow such patterning (e.g. Turicibacter sanguinis and Turicimonas muris). Our results support the need of improved taxonomic resolution for better characterization of bacterial communities to deepen our understanding of the role of the gut microbiome on host health.

RevDate: 2020-06-03

Tan SC, Chong CW, Yap IKS, et al (2020)

Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control.

Scientific reports, 10(1):8997 pii:10.1038/s41598-020-65891-4.

The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P < 0.05). The metabonome of farmers and human controls were highly similar. Notably, higher trimethylamine N-oxide (TMAO) and butyrate were detected in human control and swine, respectively. The relative abundance of TMAO was positively correlated with Prevotella copri. Overall, we compared and established the relationship between the metabolites and microbiota composition of swine, farmers and human control. Based on the data obtained, we deduced that long term occupational exposure to swine and farm environment had affected the gut bacterial composition of farmers. Nonetheless, the effect was less prominent in the metabolite profiles, suggesting the gut bacteria expressed high functional plasticity and are therefore resilience to the level of community shift detected.

RevDate: 2020-06-03

White H (2020)

Gastrointestinal Disorders and the Nervous System.

Continuum (Minneapolis, Minn.), 26(3):577-590.

PURPOSE OF REVIEW: This article describes the neurologic sequelae of various nutritional micronutrient deficiencies, celiac disease, inflammatory bowel disease, and liver disease. Where relevant, appropriate treatments for these conditions are also discussed. The developing field of the microbiome and nervous system interaction is also outlined.

RECENT FINDINGS: Pathology in the gastrointestinal system can affect the nervous system when it causes micronutrient deficiency, when immune responses created by the gastrointestinal system affect the nervous system, when toxins caused by gastrointestinal organ failure harm the nervous system, and when treatments aimed at a gastrointestinal medical condition cause damage to the nervous system as a side effect.

SUMMARY: This article addresses familiar concepts and new developments in the treatment and understanding of diseases that affect the gut and nervous system simultaneously.

RevDate: 2020-06-03

Brenes LR, Lohse MB, Hartooni N, et al (2020)

A Set of Diverse Genes Influence the Frequency of White-Opaque Switching in Candida albicans.

G3 (Bethesda, Md.) pii:g3.120.401249 [Epub ahead of print].

The fungal species Candida albicans is both a member of the human microbiome and a fungal pathogen. C. albicans undergoes several different morphological transitions, including one called white-opaque switching. Here, cells reversibly switch between two states, "white" and "opaque," and each state is heritable through many cell generations. Each cell type has a distinct cellular and colony morphology and they differ in many other properties including mating, nutritional specialization, and interactions with the innate immune system. Previous genetic screens to gain insight into white-opaque switching have focused on certain classes of genes (for example transcriptional regulators or chromatin modifying enzymes). In this paper, we examined 172 deletion mutants covering a broad range of cell functions. We identified 28 deletion mutants with at least a five-fold effect on switching frequencies; these cover a wide variety of functions ranging from membrane sensors to kinases to proteins of unknown function. In agreement with previous reports, we found that components of the pheromone signaling cascade affect white-to-opaque switching; however, our results suggest that the major effect of Cek1 on white-opaque switching occurs through the cell wall damage response pathway. Most of the genes we identified have not been previously implicated in white-opaque switching and serve as entry points to understand new aspects of this morphological transition.

RevDate: 2020-06-03

Kristensen M, Prevaes SMPJ, Kalkman G, et al (2020)

Development of the gut microbiota in early life: The impact of cystic fibrosis and antibiotic treatment.

Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society pii:S1569-1993(20)30120-X [Epub ahead of print].

OBJECTIVES: Patients with Cystic Fibrosis (CF) suffer from pancreatic insufficiency, lipid malabsorption and gastrointestinal complaints, next to progressive pulmonary disease. Altered mucosal homoeostasis due to malfunctioning chloride channels results in an adapted microbial composition of the gastrointestinal and the respiratory tract. Additionally, antibiotic treatment has the potential to distort resident microbial communities dramatically. This study aims to investigate early life development of the gut microbial community composition of children with CF compared to healthy infants and to study the independent effects of antibiotics taking into account other clinical and lifestyle factors.

STUDY DESIGN: Faecal samples from 20 infants with CF and 45 healthy infants were collected regularly during the first 18 months of life and microbial composition was determined using 16S rRNA based sequencing.

RESULTS: We observed significant differences in the overall microbiota composition between infants with CF and healthy infants (p<0.001). Akkermansia and Anaerostipes were significantly more abundant in control infants, whereas Streptococci and E. coli were significantly more abundant in infants with CF, also after correction for several clinical factors (p<0.05). Antibiotic use in infants with CF was associated with a lower alpha diversity, a reduced abundance of Bifidobacterium and Bacteroides, and a higher abundance of Enterococcus.

CONCLUSION: Microbial development of the gut is different in infants with CF compared to healthy infants from the first months of life on, and further deviates over time, in part as a result of antibiotic treatment. The resulting dysbiosis may have significant functional consequences for the microbial ecosystem in CF patients.

RevDate: 2020-06-03

Adelman MW, Woodworth MH, Langelier C, et al (2020)

The gut microbiome's role in the development, maintenance, and outcomes of sepsis.

Critical care (London, England), 24(1):278 pii:10.1186/s13054-020-02989-1.

The gut microbiome regulates a number of homeostatic mechanisms in the healthy host including immune function and gut barrier protection. Loss of normal gut microbial structure and function has been associated with diseases as diverse as Clostridioides difficile infection, asthma, and epilepsy. Recent evidence has also demonstrated a link between the gut microbiome and sepsis. In this review, we focus on three key areas of the interaction between the gut microbiome and sepsis. First, prior to sepsis onset, gut microbiome alteration increases sepsis susceptibility through several mechanisms, including (a) allowing for expansion of pathogenic intestinal bacteria, (b) priming the immune system for a robust pro-inflammatory response, and (c) decreasing production of beneficial microbial products such as short-chain fatty acids. Second, once sepsis is established, gut microbiome disruption worsens and increases susceptibility to end-organ dysfunction. Third, there is limited evidence that microbiome-based therapeutics, including probiotics and selective digestive decontamination, may decrease sepsis risk and improve sepsis outcomes in select patient populations, but concerns about safety have limited uptake. Case reports of a different microbiome-based therapy, fecal microbiota transplantation, have shown correlation with gut microbial structure restoration and decreased inflammatory response, but these results require further validation. While much of the evidence linking the gut microbiome and sepsis has been established in pre-clinical studies, clinical evidence is lacking in many areas. To address this, we outline a potential research agenda for further investigating the interaction between the gut microbiome and sepsis.

RevDate: 2020-06-03

Sánchez-Reyes A, Bretón-Deval L, Mangelson H, et al (2020)

Draft genome sequence of "Candidatus Afipia apatlaquensis" sp. nov., IBT-C3, a potential strain for decolorization of textile dyes.

BMC research notes, 13(1):265 pii:10.1186/s13104-020-05117-y.

OBJECTIVES: In order to characterize a river-associated, enriched microbiome capable of degrading an anthraquinone dye from the oil blue family, as well as assessing its functional potential, we performed a taxa-specific metagenomic deconvolution analysis based on contact probability maps at the chromosomal level. This study will allow associating the genomic content of "Candidatus Afipia apatlaquensis" strain IBT-C3 with its phenotypic potential in the context of bioremediation of textile dyes. We anticipate that this resource will be very useful in comparative genomic clinical studies, contributing to understanding the genomic basis of Afipia pathogenicity.

DATA DESCRIPTION: Here, we report the first draft genome sequence of "Candidatus Afipia apatlaquensis" sp. nov., strain IBT-C3, obtained by deconvolution of a textile-dye degrader microbiome in Mexico. The genome composite was deconvoluted using a Hi-C proximity ligation method. Whole-genome-based comparisons and phylogenomics reconstruction indicate that strain IBT-C3 represents a new species of the genus Afipia. The assembly completeness was 92.5% with 5,604,749 bp in length and 60.72% G+C content. The genome complement of IBT-C3 suggests a functional potential for decolorization of textile dyes, contrasting with previous reports of Afipia genus focused on its pathogenic potential.

RevDate: 2020-06-03

Manzoor SS, Doedens A, MB Burns (2020)

The promise and challenge of cancer microbiome research.

Genome biology, 21(1):131 pii:10.1186/s13059-020-02037-9.

Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodologies, especially culture-independent approaches, have accelerated and driven this research. Recent work has shed light on the multifaceted role that the community of organisms in and on the human body plays in cancer onset, development, detection, treatment, and outcome. Much remains to be discovered, however, as methodological variation and functional testing of statistical correlations need to be addressed for the field to advance.

RevDate: 2020-06-03

Lamas B, Martins Breyner N, E Houdeau (2020)

Impacts of foodborne inorganic nanoparticles on the gut microbiota-immune axis: potential consequences for host health.

Particle and fibre toxicology, 17(1):19 pii:10.1186/s12989-020-00349-z.

BACKGROUND: In food toxicology, there is growing interest in studying the impacts of foodborne nanoparticles (NPs, originating from food additives, food supplements or food packaging) on the intestinal microbiome due to the important and complex physiological roles of these microbial communities in host health. Biocidal activities, as described over recent years for most inorganic and metal NPs, could favour chronic changes in the composition and/or metabolic activities of commensal bacteria (namely, intestinal dysbiosis) with consequences on immune functions. Reciprocally, direct interactions of NPs with the immune system (e.g., inflammatory responses, adjuvant or immunosuppressive properties) may in turn have effects on the gut microbiota. Many chronic diseases in humans are associated with alterations along the microbiota-immune system axis, such as inflammatory bowel diseases (IBD) (Crohn's disease and ulcerative colitis), metabolic disorders (e.g., obesity) or colorectal cancer (CRC). This raises the question of whether chronic dietary exposure to inorganic NPs may be viewed as a risk factor facilitating disease onset and/or progression. Deciphering the variety of effects along the microbiota-immune axis may aid the understanding of how daily exposure to inorganic NPs through various foodstuffs may potentially disturb the intricate dialogue between gut commensals and immunity, hence increasing the vulnerability of the host. In animal studies, dose levels and durations of oral treatment are key factors for mimicking exposure conditions to which humans are or may be exposed through the diet on a daily basis, and are needed for hazard identification and risk assessment of foodborne NPs. This review summarizes relevant studies to support the development of predictive toxicological models that account for the gut microbiota-immune axis.

CONCLUSIONS: The literature indicates that, in addition to evoking immune dysfunctions in the gut, inorganic NPs exhibit a moderate to extensive impact on intestinal microbiota composition and activity, highlighting a recurrent signature that favours colonization of the intestine by pathobionts at the expense of beneficial bacterial strains, as observed in IBD, CRC and obesity. Considering the long-term exposure via food, the effects of NPs on the gut microbiome should be considered in human health risk assessment, especially when a nanomaterial exhibits antimicrobial properties.

RevDate: 2020-06-03

Harding JN, Siefker D, Vu L, et al (2020)

Altered gut microbiota in infants is associated with respiratory syncytial virus disease severity.

BMC microbiology, 20(1):140 pii:10.1186/s12866-020-01816-5.

BACKGROUND: Respiratory syncytial virus (RSV) is the number one cause of lower respiratory tract infections in infants. There are still no vaccines or specific antiviral therapies against RSV, mainly due to the inadequate understanding of RSV pathogenesis. Recent data suggest a role for gut microbiota community structure in determining RSV disease severity. Our objective was to determine the gut microbial profile associated with severe RSV patients, which could be used to help identify at-risk patients and develop therapeutically protective microbial assemblages that may stimulate immuno-protection.

RESULTS: We enrolled 95 infants from Le Bonheur during the 2014 to 2016 RSV season. Of these, 37 were well-babies and 58 were hospitalized with RSV. Of the RSV infected babies, 53 remained in the pediatric ward (moderate) and 5 were moved to the pediatric intensive care unit at a later date (severe). Stool samples were collected within 72 h of admission; and the composition of gut microbiota was evaluated via 16S sequencing of fecal DNA. There was a significant enrichment in S24_7, Clostridiales, Odoribacteraceae, Lactobacillaceae, and Actinomyces in RSV (moderate and severe) vs. controls. Patients with severe RSV disease had slightly lower alpha diversity (richness and evenness of the bacterial community) of the gut microbiota compared to patients with moderate RSV and healthy controls. Beta diversity (overall microbial composition) was significantly different between all RSV patients (moderate and severe) compared to controls and had significant microbial composition separating all three groups (control, moderate RSV, and severe RSV).

CONCLUSIONS: Collectively, these data demonstrate that a unique gut microbial profile is associated with RSV disease and with severe RSV disease with admission to the pediatric intensive care unit. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of severe RSV disease.

RevDate: 2020-06-03

Reverter M, Sasal P, Suzuki MT, et al (2020)

Insights into the Natural Defenses of a Coral Reef Fish Against Gill Ectoparasites: Integrated Metabolome and Microbiome Approach.

Metabolites, 10(6): pii:metabo10060227.

Understanding natural defense mechanisms against parasites can be a valuable tool for the development of innovative therapies. We have previously identified a butterflyfish species (Chaetodonlunulatus) that avoids gill monogenean parasites while living amongst closely related parasitized species. The metabolome and microbiome of several sympatric butterflyfish species from the island of Moorea (French Polynesia) were previously described. In this study, we used the previously generated datasets in an attempt to identify metabolites and bacteria potentially involved in parasite defense mechanisms. We investigated the interplay between the gill mucus metabolome and microbiome of the non-susceptible C.lunulatus versus sympatric butterflyfish species that were always found parasitized in the Central and Eastern Indo-Pacific. After observing significant differences between the metabolome and bacteria of susceptible versus non-susceptible fish, we obtained the discriminant metabolites and operational taxonomic units (OTUs) using a supervised analysis. Some of the most important discriminant metabolites were identified as peptides, and three new peptides derived from β-subunit hemoglobin from C.lunulatus (CLHbβ-1, CLHbβ-2, and CLHbβ-3) were purified, characterized and synthesized to confirm their structures. We also identified specific bacterial families and OTUs typical from low-oxygen habitats in C.lunulatus gill mucus. By using a correlation network between the two datasets, we found a Fusobacteriaceae strain exclusively present in C.lunulatus and highly correlated to the peptides. Finally, we discuss the possible involvement of these peptides and Fusobacteriaceae in monogenean avoidance by this fish species.

RevDate: 2020-06-03

Sánchez-Alcoholado L, Ramos-Molina B, Otero A, et al (2020)

The Role of the Gut Microbiome in Colorectal Cancer Development and Therapy Response.

Cancers, 12(6): pii:cancers12061406.

Colorectal cancer (CRC) is the third most common cancer worldwide and the leading cause of cancer-related deaths. Recently, several studies have demonstrated that gut microbiota can alter CRC susceptibility and progression by modulating mechanisms such as inflammation and DNA damage, and by producing metabolites involved in tumor progression or suppression. Dysbiosis of gut microbiota has been observed in patients with CRC, with a decrease in commensal bacterial species (butyrate-producing bacteria) and an enrichment of detrimental bacterial populations (pro-inflammatory opportunistic pathogens). CRC is characterized by altered production of bacterial metabolites directly involved in cancer metabolism including short-chain fatty acids and polyamines. Emerging evidence suggests that diet has an important impact on the risk of CRC development. The intake of high-fiber diets and the supplementation of diet with polyunsaturated fatty acids, polyphenols and probiotics, which are known to regulate gut microbiota, could be not only a potential mechanism for the reduction of CRC risk in a primary prevention setting, but may also be important to enhance the response to cancer therapy when used as adjuvant to conventional treatment for CRC. Therefore, a personalized modulation of the pattern of gut microbiome by diet may be a promising approach to prevent the development and progression of CRC and to improve the efficacy of antitumoral therapy.

RevDate: 2020-06-03

Koike Y, Kuwatsuka S, Nishimoto K, et al (2020)

Skin Mycobiome of Psoriasis Patients is Retained during Treatment with TNF and IL-17 Inhibitors.

International journal of molecular sciences, 21(11): pii:ijms21113892.

BACKGROUND: Biological treatment relieves refractory skin lesions in patients with psoriasis; however, changes in the fungal microbiome (the mycobiome) on the skin are unclear.

METHODS: The skin mycobiome of psoriasis patients treated with TNF inhibitors (TNFi, n = 5) and IL-17 inhibitors (IL-17i, n = 7) was compared with that of patients not receiving systemic therapy (n = 7). Skin swab samples were collected from non-lesional post-auricular areas. Fungal DNA was sequenced by ITS1 metagenomic analysis and taxonomic classification was performed.

RESULTS: An average of 37543 reads/sample were analyzed and fungi belonging to 31 genera were detected. The genus Malassezia accounted for >90% of reads in 7/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group. Biodiversity was low in those three groups. Few members of the genus trichophyton were detected; the genus Candida was not detected at all. Among the Malassezia species, M. restricta was the major species in 6/7 samples from the no-therapy group, 4/5 from the TNFi group, and 5/7 from the IL-17i group whose the other largest species revealed M. globosa.

CONCLUSIONS: The mycobiome is retained on post-auricular skin during systemic treatment with TNF and IL-17 inhibitors.

RevDate: 2020-06-03

Papadopoulos C, Karas PA, Vasileiadis S, et al (2020)

Host Species Determines the Composition of the Prokaryotic Microbiota in Phlebotomus Sandflies.

Pathogens (Basel, Switzerland), 9(6): pii:pathogens9060428.

Phlebotomine sandflies are vectors of the humans' and mammals' parasite Leishmania spp. Although the role of gut microbiome in the biological cycle of insects is acknowledged, we still know little about the factors modulating the composition of the gut microbiota of sandflies. We tested whether host species impose a strong structural effect on the gut microbiota of Phlebotomus spp. Sandflies were collected from the island of Leros, Greece, and classified to P.papatasi, P. neglectus, P.tobbi, and P.similis, all being negative to Leishmania spp. The prokaryotic gut microbiota was determined via 16S rRNA gene amplicon sequencing. Phlebotomus species supported distinct microbial communities (p < 0.001). P.papatasi microbiota was the most distinct over-dominated by three Spiroplasma, Wolbachia and Paenibacillus operational taxonomic units (OTUs), while another Wolbachia OTU prevailed in P. neglectus. Conversely, the microbiota of P.tobbi and P.similis was composed of several less dominant OTUs. Archaea showed low presence with the dominant OTUs belonging to methanogenic Euryarcheota, ammonia-oxidizing Thaumarcheota, and Nanoarchaeota. We provide first insights into the composition of the bacterial and archaeal community of Phlebotomus sandflies and showed that, in the absence of Leishmania, host genotype is the major modulator of Phlebotomus sandfly gut microbiota.

RevDate: 2020-06-02

Ruppel S, Franken P, K Witzel (2013)

Properties of the halophyte microbiome and their implications for plant salt tolerance.

Functional plant biology : FPB, 40(9):940-951.

Saline habitats cover a wide area of our planet and halophytes (plants growing naturally in saline soils) are increasingly used for human benefits. Beside their genetic and physiological adaptations to salt, complex ecological processes affect the salinity tolerance of halophytes. Hence, prokaryotes and fungi inhabiting roots and leaves can contribute significantly to plant performance. Members of the two prokaryotic domains Bacteria and Archaea, as well as of the fungal kingdom are known to be able to adapt to a range of changes in external osmolarity. Shifts in the microbial community composition with increasing soil salinity have been suggested and research in functional interactions between plants and micro-organisms contributing to salt stress tolerance is gaining interest. Among others, microbial biosynthesis of polymers, exopolysaccharides, phytohormones and phytohormones-degrading enzymes could be involved.

RevDate: 2020-05-26

Prommi A, Prombutara P, Watthanakulpanich D, et al (2020)

Intestinal parasites in rural communities in Nan Province, Thailand: changes in bacterial gut microbiota associated with minute intestinal fluke infection.

Parasitology pii:S0031182020000736 [Epub ahead of print].

Gastrointestinal helminth infection likely affects the gut microbiome, in turn affecting host health. To investigate the effect of intestinal parasite status on the gut microbiome, parasitic infection surveys were conducted in communities in Nan Province, Thailand. In total, 1047 participants submitted stool samples for intestinal parasite examination, and 391 parasite-positive cases were identified, equating to an infection prevalence of 37.3%. Intestinal protozoan species were less prevalent (4.6%) than helminth species. The most prevalent parasite was the minute intestinal fluke Haplorchis taichui (35.9%). Amplicon sequencing of 16S rRNA was conducted to investigate the gut microbiome profiles of H. taichui-infected participants compared with those of parasite-free participants. Prevotella copri was the dominant bacterial operational taxonomic unit (OTU) in the study population. The relative abundance of three bacterial taxa, Ruminococcus, Roseburia faecis and Veillonella parvula, was significantly increased in the H. taichui-infected group. Parasite-negative group had higher bacterial diversity (α diversity) than the H. taichui-positive group. In addition, a significant difference in bacterial community composition (β diversity) was found between the two groups. The results suggest that H. taichui infection impacts the gut microbiome profile by reducing bacterial diversity and altering bacterial community structure in the gastrointestinal tract.

RevDate: 2020-06-02

Li J, Dong T, Keerthisinghe TP, et al (2020)

Long-term oxytetracycline exposure potentially alters brain thyroid hormone and serotonin homeostasis in zebrafish.

Journal of hazardous materials, 399:123061 pii:S0304-3894(20)31050-5 [Epub ahead of print].

The impact of oxytetracycline (OTC) exposure in water on the fish still remains unclear. We hypothesized OTC exposure could alter fish gut microbiome and affect thyroid hormone and serotonin homeostasis in the brain via "chemical-gut-brain" axis. Here, ∼2-month-old juvenile zebrafish (Danio rerio) was exposed to two concentrations of OTC (1 and 100 μg/L) for one month until adulthood. Thyroxine-associated gene analysis in the brain revealed that deiodinase 2 (DIO2), deiodinase 3 (DIO3), and thyroid hormone receptor beta (THRβ) expression was significantly decreased. Quantification of thyroid hormones showed a decrease in triiodothyronine (T3) under OTC treatment, which agrees with reduced activity of DIO2. For the serotonin (5-HT) synthesis, the expression of tryptophan hydroxylase (TPH2) was 41 % and 9.3 % of the control group for 1 and 100 μg/L OTC exposed groups; respectively. The intestinal 16S rRNA analysis revealed an increased abundance of Fusobacteria and Proteobacteria, while Actinobacteria was decreased significantly. The altered microbial balance between Proteobacteria and Firmicutes have been previously reported to affect nutrient uptakes such as zinc, which can potentially reduce the activity of DIO2. In summary, this study suggests that long-term OTC exposure not only alters gut microbiome but also changes thyroid hormone and serotonin homeostasis.

RevDate: 2020-06-02

Yie Qin Lee C, Franks AE, EL Hill-Yardin (2020)

Autism-associated synaptic mutations impact the gut-brain axis in mice.

Brain, behavior, and immunity pii:S0889-1591(20)30071-4 [Epub ahead of print].

Interactions between the gut microbiome and the brain affect mood and behaviour in health and disease. Using preclinical animal models, recent discoveries begin to explain how bacteria in the gut affect our mood as well as highlighting new findings relevant to autism. Autism-associated gene mutations known to affect synapse function in the CNS also affect the inflammatory response and alter the enteric nervous system resulting in abnormal gastrointestinal motility and structure. Strikingly, these mutations additionally affect the gut microbiome in mice. This review describes the changes in gut physiology and microbiota in mouse models of autism with modified synapse function. The rationale for different regions of the gastrointestinal tract having variable susceptibility to dysfunction is also discussed. To dissect underlying biological mechanisms involving gut-brain axis dysfunction in preclinical models, a range of multidisciplinary approaches are required. This research will provide insights into the role of the gut-brain axis in health and neurodevelopmental disorders including autism.

RevDate: 2020-06-02

Basciani S, Camajani E, Contini S, et al (2020)

Very-Low-Calorie Ketogenic Diets with Whey, Vegetable or Animal Protein in Patients with Obesity: A Randomized Pilot Study.

The Journal of clinical endocrinology and metabolism pii:5850439 [Epub ahead of print].

CONTEXT: We compared the efficacy, safety and effect of 45-day isocaloric very-low-calorie ketogenic diets (VLCKDs) incorporating whey, vegetable or animal protein on the microbiota in patients with obesity and insulin resistance to test the hypothesis that protein source may modulate the response to VLCKD interventions.

SUBJECTS AND METHODS: Forty-eight patients with obesity [19 males and 29 females, HOMA index ≥ 2.5, age 56.2±6.1 years, body mass index (BMI) 35.9±4.1 kg/m2] were randomly assigned to three 45-day isocaloric VLCKD regimens (≤800 kcal/day) containing whey, plant or animal protein. Anthropometric indexes; blood and urine chemistry, including parameters of kidney, liver, glucose and lipid metabolism; body composition; muscle strength; and taxonomic composition of the gut microbiome were assessed. Adverse events were also recorded.

RESULTS: Body weight, BMI, blood pressure, waist circumference, HOMA index, insulin, and total and LDL cholesterol decreased in all patients. Patients who consumed whey protein had a more pronounced improvement in muscle strength. The markers of renal function worsened slightly in the animal protein group. A decrease in the relative abundance of Firmicutes and an increase in Bacteroidetes were observed after the consumption of VLCKDs. This pattern was less pronounced in patients consuming animal protein.

CONCLUSIONS: VLCKDs led to significant weight loss and a striking improvement in metabolic parameters over a 45-day period. VLCKDs based on whey or vegetable protein have a safer profile and result in a healthier microbiota composition than those containing animal proteins. VLCKDs incorporating whey protein are more effective in maintaining muscle performance.

RevDate: 2020-06-02

Capone K, Kirchner F, Klein SL, et al (2020)

Effects of Colloidal Oatmeal Topical Atopic Dermatitis Cream on Skin Microbiome and Skin Barrier Properties.

Journal of drugs in dermatology : JDD, 19(5):524-531.

Atopic dermatitis is characterized by dry, itchy, inflamed skin with a dysbiotic microbiome. In this clinical study (NCT03673059), we compared the effects of an eczema cream containing 1% colloidal oat and a standard moisturizer on the skin microbiome and skin barrier function of patients with mild to moderate eczema. Patients were randomly assigned to treatment with 1% colloidal oat eczema cream or a standard, non-fragranced daily moisturizer. Treatment lasted 14 days, followed by a 7-day regression period. Of 61 patients who completed the study, 30 received the 1% colloidal oat eczema cream and 31 received the standard moisturizer. At 14 days, the 1% colloidal oat eczema cream reduced mean Eczema Area Severity Index and Atopic Dermatitis Severity Index scores by 51% and 54%, respectively. Unlike treatment with the standard moisturizer, treatment with the 1% colloidal oat eczema cream was associated with trends towards lower prevalence of Staphylococcus species and higher microbiome diversity at lesion sites. The 1% colloidal oat eczema cream significantly improved skin pH, skin barrier function, and skin hydration from baseline to day 14, whereas the standard moisturizer improved hydration. Overall, the results demonstrate that topical products can have differing effects on the skin barrier properties and the microbiome. Importantly, we show that the use of a 1% colloidal oat eczema cream improves microbiome composition and significantly repairs skin barrier defects. J Drugs Dermatol. 2020;19(5): &nbsp; doi:10.36849/JDD.2020.4924.

RevDate: 2020-06-02

Khurshid M, MS Akash (2020)

Probiotic preparations for infantile gastroenteritis: the clinical and economic perspective.

RevDate: 2020-06-02

Villela H (2020)

Microbiome Flexibility Provides New Perspectives in Coral Research.

BioEssays : news and reviews in molecular, cellular and developmental biology [Epub ahead of print].

RevDate: 2020-06-02

Garland M, Hryckowian AJ, Tholen M, et al (2020)

The Clinical Drug Ebselen Attenuates Inflammation and Promotes Microbiome Recovery in Mice after Antibiotic Treatment for CDI.

Cell reports medicine, 1(1):.

Clostridium difficile infection (CDI) is an enteric bacterial disease that is increasing in prevalence worldwide. C. difficile capitalizes on gut inflammation and microbiome dysbiosis to establish infection, with symptoms ranging from watery diarrhea to toxic megacolon. We reported that the safe-in-human clinical drug ebselen ( NCT03013400, NCT01452607, NCT00762671, and NCT02603081) has biochemical, cell-based, and in vivo efficacy against the toxins of C. difficile. Here, we show that ebselen treatment reduces recurrence rates and decreases colitis in a hamster model of relapsing CDI. Furthermore, ebselen treatment does not alter microbiome diversity and promotes recovery back to that of healthy controls after antibiotic-induced dysbiosis in healthy and C. difficile-infected mice. This increased microbiome recovery upon ebselen treatment correlates with a decrease in host-derived inflammatory markers, suggesting that the anti-inflammatory properties of ebselen, combined with its anti-toxin function, help to mitigate the major clinical challenges of CDI, including recurrence, microbial dysbiosis, and colitis.

RevDate: 2020-06-02

Lv W, Graves DT, He L, et al (2020)

Depletion of the diabetic gut microbiota resistance enhances stem cells therapy in type 1 diabetes mellitus.

Theranostics, 10(14):6500-6516 pii:thnov10p6500.

Microbiome, considered as the "second genome" of the host, is altered in type 1 diabetes mellitus (T1DM) patients to a state of dysbiosis. Mesenchymal stem cell (MSC) transplantation is a promising treatment for T1DM but is limited by several factors in the diabetic host. In this study, we tested the hypothesis that dysbiotic gut microbiota may limit MSC therapy, and modulating gut microbiota may help to improve the effects of MSC transplantation. Methods: NOD/Ltj mice, treated with adipose-derived stem cells (ADSCs), were fed with an antibiotics cocktails (Abx) for 1 week. The blood glucose levels, insulitis, intestinal permeability and gut bacteria translocation to the pancreas were evaluated. 16s rRNA and colon tissue transcription sequencing were performed to analyze beneficial bacteria and reactive host biomolecules in the ADSCs+Abx group. Based on the sequencing results, specific bacteria were gavaged orally to diabetic mice to confirm their effect on ADSCs transplantation in T1DM was determined. Results: We found that the recolonized the diabetic gut microbiota abolished the therapeutic effect of ADSCs. On the contrary, depletion of the diabetic gut microbiota by antibiotics treatment in diabetic mice significantly enhanced the therapeutic effects of ADSCs as measured by reversal of hyperglycemia, insulitis, and increased insulin output. Mechanistically, treatment with antibiotics increased the abundance of Bifidobacterium in the gut and reduced bacterial translocation to the pancreas by promoting Mucin2 expression and thickening the mucus layer through TRPM7. The mechanism was confirmed the re-colonization of the gut by B.breve through oral gavage that produced similar results. Conclusions: These results provide the rationale for a new approach to improve MSC therapy for T1DM by altering the gut microbiota.

RevDate: 2020-06-02

Emamat H, Ghalandari H, Tangestani H, et al (2020)

Artificial sweeteners are related to non-alcoholic fatty liver disease: Microbiota dysbiosis as a novel potential mechanism.

EXCLI journal, 19:620-626 pii:Doc620.

Non-alcoholic fatty liver disease (NAFLD) is a systemic and wide-spread disease characterized by accumulation of excess fat in the liver of people who drink little or no alcohol. Artificial sweeteners (ASs) or sugar substitutes are food additives that provide a sweet taste, and are also known as low-calorie or non-calorie sweeteners. Recently people consume increasingly more ASs to reduce their calorie intake. Gut microbiome is a complex ecosystem where 1014 microorganisms play several roles in host nutrition, bone mineralization, immune system regulation, xenobiotics metabolism, proliferation of intestinal cells, and protection against pathogens. A disruption in composition of the normal microbiota is known as 'gut dysbiosis' which may adversely affect body metabolism. It has recently been suggested that dysbiosis may contribute to the occurrence of NAFLD. The aim of the present study was to investigate the effects of ASs on the risk of NAFLD. The focus of this review is on microbiota changes and dysbiosis. Increasing evidence shows that ASs have a potential role in microbiota alteration and dysbiosis. We speculate that increased consumption of ASs can further raise the prevalence of NAFLD. However, further human studies are needed to determine this relationship definitively.

RevDate: 2020-06-02

Calusinska M, Marynowska M, Bertucci M, et al (2020)

Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes.

Communications biology, 3(1):275 pii:10.1038/s42003-020-1004-3.

Miscanthus sp. biomass could satisfy future biorefinery value chains. However, its use is largely untapped due to high recalcitrance. The termite and its gut microbiome are considered the most efficient lignocellulose degrading system in nature. Here, we investigate at holobiont level the dynamic adaptation of Cortaritermes sp. to imposed Miscanthus diet, with a long-term objective of overcoming lignocellulose recalcitrance. We use an integrative omics approach combined with enzymatic characterisation of carbohydrate active enzymes from termite gut Fibrobacteres and Spirochaetae. Modified gene expression profiles of gut bacteria suggest a shift towards utilisation of cellulose and arabinoxylan, two main components of Miscanthus lignocellulose. Low identity of reconstructed microbial genomes to closely related species supports the hypothesis of a strong phylogenetic relationship between host and its gut microbiome. This study provides a framework for better understanding the complex lignocellulose degradation by the higher termite gut system and paves a road towards its future bioprospecting.

RevDate: 2020-06-02

Roach TNF, Little M, Arts MGI, et al (2020)

A multiomic analysis of in situ coral-turf algal interactions.

Proceedings of the National Academy of Sciences of the United States of America pii:1915455117 [Epub ahead of print].

Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.

RevDate: 2020-06-02

Wu H, Singer J, Kwan TK, et al (2020)

Gut Microbial Metabolites Induce Donor-Specific Tolerance of Kidney Allografts through Induction of T Regulatory Cells by Short-Chain Fatty Acids.

Journal of the American Society of Nephrology : JASN pii:ASN.2019080852 [Epub ahead of print].

BACKGROUND: Short-chain fatty acids derived from gut microbial fermentation of dietary fiber have been shown to suppress autoimmunity through mechanisms that include enhanced regulation by T regulatory cells (Tregs).

METHODS: Using a murine kidney transplantation model, we examined the effects on alloimmunity of a high-fiber diet or supplementation with the short-chain fatty acid acetate. Kidney transplants were performed from BALB/c(H2d) to B6(H2b) mice as allografts in wild-type and recipient mice lacking the G protein-coupled receptor GPR43 (the metabolite-sensing receptor of acetate). Allograft mice received normal chow, a high-fiber diet, or normal chow supplemented with sodium acetate. We assessed rejection at days 14 (acute) and 100 (chronic), and used 16S rRNA sequencing to determine gut microbiota composition pretransplantation and post-transplantation.

RESULTS: Wild-type mice fed normal chow exhibited dysbiosis after receiving a kidney allograft but not an isograft, despite the avoidance of antibiotics and immunosuppression for the latter. A high-fiber diet prevented dysbiosis in allograft recipients, who demonstrated prolonged survival and reduced evidence of rejection compared with mice fed normal chow. Allograft mice receiving supplemental sodium acetate exhibited similar protection from rejection, and subsequently demonstrated donor-specific tolerance. Depletion of CD25+ Tregs or absence of the short-chain fatty acid receptor GPR43 abolished this survival advantage.

CONCLUSIONS: Manipulation of the microbiome by a high-fiber diet or supplementation with sodium acetate modified alloimmunity in a kidney transplant model, generating tolerance dependent on Tregs and GPR43. Diet-based therapy to induce changes in the gut microbiome can alter systemic alloimmunity in mice, in part through the production of short-chain fatty acids leading to Treg cell development, and merits study as a potential clinical strategy to facilitate transplant acceptance.

RevDate: 2020-06-02

Araghi A (2020)

The lung microbiome and pneumonia: Where precision medicine meets pulmonology.

RevDate: 2020-06-02

Chu W, Han Q, Xu J, et al (2020)

Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome.

Fertility and sterility, 113(6):1286-1298.e4.

OBJECTIVE: To identify different microbial species in women with polycystic ovary syndrome (PCOS) and reveal a possible relationship between gut dysbiosis and pathological changes.

DESIGN: Cross-sectional study.

SETTING: Academic institution.

PATIENT(S): Reproductive-aged women with PCOS (n = 14) and controls (n = 14) from the Centre for Reproductive Medicine.

INTERVENTION(S): Shotgun metagenomic sequencing on fecal samples from patients, and clinical parameters (including body mass index, endocrine hormone levels, and glycemia level) gathered for correlation analysis.

MAIN OUTCOME MEASURE(S): Identification of different gut microbial strains and relativity between microbiota and clinical parameters.

RESULT(S): We found several microbial strains were statistically significantly more abundant in the PCOS group, including Parabacteroides merdae, Bacteroides fragilis, and strains of Escherichia and Shigella, whereas Faecalibacterium prausnitzii was enriched in the control group. Metagenomic species (MGS) analysis revealed that the microbes of the PCOS group were negatively correlated with those of the control group. Of note, we observed a positive correlation between MGS relevant to PCOS and endocrine disorders, including body mass index and elevated levels of serum testosterone, luteinizing hormone, and antimüllerian hormone. Functional alterations, reflected by Kyoto Encyclopedia of Genes and Genomes orthologues, could imply potential mechanisms of microbial involvement in the developmental progress of PCOS.

CONCLUSION(S): Our findings suggest an intimate association and potential mechanisms linking microbial dysbiosis and the pathophysiologic changes of PCOS. We address the importance of monitoring and modulating microbial composition and functional shifts in future clinical practice.

RevDate: 2020-06-02

Ribeiro IM, Souto PCS, Borbely AU, et al (2020)

The limited knowledge of placental damage due to neglected infections: ongoing problems in Latin America.

Systems biology in reproductive medicine, 66(3):151-169.

The placenta works as a selective barrier, protecting the fetus from potential infections that may affect the maternal organism during pregnancy. In this review, we will discuss several challenging infections that are common within Latin American countries and that may affect the maternal-fetal interface and pose risks to fetal development. Specifically, we will focus on emerging infectious diseases including the arboviruses, malaria, leishmaniasis, and the bacterial foodborne disease caused by Shiga toxin-producing Escherichia coli. We will also highlight some topics of interest currently being studied by research groups that comprise an international effort aimed at filling the knowledge gaps in this field. These topics address the relationship between exposure to microorganisms and placental abnormalities, congenital anomalies, and complications of pregnancy.

ABBREVIATIONS: ADE: antibody-dependent enhancement; CCL2: monocyte chemoattractant protein-1; CCL3: macrophage inflammatory protein-1 α; CCL5: chemokine (C-C motif) ligand 5; CHIKV: chikungunya virus; DCL: diffuse cutaneous leishmaniasis; DENV: dengue virus; Gb3: glycolipid globotriaosylceramyde; HIF: hypoxia-inducible factor; HUS: hemolytic uremic syndrome; IFN: interferon; Ig: immunoglobulins; IL: interleukin; IUGR: intrauterine growth restriction; LCL: localized cutaneous leishmaniasis; LPS: lipopolysaccharid; MCL: mucocutaneous leishmaniasis; NO: nitric oxide; PCR: polymerase chain reaction; PGF: placental growth factor; PM: placental malaria; RIVATREM: Red Iberoamericana de Alteraciones Vasculares em transtornos del Embarazo; sVEGFR: soluble vascular endothelial growth factor receptor; STEC: shiga toxin-producing Escherichia coli; stx: shiga toxin protein; TNF: tumor necrosis factor; TOAS: T cell original antigenic sin; Var2CSA: variant surface antigen 2-CSA; VEGF: vascular endothelial growth factor; VL: visceral leishmaniasis; WHO: world health organization; YFV: yellow fever virus; ZIKV: Zika virus.

RevDate: 2020-06-02

Blake S, Thanissery R, Rivera AJ, et al (2020)

Salicylanilide analog minimizes relapse of Clostridioides difficile infection in mice.

Journal of medicinal chemistry [Epub ahead of print].

Clostridioides difficile infection (CDI) causes serious and sometimes fatal symptoms like diarrhea and pseudomembraneous colitis. Although antibiotics for CDI exist, they are either expensive or cause recurrence of the infection due to their altering the colonic microbiota which is necessary to suppress the infection. Here, we leverage a class of known membrane-targeting compounds that we previously showed to have broad inhibitory activity across multiple C. difficile strains while preserving the microbiome to develop an efficacious agent. A new series of salicylanilides was synthesized and the most potent analog was selected through an in vitro inhibitory assay to evaluate its pharmacokinetic parameters and potency in a CDI mouse model. The results revealed reduced recurrence of CDI and disturbance of the microbiota in mice compared to standard-of-care vancomycin, thus paving the way for novel therapy that can potentially target the cell membrane of C. difficile to minimize relapse in the recovering patient.

RevDate: 2020-06-02

Zollner-Schwetz I, Scarpatetti M, Pichler G, et al (2020)

Effect of a Multispecies Probiotic on Intestinal and Skin Colonization by Multidrug-Resistant Gram-Negative Bacteria in Patients in a Long-Term Care Facility: A Pilot Study.

Nutrients, 12(6): pii:nu12061586.

Residents in long-term care facilities (LTCFs) are frequently colonized by multidrug-resistant Gram-negative bacteria, putting them at risk for subsequent infections. We aimed to evaluate the effect of the multispecies probiotic Omnibiotic10AAD® on the intestinal and inguinal skin colonization of patients by multidrug-resistant Gram-negative bacteria in LTCFs. Patients colonized by multidrug-resistant Gram-negative bacteria received a 12 week oral course of Omnibiotic10AAD®. Inguinal swabs and stool samples were collected during and after treatment for microbiological and microbiome analysis. The median age of patients was 76 years. Twelve patients completed the pilot study. Intestinal colonization was reduced to 42% of patients 8 weeks after the end of treatment, but increased to 66% 24 weeks after the end of probiotic treatment. Colonization of inguinal skin was lowest during probiotic treatment and increased thereafter. Fecal microbiome analysis revealed statistically significant increases of the genus Enterococcus comparing start and end of probiotic treatment. In conclusion, a 12 week course of a multispecies probiotic led to a transient reduction of intestinal colonization 8 weeks after the end of treatment. The findings of our pilot study warrant further research in the area of probiotics and intestinal colonization by multidrug-resistant bacteria.

RevDate: 2020-06-02

Chichlowski M, Shah N, Wampler JL, et al (2020)

Bifidobacterium longum Subspecies infantis (B. infantis) in Pediatric Nutrition: Current State of Knowledge.

Nutrients, 12(6): pii:nu12061581.

Abstract: Since originally isolated in 1899, the genus Bifidobacterium has been demonstrated to predominate in the gut microbiota of breastfed infants and to benefit the host by accelerating maturation of the immune response, balancing the immune system to suppress inflammation, improving intestinal barrier function, and increasing acetate production. In particular, Bifidobacterium longum subspecies infantis (B. infantis) is well adapted to the infant gut and has co-evolved with the mother-infant dyad and gut microbiome, in part due to its ability to consume complex carbohydrates found in human milk. B. infantis and its human host have a symbiotic relationship that protects the preterm or term neonate and nourishes a healthy gut microbiota prior to weaning. To provide benefits associated with B. infantis to all infants, a number of commercialized strains have been developed over the past decades. As new ingredients become available, safety and suitability must be assessed in preclinical and clinical studies. Consideration of the full clinical evidence for B. infantis use in pediatric nutrition is critical to better understand its potential impacts on infant health and development. Herein we summarize the recent clinical studies utilizing select strains of commercialized B. infantis.

RevDate: 2020-06-02

Havlik J, Marinello V, Gardyne A, et al (2020)

Dietary Fibres Differentially Impact on the Production of Phenolic Acids from Rutin in an In Vitro Fermentation Model of the Human Gut Microbiota.

Nutrients, 12(6): pii:nu12061577.

Polyphenols are often ingested alongside dietary fibres. They are both catabolised by, and may influence, the intestinal microbiota; yet, interactions between them and the impact on their resultant microbial products are poorly understood. Dietary fibres (inulin, pectin, psyllium, pyrodextrin, wheat bran, cellulose-three doses) were fermented in vitro with human faeces (n = 10) with and without rutin (20 µg/mL), a common dietary flavonol glycoside. Twenty-eight phenolic metabolites and short chain fatty acids (SCFA) were measured over 24 h. Several phenolic metabolites were produced during fibre fermentation, without rutin. With rutin, 3,4-dihydroxyphenylacetic acid (3,4diOHPAA), 3-hydroxyphenylacetic acid (3OHPAA), 3-(3 hydroxyphenyl)propionic acid (3OHPPA) and 3-(3,4-dihydroxyphenyl)propionic acid (3,4diOHPPA; DOPAC) were produced, with 3,4diOHPAA the most abundant, confirmed by fermentation of 13C labelled quercetin. The addition of inulin, wheat bran or pyrodextrin increased 3,4diOHPAA 2 2.5-fold over 24 h (p < 0.05). Rutin affected SCFA production, but this depended on fibre, fibre concentration and timepoint. With inulin, rutin increased pH at 6 h from 4.9 to 5.6 (p = 0.01) but increased propionic, butyric and isovaleric acid (1.9, 1.6 and 5-fold, p < 0.05 at 24 h). Interactions between fibre and phenolics modify production of phenolic acids and SCFA and may be key in enhancing health benefits.

RevDate: 2020-06-02

Ostendorf F, Metzdorf J, Gold R, et al (2020)

Propionic Acid and Fasudil as Treatment Against Rotenone Toxicity in an In Vitro Model of Parkinson's Disease.

Molecules (Basel, Switzerland), 25(11): pii:molecules25112502.

Parkinson's disease (PD) is a multifactorial neurodegenerative disease. In recent years, several studies demonstrated that the gastroenteric system and intestinal microbiome influence central nervous system function. The pathological mechanisms triggered thereby change neuronal function in neurodegenerative diseases including dopaminergic neurons in Parkinson´s disease. In this study, we employed a model system for PD of cultured primary mesencephalic cells and used the pesticide rotenone to model dopaminergic cell damage. We examined neuroprotective effects of the Rho kinase inhibitor Fasudil and the short chain fatty acid (SCFA) propionic acid on primary neurons in cell morphological assays, cell survival, gene and protein expression. Fasudil application resulted in significantly enhanced neuritic outgrowth and increased cell survival of dopaminergic cells. The application of propionic acid primarily promoted cell survival of dopaminergic cells against rotenone toxicity and increased neurite outgrowth to a moderate extent. Interestingly, Fasudil augmented gene expression of synaptophysin whereas gene expression levels of tyrosine hydroxylase (TH) were substantially increased by propionic acid. Concerning protein expression propionic acid treatment increased STAT3 levels but did not lead to an increased phosphorylation indicative of pathway activation. Our findings indicate that both Fasudil and propionic acid treatment show beneficial potential in rotenone-lesioned primary mesencephalic cells.

RevDate: 2020-06-02

Timmusk S, Nevo E, Ayele F, et al (2020)

Fighting Fusarium Pathogens in the Era of Climate Change: A Conceptual Approach.

Pathogens (Basel, Switzerland), 9(6): pii:pathogens9060419.

Fusarium head blight (FHB) caused by Fusarium pathogens is one of the most devastating fungal diseases of small grain cereals worldwide, substantially reducing yield quality and food safety. Its severity is increasing due to the climate change caused by weather fluctuations. Intensive research on FHB control methods has been initiated more than a decade ago. Since then, the environment has been rapidly changing at regional to global scales due to increasing anthropogenic emissions enhanced fertilizer application and substantial changes in land use. It is known that environmental factors affect both the pathogen virulence as well as plant resistance mechanisms. Changes in CO2 concentration, temperature, and water availability can have positive, neutral, or negative effects on pathogen spread depending on the environmental optima of the pathosystem. Hence, there is a need for studies of plant-pathogen interactions in current and future environmental context. Long-term monitoring data are needed in order to understand the complex nature of plants and its microbiome interactions. We suggest an holobiotic approach, integrating plant phyllosphere microbiome research on the ecological background. This will enable the development of efficient strategies based on ecological know-how to fight Fusarium pathogens and maintain sustainable agricultural systems.

RevDate: 2020-06-02

Chan CWH, Leung TF, Choi KC, et al (2020)

Effects of gut microbiome and environment on the development of eczema in Chinese infants.

Medicine, 99(21):e20327.

BACKGROUND: Eczema is a relapsing and persistent inflammatory skin disease affecting about one-fifth of children worldwide. As in other developed countries, the prevalence of this chronic disease in Hong Kong is approximately 30%. Moreover, the number of local cases reported has been on a rising trend since 1995. Eczema frequently starts in early infancy. A total of 45% of all cases begin within the first six months of life, 60% during the first year and 85% before the age of 5. The pathophysiology of eczema is multi-factorial and is a complex inter-relationship between skin barrier, genetic predisposition, immunologic development, microbiome, environment, nutrition, and pharmacological and psychological factors.

OBJECTIVE: To characterize the longitudinal changes of gut microbial profile in early childhood and to examine the association between gut microbiome diversity, environmental factors and the development of eczema in early childhood.

METHOD: We will conduct a longitudinal cohort study that follows 1250 Hong Kong Chinese infants for 2 years and assess the gut microbiome and other potential environmental factors in the aetiology of eczema. Parents will be asked to provide demographic data, their infant birth data, allergy condition, diet, environmental conditions as well as the data on maternal stress. Stool specimen will be collected for gut microbiome diversity analysis. We will examine newborn infants at enrollment, at 4 months, 1 year and 2 years after birth.

EXPECTED RESULTS: This study will evaluate the association between gut microbiome, environmental factors and the development of eczema in Chinese infants. Findings from this study may be used to develop a predictive path model to guide effective health promotion, disease prevention and management.

RevDate: 2020-06-01

Bernstein RC, Maier LA, E Crouser (2018)

Proceedings of the Americas Association of Sarcoidosis and Other Granulomatous Diseases (AASOG) 2017 annual meeting.

Sarcoidosis, vasculitis, and diffuse lung diseases : official journal of WASOG, 35(1):91-94.

On April 7th and 8th, 2017; the Americas Association for Sarcoidosis and Other Granulomatous Diseases (AASOG) held its annual scientific conference titled "Combining Transformative Sarcoidosis Research and Outreach to Improve Health Disparities" at the Penn State Health, Hershey Campus Conference Center. Participants came from geographically diverse areas of the United States. The demographics of meeting speakers and attendees reflected the gender, racial and ethnic diversity of those who are engaged in the treatment of the disease. The AASOG meeting was held in conjunction with an FSR-sponsored sarcoidosis patient-physician conference, providing a unique forum to enhance communication between patients, providers and researchers. Cutting edge topics at the meeting included immunology, microbiome, genomics, and challenges in diagnosis and treatment of vulnerable populations. The meeting's clinical foci were neurosarcoidosis, fatigue, and small fiber neuropathy. (Sarcoidosis Vasc Diffuse Lung Dis 2018; 35: 91-94).

RevDate: 2020-06-01

Singh A, Nayak N, Rathi P, et al (2020)

Microbiome and host crosstalk: A new paradigm to cancer therapy.

Seminars in cancer biology pii:S1044-579X(20)30110-3 [Epub ahead of print].

The commensal microbiome of humans has co-evolved for thousands of years. The microbiome regulates human health and is also linked to several diseases, including cancer. The advances in next-generation sequencing have significantly contributed to our understanding of the microbiome and its association with cancer and cancer therapy. Recent studies have highlighted a close relationship of the microbiome to the pharmacological effect of chemotherapy and immunotherapy. The chemo-drugs usually interfere with the host immune system and reduces the microbiome diversity inside the body, which in turn leads to decreased efficacy of these drugs. The human microbiome, specifically the gut microbiome, increases the potency of chemo-drugs through metabolism, enzymatic degradation, ecological differences, and immunomodulation. Recent research exploits the involvement of microbiome to shape the efficacy and decrease the toxicity of these chemo-drugs. In this review, we have highlighted the recent development in understanding the relationship of the human microbiome with cancer and also emphasize on various roles of the microbiome in the modulation of cancer therapy. Additionally, we also summarize the ongoing research focussed on the improved efficacy of chemotherapy and immunotherapy using the host microbiome.

RevDate: 2020-06-01

Chen C, Zhang Q, Yu W, et al (2020)

Oral Mucositis: An Update on Innate Immunity and New Interventional Targets.

Journal of dental research [Epub ahead of print].

Oral mucositis (OM), a common debilitating toxicity associated with chemo- and radiation therapies, is a significant unmet clinical need for head and neck cancer patients. The biological complexities of chemoradiotherapy-induced OM involve interactions among disrupted tissue structures, inflammatory infiltrations, and oral microbiome, whereby several master inflammatory pathways constitute the complicated regulatory networks. Oral mucosal damages triggered by chemoradiotherapy-induced cell apoptosis were further exacerbated by the amplified inflammatory cascades dominantly governed by the innate immune responses. The coexistence of microbiome and innate immune components in oral mucosal barriers indicates that a signaling hub coordinates the interaction between environmental cues and host cells during tissue and immune homeostasis. Dysbiotic shifts in oral microbiota caused by cytotoxic cancer therapies may also contribute to the progression and severity of chemoradiotherapy-induced OM. In this review, we have updated the mechanisms involving innate immunity-governed inflammatory cascades in the pathobiology of chemoradiotherapy-induced OM and the development of new interventional targets for the management of this severe morbidity in head and neck cancer patients.

RevDate: 2020-06-01

Kreth J, Merritt J, Pfeifer CS, et al (2020)

Interaction between the Oral Microbiome and Dental Composite Biomaterials: Where We Are and Where We Should Go.

Journal of dental research [Epub ahead of print].

Dental composites are routinely placed as part of tooth restoration procedures. The integrity of the restoration is constantly challenged by the metabolic activities of the oral microbiome. This activity directly contributes to a less-than-desirable half-life for the dental composite formulations currently in use. Therefore, many new antimicrobial dental composites are being developed to counteract the microbial challenge. To ensure that these materials will resist microbiome-derived degradation, the model systems used for testing antimicrobial activities should be relevant to the in vivo environment. Here, we summarize the key steps in oral microbial colonization that should be considered in clinically relevant model systems. Oral microbial colonization is a clearly defined developmental process that starts with the formation of the acquired salivary pellicle on the tooth surface, a conditioned film that provides the critical attachment sites for the initial colonizers. Further development includes the integration of additional species and the formation of a diverse, polymicrobial mature biofilm. Biofilm development is discussed in the context of dental composites, and recent research is highlighted regarding the effect of antimicrobial composites on the composition of the oral microbiome. Future challenges are addressed, including the potential of antimicrobial resistance development and how this could be counteracted by detailed studies of microbiome composition and gene expression on dental composites. Ultimately, progress in this area will require interdisciplinary approaches to effectively mitigate the inevitable challenges that arise as new experimental bioactive composites are evaluated for potential clinical efficacy. Success in this area could have the added benefit of inspiring other fields in medically relevant materials research, since microbial colonization of medical implants and devices is a ubiquitous problem in the field.

RevDate: 2020-06-01

Asad F, Anwar H, Yassine HM, et al (2020)

White Button Mushroom, Agaricus bisporus (Agaricomycetes), and a Probiotics Mixture Supplementation Correct Dyslipidemia without Influencing the Colon Microbiome Profile in Hypercholesterolemic Rats.

International journal of medicinal mushrooms, 22(3):235-244.

Consumption of foods rich in dietary fiber has attracted considerable attention for lowering blood cholesterol and triglycerides through attenuation of gut microbiome. Diets rich in fiber may provide substrates for microbes to digest and proliferate. In response, products of microbial digestion enter systemic circulation and support host energy homeostasis. In the present study, rats with hypercholesterolemia (HC) were supplemented with probiotics (PB) and Agaricus bisporus mushroom to examine the antidyslipidemia effects. Forty adult rats were divided into five treatment groups. The rats in the control group were fed only a chow maintenance diet (CON; n = 8), whereas an atherogenic diet (chow diet supplemented with 1.5% cholesterol and 0.5% cholic acid) was offered to the remaining rats to induce hypercholesterolemia (HC group; n = 32). Rats developed HC following a 24-day continuous supplementation with the atherogenic diet. From day 25 onward, the HC group was further divided into HC-CON, HC-PB (supplemented with PB at 1 mg/rat/day), HC-AB (supplemented with A. bisporus at 5% of diet), and HC-AB.PB (supplemented with both A. bisporus and PB). After 6 weeks of supplementation, rats were killed to collect blood to determine serum lipid profile, oxidative stress, and for metagenomics analysis of colon contents. Results showed that all supplementations corrected HC-induced oxidative stress. Furthermore, A. bisporus supplementation corrected HC-induced dyslipidemia (P ≤ .05). Blautia and Bifidobacterium were the most dominant bacterial genera in HC-AB and HC-PB groups, respectively. Phylum Firmicutes and class Clostridia predominantly occupied the gut microbiome in all groups. However, no significant differences were observed in microbiome diversity and clustering patterns among study groups. In conclusion, supplementation of A. bisporus mushroom and probiotics can lower oxidative stress and dyslipidemia with partial effects on the phylogenetic makeup in the gut microbiome.

RevDate: 2020-06-01

Awany D, Allali I, ER Chimusa (2020)

Dissecting Genome-wide Studies for Microbiome-related Metabolic Diseases.

Human molecular genetics pii:5849428 [Epub ahead of print].

Despite the meteoric rise in genome-wide association studies for metabolic diseases (MetD) over the last few years, our understanding of the pathogenesis of these diseases is still far from complete. Recent developments have established that MetD arises from complex interactions between host genetics, the gut microbiome, and the environment. However, our knowledge of the genetic and microbiome components involved, and the underlying molecular mechanisms remains limited. Here, we review and summarize recent studies investigating the genetic and microbiome basis of MetD. Then, given the critical importance of study-individual's ancestry in these studies, we leverage 4932 whole genome sequence (WGS) samples from 18 world-wide ethnic groups to examine genetic diversity in currently reported variants associated with metabolic diseases. The analyses show marked differences in gene-specific proportion of pathogenic SNPs, and gene-specific SNPs minor allele frequencies across ethnic groups, highlighting the importance of population- and ethnic-specific investigations in pinpointing the causative factors for MetD. We conclude with a discussion of research areas where further investigation on interactions between host genetics, microbiome, and the environment is needed.

RevDate: 2020-06-01

Chen J, Sali A, L Vitetta (2020)

The gallbladder and vermiform appendix influence the assemblage of intestinal microorganisms.

Future microbiology [Epub ahead of print].

Surgical procedures for the symptomatic removal of the gallbladder and the vermiform appendix have been posited to adversely shift the assemblage of the intestinal microbiome increasing the risk of disease. The associated mechanisms have been linked with dysbiosis of the gut microbiota. Cholecystectomy causes changes of bile acid compositions and bile secretion patterns as bile acids interact with the intestinal microbiota in a bidirectional capacity. An appendectomy precludes the further recolonization of the proximal colon with a commensal biofilm that could maintain a stable intestinal microbiome. Epidemiological studies indicate that there is an increased risk of disease rather than causality following a cholecystectomy and appendectomy. This narrative review summarizes studies that report on the role that bile salts and the appendix, contribute to the assemblage of the intestinal microbiome in health and disease.

RevDate: 2020-06-01

Cullings K, Stott MB, Marinkovich N, et al (2020)

Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert.

MicrobiologyOpen [Epub ahead of print].

We used high-throughput DNA sequencing methods combined with bio-geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography-mass spectrometry (GC-MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high-throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS-2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.

RevDate: 2020-06-01

Rettedal EA, Cree JME, Adams SE, et al (2020)

Short-term high intensity interval training (HIIT) exercise does not affect gut bacterial community diversity or composition of lean and overweight men.

Experimental physiology [Epub ahead of print].

NEW FINDINGS: What is the central question of this study? Does short-term high intensity interval training alter microbiome composition, and does this associate with exercise-induced improvements in cardiorespiratory fitness and insulin sensitivity? What is the main finding and its importance? Despite high intensity interval training increasing insulin sensitivity and cardiovascular fitness it did not alter microbiome composition. This suggests microbiome composition changes that occur with prolonged exercise training may respond to changes in metabolic health rather than drive exercise training induced adaptations.

ABSTRACT: Regular exercise reduces the risk of metabolic diseases, and gut microbiome composition has been associated with metabolic function. We investigated whether short-term high-intensity interval training (HIIT) alters bacterial community diversity and composition, and whether there were associations with markers of insulin sensitivity or aerobic fitness. Cardiorespiratory fitness (VO2 peak) and body composition (DXA scan) were assessed, and faecal and fasted blood samples collected from 14 lean (fat mass 21 ± 2%, aged 29 ± 2 y) and 15 overweight (fat mass 33 ± 2%, aged 31 ± 2 y) men before and following 3 weeks of HIIT training (8-12 × 60 s cycle ergometer bouts at VO2 peak power output interspersed by 75 s rest, 3 times per week). Gut microbiome composition was analysed by 16S rRNA gene amplicon sequencing. HIIT significantly increased aerobic fitness of both groups (p < 0.001), and improved markers of insulin sensitivity (lowered fasted insulin and HOMA-IR; p < 0.001) in the overweight group. Despite differences in the abundance of several bacterial taxa being evident between the lean and overweight group, HIIT did not affect the overall bacterial diversity or community structure (α-diversity or β-diversity). No associations were found between the top 50 most abundant bacteria genera and cardiorespiratory fitness markers, however, significant associations (p < 0.05) were observed between the bacterial species Coprococcus_3, Blautia, Lachnospiraceae_ge and Dorea abundance and insulin sensitivity markers in the overweight group. Our results suggest short-term HIIT does not greatly impact the overall composition of the gut microbiome, however certain microbiome genera associate with insulin sensitivity markers that were improved by HIIT in overweight participants. This article is protected by copyright. All rights reserved.

RevDate: 2020-06-01

Paës C, Gidenne T, Bébin K, et al (2020)

Early Introduction of Solid Feeds: Ingestion Level Matters More Than Prebiotic Supplementation for Shaping Gut Microbiota.

Frontiers in veterinary science, 7:261.

Early introduction of a nutritional substrate is a promising biomimetic strategy for controlling the implantation of the microbiota and preserving the health of young animals. In this study, we provided experimental solid substrate in a gel form to stimulate suckling rabbits' intake and to investigate its effects on microbiota implantation and colonization. All the rabbits had access to solid feed outside the nest as of 15 days of age. Except for the control group, rabbits were offered starter feed gels inside the nests from 3 to 18 days of age. These gels were either free of additives (AF_GEL) or contained 4% of fructo-oligosaccharides (FOS_GEL) or 4% of mannan-oligosaccharides and β-glucans mixtures (MOS_GEL). The cecal content of 160 rabbits was sampled at 18, 29, 38, and 57 days of age and analyzed using 16S rRNA gene sequencing. Pups consumed an average of 3.95 ± 1.07 g of starter feed gel with a higher intake when it was supplemented with fructo-oligosaccharides (+1.2 g; P < 0.05). Starter feed gel consumption increased the ensuing intake of pellets (+17 g from 15 to 21 days; P < 0.05). Alpha-diversity indexes were similar between groups and prebiotic supplementation did not induce a clear shift in microbiota pattern. Conversely, when considering rabbits that consumed more starter feed, the highest proportions of bacteria with plant-degrading abilities, such as species from the Lachnospiraceae and Ruminococcaceae families, were observed at 18 days of age. However, fermentative activities were not affected by starter feed intake at 29, 38, and 57 days of age. By providing comprehensive results on the regulation of microbial community structure at the onset of solid feed intake, this research paves the way for further studies on digestive ecosystem maturation.

RevDate: 2020-06-01

Chen XY, Fan HN, Zhang HK, et al (2020)

Rewiring of Microbiota Networks in Erosive Inflammation of the Stomach and Small Bowel.

Frontiers in bioengineering and biotechnology, 8:299.

The development of non-invasive, inexpensive, and effective early diagnosis tests for gastric and small-bowel lesions is an urgent requirement. The introduction of magnetically guided capsule endoscopy (MGCE) has aided examination of the small bowel for diagnoses. However, the distribution of the fecal microbiome in abnormal erosions of the stomach and small bowel remains unclear. Herein, alternations in the fecal microbiome in three groups [normal, small-bowel inflammation, and chronic gastritis (CG)] were analyzed by metagenomics and our well-developed method [individual-specific edge-network analysis (iENA)]. In addition to the dominant microbiota identified by the conventional differential analysis, iENA could recognize novel network biomarkers of microbiome communities, such as the genus Bacteroide in CG and small-bowel inflammation. Combined with differential network analysis, the network-hub microbiota within rewired microbiota networks revealed high-ranked iENA microbiota markers, which were disease specific and had particular pathogenic functions. Our findings illuminate the components of the fecal microbiome and the importance of specific bacteria in CG and small-bowel erosions, and could be employed to develop preventive and non-invasive therapeutic strategies.

RevDate: 2020-06-01

Welp AL, JM Bomberger (2020)

Bacterial Community Interactions During Chronic Respiratory Disease.

Frontiers in cellular and infection microbiology, 10:213.

Chronic respiratory diseases including chronic rhinosinusitis, otitis media, asthma, cystic fibrosis, non-CF bronchiectasis, and chronic obstructive pulmonary disease are a major public health burden. Patients suffering from chronic respiratory disease are prone to persistent, debilitating respiratory infections due to the decreased ability to clear pathogens from the respiratory tract. Such infections often develop into chronic, life-long complications that are difficult to treat with antibiotics due to the formation of recalcitrant biofilms. The microbial communities present in the upper and lower respiratory tracts change as these respiratory diseases progress, often becoming less diverse and dysbiotic, correlating with worsening patient morbidity. Those with chronic respiratory disease are commonly infected with a shared group of respiratory pathogens including Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis, among others. In order to understand the microbial landscape of the respiratory tract during chronic disease, we review the known inter-species interactions among these organisms and other common respiratory flora. We consider both the balance between cooperative and competitive interactions in relation to microbial community structure. By reviewing the major causes of chronic respiratory disease, we identify common features across disease states and signals that might contribute to community shifts. As microbiome shifts have been associated with respiratory disease progression, worsening morbidity, and increased mortality, these underlying community interactions likely have an impact on respiratory disease state.

RevDate: 2020-06-01

Hagenfeld D, Matern J, Prior K, et al (2020)

Significant Short-Term Shifts in the Microbiomes of Smokers With Periodontitis After Periodontal Therapy With Amoxicillin & Metronidazole as Revealed by 16S rDNA Amplicon Next Generation Sequencing.

Frontiers in cellular and infection microbiology, 10:167.

The aim of this follow-up study was, to compare the effects of mechanical periodontal therapy with or without adjunctive amoxicillin and metronidazole on the subgingival microbiome of smokers with periodontitis using 16S rDNA amplicon next generation sequencing. Fifty-four periodontitis patients that smoke received either non-surgical periodontal therapy with adjunctive amoxicillin and metronidazole (n = 27) or with placebos (n = 27). Subgingival plaque samples were taken before and two months after therapy. Bacterial genomic DNA was isolated and the V4 hypervariable region of the bacterial 16S rRNA genes was amplified. Up to 96 libraries were normalized and pooled for Illumina MiSeq paired-end sequencing with almost fully overlapping 250 base pairs reads. Exact ribosomal sequence variants (RSVs) were inferred with DADA2. Microbial diversity and changes on the genus and RSV level were analyzed with non-parametric tests and a negative binomial regression model, respectively. Before therapy, the demographic, clinical, and microbial parameters were not significantly different between the placebo and antibiotic groups. Two months after the therapy, clinical parameters improved and there was a significantly increased dissimilarity of microbiomes between the two groups. In the antibiotic group, there was a significant reduction of genera classified as Porphyromonas, Tannerella, and Treponema, and 22 other genera also decreased significantly, while Selenomonas, Capnocytophaga, Actinomycetes, and five other genera significantly increased. In the placebo group, however, there was not a significant decrease in periodontal pathogens after therapy and only five other genera decreased, while Veillonella and nine other genera increased. We conclude that in periodontitis patients who smoke, microbial shifts occurred two months after periodontal therapy with either antibiotics or placebo, but genera including periodontal pathogens decreased significantly only with adjunctive antibiotics.

RevDate: 2020-06-01

Garcia K, Bücking H, SD Zimmermann (2020)

Editorial: Importance of Root Symbiomes for Plant Nutrition: New Insights, Perspectives and Future Challenges.

Frontiers in plant science, 11:594.

RevDate: 2020-06-01

Sharma P, Rani J, Chauhan C, et al (2020)

Altered Gut Microbiota and Immunity Defines Plasmodium vivax Survival in Anopheles stephensi.

Frontiers in immunology, 11:609.

Blood-feeding enriched gut-microbiota boosts mosquitoes' anti-Plasmodium immunity. Here, we ask how Plasmodium vivax alters gut-microbiota, anti-Plasmodial immunity, and impacts tripartite Plasmodium-mosquito-microbiota interactions in the gut lumen. We used a metagenomics and RNAseq strategy to address these questions. In naïve mosquitoes, Elizabethkingia meningitis and Pseudomonas spp. are the dominant bacteria and blood-feeding leads to a heightened detection of Elizabethkingia, Pseudomonas and Serratia 16S rRNA. A parallel RNAseq analysis of blood-fed midguts also shows the presence of Elizabethkingia-related transcripts. After, P. vivax infected blood-meal, however, we do not detect bacterial 16S rRNA until circa 36 h. Intriguingly, the transcriptional expression of a selected array of antimicrobial arsenal cecropins 1-2, defensin-1, and gambicin remained low during the first 36 h-a time frame when ookinetes/early oocysts invaded the gut. We conclude during the preinvasive phase, P. vivax outcompetes midgut-microbiota. This microbial suppression likely negates the impact of mosquito immunity which in turn may enhance the survival of P. vivax. Detection of sequences matching to mosquito-associated Wolbachia opens a new inquiry for its exploration as an agent for "paratransgenesis-based" mosquito control.

RevDate: 2020-06-01

Corbin KR, Bolt B, CM Rodríguez López (2020)

Breeding for Beneficial Microbial Communities Using Epigenomics.

Frontiers in microbiology, 11:937.

RevDate: 2020-06-01

Schwan B, Abendroth C, Latorre-Pérez A, et al (2020)

Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility.

Frontiers in microbiology, 11:867.

Anaerobic digestion is a technology known for its potential in terms of methane production. During the digestion process, multiple metabolites of high value are synthesized. However, recent works have demonstrated the high robustness and resilience of the involved microbiomes; these attributes make it difficult to manipulate them in such a way that a specific metabolite is predominantly produced. Therefore, an exact understanding of the manipulability of anaerobic microbiomes may open up a treasure box for bio-based industries. In the present work, the effect of nalidixic acid, γ-aminobutyric acid (GABA), and sodium phosphate on the microbiome of digested sewage sludge from a water treatment plant fed with glucose was investigated. Despite of the induced process perturbations, high stability was observed at the phylum level. However, strong variations were observed at the genus level, especially for the genera Trichococcus, Candidatus Caldatribacterium, and Phascolarctobacterium. Ecological interactions were analyzed based on the Lotka-Volterra model for Trichococcus, Rikenellaceae DMER64, Sedimentibacter, Candidatus Cloacimonas, Smithella, Cloacimonadaceae W5 and Longilinea. These genera dynamically shifted among positive, negative or no correlation, depending on the applied stressor, which indicates a surprisingly dynamic behavior. Globally, the presented work suggests a massive resilience and stability of the methanogenic communities coupled with a surprising flexibility of the particular microbial key players involved in the process.

RevDate: 2020-06-01

Ding Z, Bai J, Xu D, et al (2020)

Microbial Community Dynamics and Natural Fermentation Profiles of Ensiled Alpine Grass Elymus nutans Prepared From Different Regions of the Qinghai-Tibetan Plateau.

Frontiers in microbiology, 11:855.

Feed deficiency during the long cold period of a year is one of the major problems that the traditional year-round animal grazing system has faced on the Qinghai-Tibetan plateau (QTP) since ancient time. Therefore, ensiling the grasses from grassland could be a desirable feeding regime to preserve high quality forage and to alleviate the seasonal unbalanced feed supply problem on this plateau. The present study was designed to investigate dynamics of bacterial community and natural fermentation quality of ensiled Elymus nutans collected from grasslands in four different areas with different elevations [Tianzhu County (TZ), 2965 m; Golog Prefecture (GL), 3763 m; Damxung County (DX), 4228 m, and Nagqu Prefecture (NQ), 4752 m] on the QTP. The bacterial community was characterized by using the PacBio single molecule with real-time sequencing technology (SMRT). The harvested fresh E. nutans grasses were ensiled in vacuum-sealed polyethylene bags for 14, 30, 60, and 90 days. Obvious differences in the epiphytic bacterial community of the fresh E. nutans samples from the four areas were observed, which resulted in various bacterial community dynamics and fermentation qualities of ensiled E. nutans. Higher fermentation quality was observed in silage samples from Nagqu than in those from the other areas (P < 0.05). Lactic acid bacteria (LAB) involved in fermentation of E. nutans from low altitude areas consisted of Pediococcus pentosaceus, Lactobacillus sp., Leuconostoc mesenteroides, and Lactobacillus coryniformis, whereas major LAB species involved in the fermentation of E. nutans silage from high altitudes included L. mesenteroides, Lactobacillus brevis, and Lactobacillus sp. Correlation analysis between bacterial composition and fermentation quality of E. nutans silages made from the four different areas in the QTP indicated that the LAB species responsible for silage fermentation in different areas were totally different, which was mainly due to the different epiphytic bacterial compositions in fresh E. nutans before ensiling. The present results provide important information on revealing the bacterial communities and fermentation quality of ensiled E. nutans, and on future screening of LAB isolates for making high quality silage in order to alleviate feed shortage of the traditional year-round grazing system on the QTP.

RevDate: 2020-06-01

Alushi B, Curini L, Christopher MR, et al (2020)

Calcific Aortic Valve Disease-Natural History and Future Therapeutic Strategies.

Frontiers in pharmacology, 11:685.

Calcific aortic valve disease (CAVD) is the most frequent heart valve disorder. It is characterized by an active remodeling process accompanied with valve mineralization, that results in a progressive aortic valve narrowing, significant restriction of the valvular area, and impairment of blood flow.The pathophysiology of CAVD is a multifaceted process, involving genetic factors, chronic inflammation, lipid deposition, and valve mineralization. Mineralization is strictly related to the inflammatory process in which both, innate, and adaptive immunity are involved. The underlying pathophysiological pathways that go from inflammation to calcification and, finally lead to severe stenosis, remain, however, incompletely understood. Histopathological studies are limited to patients with severe CAVD and no samples are available for longitudinal studies of disease progression. Therefore, alternative routes should be explored to investigate the pathogenesis and progression of CAVD.Recently, increasing evidence suggests that epigenetic markers such as non-coding RNAs are implicated in the landscape of phenotypical changes occurring in CAVD. Furthermore, the microbiome, an essential player in several diseases, including the cardiovascular ones, has recently been linked to the inflammation process occurring in CAVD. In the present review, we analyze and discuss the CAVD pathophysiology and future therapeutic strategies, focusing on the real and putative role of inflammation, calcification, and microbiome.

RevDate: 2020-06-01

Dias AM, Cordeiro G, Estevinho MM, et al (2020)

Gut bacterial microbiome composition and statin intake-A systematic review.

Pharmacology research & perspectives, 8(3):e00601.

Recently, the gut microbiome has become an important field of interest. Indeed, the microbiome has been associated to numerous drug interactions and it is thought to influence the efficacy of pharmacologic treatments. Although statins are widely prescribed medications, there remains considerable variability in its therapeutic response. In this context, we aimed to investigate how statins modulate the gut microbiome and, reversely, how can the microbiome influence the course of anti-hypercholesterolemic treatment. We conducted a systematic review by searching four online databases, in accordance with PRISMA guidelines. Studies addressing gut microbiome changes following statin treatment and those assessing statins' response and associating it with patients' microbiome were included. Due to the limited number of results, we decided to include studies enrolling both humans and animals. We summarized information from three human and seven animal studies and aimed to assess the influence of gut microbiome composition on statin response (Outcome 1) and to evaluate the impact of statin treatment on the gut microbiome (Outcome 2). An association between a certain microbiome composition that promoted the lipid-lowering effect of statins was found. However, what kind of microorganisms and how they can exert this effect remains uncertain. Furthermore, statins might have a role in the modulation of the gut microbiome, but then again, it is still unknown whether this change is directly caused by the drug or another metabolic mechanism. Even though gut microbiota may have several potential therapeutic implications, its use as a personalized predictive biomarker requires further studies.

RevDate: 2020-06-01

Shi H, KC Huang (2020)

Pictures of Tongues Sticking Out.

Trends in endocrinology and metabolism: TEM pii:S1043-2760(20)30115-6 [Epub ahead of print].

Despite their small sizes, bacterial cells within a host-associated microbial community often form highly structured complexes determined by environmental factors and interspecies interactions. Wilbert et al. combined species-specific fluorescent labels and high-resolution microscopy to visualize human tongue dorsum microbiomes and to highlight their structure and dynamics.

RevDate: 2020-06-01

Wang X, Yang Z, Xu X, et al (2020)

Odd-numbered agaro-oligosaccharides alleviate type 2 diabetes mellitus and related colonic microbiota dysbiosis in mice.

Carbohydrate polymers, 240:116261.

Agaro- and neoagaro-oligosaccharides with even-numbered sugar units possess a variety of biological activities. However, the effects of the odd-numbered oligosaccharides from Gracilaria agarose (OGAOs) on type 2 diabetes mellitus (T2DM) have not been reported. In this study, we aimed to evaluate the effects of OGAOs on anti-T2DM from different aspects. We found that OGAOs treatment could alleviate oxidative stress, inflammation, and the related hyperglycemia, insulin resistance, lipid accumulation, and obesity in high-fat diet (HFD) induced T2DM. Investigation of the underlying mechanism showed that colitis and colonic microbiota dysbiosis in T2DM mice were ameliorated after OGAOs treatment. First, OGAOs increased the expression of ZO-1, occludin, and AMPK, and suppressed the TLR4/MAPK/NF-κB pathway in colon indicating that OGAOs enhance intestinal integrity and conduct the anti-apoptosis effects to prevent the invasion of toxins and harmful microorganisms. Moreover, the relative abundance of Akkermansia was significantly upregulated in the gut microbiome of T2DM mice associated with a dramatic decrease of the relative abundance of Helicobacter, which are both beneficial for alleviating colitis and T2DM. In addition, Spearman's correlation analysis indicated that changes in the colonic microbiota could regulate oxidative stress, inflammation, and hyperlipidemia. In summary, the underlying mechanism of OGAOs on alleviating colitis and colonic microbiota dysbiosis in T2DM has been intensively studied, illustrating that OGAOs could be further developed as a potential pharmaceutical agent for T2DM.

RevDate: 2020-06-01

Xia Y (2020)

Correlation and association analyses in microbiome study integrating multiomics in health and disease.

Progress in molecular biology and translational science, 171:309-491.

Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.

RevDate: 2020-06-01

Chan SL (2020)

Microbiome and cancer treatment: Are we ready to apply in clinics?.

Progress in molecular biology and translational science, 171:301-308.

Cancer treatment has been evolving in recent decades from surgery, conventional chemotherapy and radiation therapy to targeted therapies and more recently immunotherapies. Despite significant improvement in the efficacy of treatment with the discovery of novel therapies targeting particular cancer-related gene and proteins and more recently the immune system-modulating biologics, still only patients with specific subtypes of cancer benefit from those targeted therapies and there is room for further improvement of survival outcomes. As failure of cancer treatment is not uncommon in clinical practice, a lot of biomarker studies have been carried out with an aim to identify factors contributing to disease relapse and treatment failure. Gut microbiome is one of the research areas which warrants further investigation of its impact on cancer treatment as microbiota has long been proven to profoundly shape mammalian immunity. As there is increasing evidence showing a strong association between gut microbiota and clinical outcomes of immunotherapy, modulation of intestinal micro-ecological system may be a possible strategy to help improve therapeutic impact of immunotherapy in oncology practice.

RevDate: 2020-06-01

Dahl WJ, Rivero Mendoza D, JM Lambert (2020)

Diet, nutrients and the microbiome.

Progress in molecular biology and translational science, 171:237-263.

Although there is associative evidence linking fecal microbiome profile to health and disease, many studies have not considered the confounding effects of dietary intake. Consuming food provides fermentable substrate which sustains the microbial ecosystem that resides with most abundance in the colon. Western, Mediterranean and vegetarian dietary patterns have a role in modulating the gut microbiota, as do trending restrictive diets such the paleolithic and ketogenic. Altering the amount or ratio of carbohydrate, protein and fat, particularly at the extremes of intake, impacts the microbiome. Diets high in fermentable carbohydrates support the relative abundance of Bifidobacterium, Prevotella, Ruminococcus, Dorea and Roseburia, among others, capable of degrading polysaccharides, oligosaccharides and sugars. Conversely, very high fat diets increase bile-resistant organisms such as Bilophila and Bacteroides. Food form, whole foods vs. ultra-processed, alters the provision of macronutrient substrate to the colon due to differing digestibility, and thereby may impact the microbiota and its metabolic activity. In addition, phytochemicals in plant-based foods have specific and possibly prebiotic effects on the microbiome. Further, food ingredients such as certain low-calorie sweeteners enhance Bifidobacterium spp. The weight of evidence to date suggests a high level of interindividual variability in the human microbiome vs. clearly defined, dietary-induced profiles. Healthful dietary patterns, emphasizing plant foods high in microbial-available carbohydrate, support favorable microbiome profiles active in saccharolytic fermentation. Future research into diet and microbiome should consider the balance of gut microbial-generated metabolites, an important link between microbiome profile and human health.

RevDate: 2020-06-01

Tillett BJ, EE Hamilton-Williams (2020)

Microbiota derived factors as drivers of type 1 diabetes.

Progress in molecular biology and translational science, 171:215-235.

Type 1 diabetes (T1D) is an autoimmune disease caused by complex interactions between host genetics and environmental factors, culminating in the T-cell mediated destruction of the insulin producing cells in the pancreas. The rapid increase in disease frequency over the past 50 years or more has been too rapid to attribute to genetics. Dysbiosis of the gut microbiota is currently being widely investigated as a major contributor to environmental change driving increased T1D onset. In this chapter, we discuss the major changes in gut microbiota composition and function linked to T1D risk as well as the potential origin of these changes including infant diet, antibiotic use and host genetics. We examine the interaction between inflammation and gut barrier function and the dysbiotic gut microbiota that have been linked to T1D.

RevDate: 2020-06-01

Wang Z, Ren R, Y Yang (2020)

Mucosa microbiome of gastric lesions: Fungi and bacteria interactions.

Progress in molecular biology and translational science, 171:195-213.

Many components of the gastric non-Helicobacter pylori microbiota have been identified recently thanks to advances in DNA sequencing techniques. Several lines of evidence support the hypothesis that the gastric microbiome is essential for gastric disorders such as gastric cancer. Microbial interactions impact the pathophysiology of various gastric disorders. This chapter provides an overview of recent findings regarding general gastric microbial community profiling, microbial interactions in the stomach, and microbial characteristics in various gastric disorders.

RevDate: 2020-06-01

Silbergleit M, Vasquez AA, Miller CJ, et al (2020)

Oral and intestinal bacterial exotoxins: Potential linked to carcinogenesis.

Progress in molecular biology and translational science, 171:131-193.

Growing evidence suggests that imbalances in resident microbes (dysbiosis) can promote chronic inflammation, immune-subversion, and production of carcinogenic metabolites, thus leading to neoplasia. Yet, evidence to support a direct link of individual bacteria species to human sporadic cancer is still limited. This chapter focuses on several emerging bacterial toxins that have recently been characterized for their potential oncogenic properties toward human orodigestive cancer and the presence of which in human tissue samples has been documented. These include cytolethal distending toxins produced by various members of gamma and epsilon Proteobacteria, Dentilisin from mammalian oral Treponema, Pasteurella multocida toxin, two Fusobacterial toxins, FadA and Fap2, Bacteroides fragilis toxin, colibactin, cytotoxic necrotizing factors and α-hemolysin from Escherichia coli, and Salmonella enterica AvrA. It was clear that these bacterial toxins have biological activities to induce several hallmarks of cancer. Some toxins directly interact with DNA or chromosomes leading to their breakdowns, causing mutations and genome instability, and others modulate cell proliferation, replication and death and facilitate immune evasion and tumor invasion, prying specific oncogene and tumor suppressor pathways, such as p53 and β-catenin/Wnt. In addition, most bacterial toxins control tumor-promoting inflammation in complex and diverse mechanisms. Despite growing laboratory evidence to support oncogenic potential of selected bacterial toxins, we need more direct evidence from human studies and mechanistic data from physiologically relevant experimental animal models, which can reflect chronic infection in vivo, as well as take bacterial-bacterial interactions among microbiome into consideration.

RevDate: 2020-06-01

Parsons E, Claud K, EO Petrof (2020)

The infant microbiome and implications for central nervous system development.

Progress in molecular biology and translational science, 171:1-13.

Neurodevelopmental impairment remains a significant morbidity in former very low birth weight premature infants. There is increasing evidence the microbiome affects neurodevelopment but mechanistic causes are largely unknown. There are many factors which affect the developing microbiome in infants including mode of delivery, feeding, medications, and environmental exposures. The overall impact of these factors may differ between premature and term infants. The microbiome and brain have well recognized bidirectional communication pathways via neural, hormonal, and immunologic mechanisms. Understanding the interplay between these different pathways has been possible with the use of animal models, particularly germ-free mice. The intricate relationship between the microbiome and the brain remains a research priority not only to improve the care, but to also improve the long-term neurodevelopmental outcomes in this vulnerable population.

RevDate: 2020-06-01

Nedorost ST (2020)

Allergic Contact Sensitization in Healthy Skin Differs from Sensitization in Chronic Dermatitis: Atopic, Occupational Wet Work, and Stasis Dermatitis.

Dermatologic clinics, 38(3):301-308.

The duration of cutaneous inflammation preceding sensitization influences the resulting allergic response; the innate immune system instructs the adaptive immune response. Potent allergens that function as their own irritant cause classic T helper cell type 1 skewed dermatitis. Examples include poison ivy, epoxy resin, and methylchloroisothiazolinone. Less potent allergens, such as food proteins and propylene glycol, sensitize skin affected by chronic dermatitis resulting in a T helper cell type 2 skewed response, sometimes with associated systemic contact dermatitis. Systemic contact dermatitis should therefore be suspected in patients with positive patch tests to ingested allergens in the setting of chronic dermatitis.


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 )