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24 Feb 2020 at 01:38
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Bibliography on: Microbiome


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RJR: Recommended Bibliography 24 Feb 2020 at 01:38 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: 2020-02-23

Law CKY, De Henau R, J De Vrieze (2020)

Feedstock thermal pretreatment selectively steers process stability during the anaerobic digestion of waste activated sludge.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10472-8 [Epub ahead of print].

Strategies to enhance process performance of anaerobic digestion remain of key importance to promote wider usage of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e. organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process stability of the digesters fed sterile WAS, with a 92 ± 45% decrease in methane production, compared to a 42 ± 31% increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process stability between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na+ L-1. Feedstock sterilization through thermal pretreatment strongly impacted the microbial community in the digesters. In conclusion, feedstock thermal pretreatment strongly impacted anaerobic digestion process stability, due to feedstock inoculation and compositional modification.

RevDate: 2020-02-23

Abbas A, JP Zackular (2020)

Microbe-microbe interactions during Clostridioides difficile infection.

Current opinion in microbiology, 53:19-25 pii:S1369-5274(20)30020-5 [Epub ahead of print].

Clostridioides difficile is the leading cause of hospital-acquired gastrointestinal infections and a major public health burden in the United States. C. difficile infection causes a spectrum of disease from mild diarrhea to severe complications such as pseudomembranous colitis, toxic megacolon and death. This broad range of disease is only partially explained by bacterial genetic factors, host genetics, comorbidities and previous drug exposures. Another important factor is the gut microbiome, the disruption of which results in a loss of colonization resistance to C. difficile. Here, we review how gut microbiota and their metabolites impact C. difficile virulence and influence disease.

RevDate: 2020-02-23

Woo Kim S, Goossens A, Libert C, et al (2020)

Phytohormones: Multifunctional nutraceuticals against metabolic syndrome and comorbid diseases.

Biochemical pharmacology pii:S0006-2952(20)30094-0 [Epub ahead of print].

Metabolic syndrome is characterized by the co-occurrence of diverse symptoms initiating the development of type 2 diabetes, cardiovascular diseases, and a variety of comorbid diseases. The complex constellation of numerous comorbidities makes it difficult to develop common therapeutic approaches that ameliorate these pathological features simultaneously. The plant hormones abscisic acid, salicylic acid, auxin, and cytokinins, have shown promising anti-inflammatory and pro-metabolic effects that could mitigate several disorders relevant to metabolic syndrome. Intriguingly, besides plants, human cells and gut microbes also endogenously produce these molecules, indicating a role in the complex interplay between inflammatory responses associated with metabolic syndrome, the gut microbiome, and nutrition. Here, we introduce how bioactive phytohormones can be generated endogenously and through the gut microbiome. These molecules subsequently influence immune responses and metabolism. We also elaborate on how phytohormones can beneficially modulate metabolic syndrome comorbidities, and propose them as nutraceuticals.

RevDate: 2020-02-23

Schneider AM, Cook LC, Zhan X, et al (2020)

Response to Ring: In silico predictive metagenomic analyses highlight key metabolic pathways impacted in the HS skin microbiome.

The Journal of investigative dermatology pii:S0022-202X(20)30150-0 [Epub ahead of print].

RevDate: 2020-02-18

Nagao-Kitamoto H, Leslie JL, Kitamoto S, et al (2020)

Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota.

Nature medicine pii:10.1038/s41591-020-0764-0 [Epub ahead of print].

The involvement of host immunity in the gut microbiota-mediated colonization resistance to Clostridioides difficile infection (CDI) is incompletely understood. Here, we show that interleukin (IL)-22, induced by colonization of the gut microbiota, is crucial for the prevention of CDI in human microbiota-associated (HMA) mice. IL-22 signaling in HMA mice regulated host glycosylation, which enabled the growth of succinate-consuming bacteria Phascolarctobacterium spp. within the gut microbiome. Phascolarctobacterium reduced the availability of luminal succinate, a crucial metabolite for the growth of C. difficile, and therefore prevented the growth of C. difficile. IL-22-mediated host N-glycosylation is likely impaired in patients with ulcerative colitis (UC) and renders UC-HMA mice more susceptible to CDI. Transplantation of healthy human-derived microbiota or Phascolarctobacterium reduced luminal succinate levels and restored colonization resistance in UC-HMA mice. IL-22-mediated host glycosylation thus fosters the growth of commensal bacteria that compete with C. difficile for the nutritional niche.

RevDate: 2020-02-22

Wang Y, Gong J, Li J, et al (2020)

Insights into bacterial diversity in compost: Core microbiome and prevalence of potential pathogenic bacteria.

The Science of the total environment, 718:137304 pii:S0048-9697(20)30814-7 [Epub ahead of print].

Fertilizer-replacement programs by the ministry of agriculture and rural affairs are extraordinary actions for environment protection and sustainable agriculture in China. A national-level survey was performed to acquire consensuses of bio-physiochemical properties for composts. A total of 116 compost samples collected from 16 provinces in China were analyzed by high throughput sequencing of bacterial 16S rRNA gene amplicons. The germination index and bacterial alpha-diversity were lower in composts from poultry manure than others. This large-scale survey revealed that bacterial communities were distinct among different composts and slightly explained by pH, moisture and total nitrogen, but not by raw material or composting process. Nevertheless, 26 OTUs affiliated with Firmicutes (Cerasibacillus, Atopostipes and Bacillus) and Actinobacteria (Thermobifida, Actinomadura and Nocardiopsis) were present in most (>90%) composts and majority of these bacterial species were possibly associated with the biodegradation of organic materials. Surprisingly, 629 potential human or animal bacterial pathogens accounting an average of 1.21% of total 16S rRNA gene were detected and these bacteria were mainly affiliated with Helicobacter, Staphylococcus, Acinotobacter, Streptococcus, Mycobacterium and Enterococcus. In summary, this study provides baseline data for the diversity and abundance of core microbiome and potential pathogens in composts.

RevDate: 2020-02-22

Jiang ZH, J Meng (2020)

[Advances in the endotypes of chronic rhinosinusitis].

Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology, head, and neck surgery, 34(1):13-18.

The pathogenesis of chronic rhinosinusitis(CRS) is complex. There are differences in the clinical manifestations and therapeutic effects of CRS dominated by different causes. At present, there is a lack of uniform classification standards in clinical practice. In this paper, the research progress in the endotype of CRS in recent years was discussed.

RevDate: 2020-02-22

Younis N, Zarif R, R Mahfouz (2020)

Inflammatory bowel disease: between genetics and microbiota.

Molecular biology reports pii:10.1007/s11033-020-05318-5 [Epub ahead of print].

Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory disease that can involve any part of the gastrointestinal tract. It includes two main disorders: Crohn's disease (CD) and Ulcerative colitis (UC). CD and UC often share a similar clinical presentation; however, they affect distinct parts of the GI Tract with a different gut wall inflammatory extent. Ultimately, IBD seems to emanate from an uncontrollably continuous inflammatory process arising against the intestinal microbiome in a genetically susceptible individual. It is a multifactorial disease stemming from the impact of both environmental and genetic components on the intestinal microbiome. Furthermore, IBD genetics has gained a lot of attention. Around 200 loci were identified as imparting an increased risk for IBD. Few of them were heavily investigated and determined as highly linked to IBD. These genes, as discussed below, include NOD2, ATG16L1, IRGM, LRRK2, PTPN2, IL23R, Il10, Il10RA, Il10RB, CDH1 and HNF4α among others. Consequently, the incorporation of a genetic panel covering these key genes would markedly enhance the diagnosis and evaluation of IBD.

RevDate: 2020-02-22

Blacutt A, Ginnan N, Dang T, et al (2020)

An in vitro pipeline to screen and select citrus-associated microbiota with potential anti-Candidatus Liberibacter asiaticus properties.

Applied and environmental microbiology pii:AEM.02883-19 [Epub ahead of print].

Huanglongbing (HLB) is a destructive citrus disease that is lethal to all commercial citrus making it the most serious citrus disease and one of the most serious plant diseases. Because of the severity of HLB and the paucity of effective control measures, we structured this study to encompass the entirety of the citrus microbiome and the chemistries associated with that microbial community. We describe the spatial niche diversity of bacteria and fungi associated with citrus roots, stems and leaves using traditional microbial culturing integrated with culture-independent methods. Using the culturable sector of the citrus microbiome, we created a microbial repository using a high-throughput bulk culturing and microbial identification pipeline. We integrated an in vitro agar-diffusion inhibition bioassay into our culturing pipeline that queried the repository for antimicrobial activity against Liberibacter crescens, a culturable surrogate for the non-culturable Candidatus Liberibacter asiaticus bacterium associated with HLB. We identified microbes with robust inhibitory activity against L. crescens that include the fungi Cladosporium cladosporioides and Epicoccum nigrum and bacteria Pantoea, Bacillus and Curtobacterium Purified bioactive natural products with anti-CLas activity, were identified from the fungus, C. cladosporiodes Bioassay-guided fractionation of an organic extract of C. cladosporioides yielded the natural products cladosporols A, C and D as the active agents against L. crescens This work serves as a foundation for unraveling the complex chemistries associated with the citrus microbiome to begin to understand functional roles of members of the microbiome with the long-term goal of developing anti-CLas bioinoculants that thrive in the citrus holosystem.IMPORTANCEGlobally, citrus is threatened by Huanglongbing (HLB) and the lack of effective control measures is a major concern of farmers, markets and consumers. There is compelling evidence that plant health is a function of the activities of its associated microbiome. Using Liberibacter crescens, a culturable surrogate for the unculturable HLB-associated bacterium, Candidatus Liberibacter asiaticus (CLas), we tested the hypothesis that members of the citrus microbiome produce potential anti-CLas natural products with potential anti-CLas activity. A sub-set of isolates obtained from the microbiome inhibited L. crescens growth in an agar-diffusion inhibition assay. Further fractionation experiments linked the inhibitory activity of the fungus Cladosporium cladosporioides to the fungus-produced natural products, cladosporols A, C and D, demonstrating dose-dependent antagonism to L. crescens.

RevDate: 2020-02-22

Li Y, Dai S, Wang B, et al (2020)

Autotoxic ginsenoside disrupts soil fungal microbiomes by stimulating potentially pathogenic microbes.

Applied and environmental microbiology pii:AEM.00130-20 [Epub ahead of print].

Autotoxic ginsenosides have been implicated as one of the major causes for replant failure of Sanqi ginseng (Panax notoginseng), however, the impact of autotoxic ginsenosides on the fungal microbiome, especially on soil-borne fungal pathogens, remain poorly understood. In this study, we aimed to investigate the influence of ginsenoside monomers Rg1, Rb1, Rh1, and their mixture (Mix) on the composition and diversity of the soil fungal community as well as the abundance and growth of soil-borne pathogen Fusarium oxysporum in pure culture. The addition of autotoxic ginsenosides altered the composition of the total fungal microbiome as well as the taxa within the shared and unique treatment-based components, but not α-diversity. In particular, autotoxic ginsenosides enriched potentially pathogenic taxa, such as Alternaria, Cylindrocarpon, Gibberella, Phoma, and Fusarium, and decreased the abundances of beneficial taxa such as Acremonium, Mucor, and Ochroconis Relative abundances of pathogenic taxa were significantly and negatively correlated with that of beneficial taxa. Among the pathogenic fungi, the Fusarium genus was most responsive to ginsenoside addition with the abundance of F. oxysporum consistently enhanced in the ginsenoside-treated soils. Validation tests confirmed that autotoxic ginsenosides promoted mycelial growth and conidial germination of the root-rot pathogen F. oxysporum In addition, the autotoxic ginsenoside mixture exhibited synergistic effects on pathogen proliferation. Collectively, these results highlight that autotoxic ginsenosides are capable of disrupting the equilibrium of fungal microbiomes through the stimulation of potential soil-borne pathogens which presents a significant hurdle in remediating replant failure of Sanqi ginseng.IMPORTANCESanqi ginseng (Panax notoginseng (Burk.) F. H. Chen) could be geo-authentically produced in a restricted area of southwest China and successful replanting requires a rotation cycle of more than 15-30 years. The increasing demands of Sanqi ginseng and diminishing arable land resources drive the farmers to employ consecutive monoculture systems. Replant failure has severely threatened the sustainable production of Sanqi ginseng and causes great economic losses annually. Worse still, the acreage and severity of replant failure are yearly increased, that may destroy the Sanqi ginseng industry in the near future. The significance of this work is to decipher the mechanism of how autotoxic ginsenosides promote the accumulation of soil-borne pathogens and disrupt the equilibrium of soil fungal microbiomes. This result may help us to develop effective approaches to successfully conquer the replant failure of Sanqi ginseng.

RevDate: 2020-02-22

Won MY, Oyama LB, Courtney SJ, et al (2020)

Can rumen bacteria communicate to each other?.

Microbiome, 8(1):23 pii:10.1186/s40168-020-00796-y.

BACKGROUND: The rumen contains a myriad of microbes whose primary role is to degrade and ferment dietary nutrients, which then provide the host with energy and nutrients. Rumen microbes commonly attach to ingested plant materials and form biofilms for effective plant degradation. Quorum sensing (QS) is a well-recognised form of bacterial communication in most biofilm communities, with homoserine lactone (AHL)-based QS commonly being used by Gram-negative bacteria alone and AI-2 Lux-based QS communication being used to communicate across Gram-negative and Gram-positive bacteria. However, bacterial cell to cell communication in the rumen is poorly understood. In this study, rumen bacterial genomes from the Hungate collection and Genbank were prospected for QS-related genes. To check that the discovered QS genes are actually expressed in the rumen, we investigated expression levels in rumen metatranscriptome datasets.

RESULTS: A total of 448 rumen bacterial genomes from the Hungate collection and Genbank, comprised of 311 Gram-positive, 136 Gram-negative and 1 Gram stain variable bacterium, were analysed. Abundance and distribution of AHL and AI-2 signalling genes showed that only one species (Citrobacter sp. NLAE-zl-C269) of a Gram-negative bacteria appeared to possess an AHL synthase gene, while the Lux-based genes (AI-2 QS) were identified in both Gram-positive and Gram-positive bacteria (191 genomes representing 38.2% of total genomes). Of these 192 genomes, 139 are from Gram-positive bactreetteria and 53 from Gram-negative bacteria. We also found that the genera Butyrivibrio, Prevotella, Ruminococcus and Pseudobutyrivibrio, which are well known as the most abundant bacterial genera in the rumen, possessed the most lux-based AI-2 QS genes. Gene expression levels within the metatranscriptome dataset showed that Prevotella, in particular, expressed high levels of LuxS synthase suggesting that this genus plays an important role in QS within the rumen.

CONCLUSION: This is the most comprehensive study of QS in the rumen microbiome to date. This study shows that AI-2-based QS is rife in the rumen. These results allow a greater understanding on plant-microbe interactions in the rumen.

RevDate: 2020-02-22

Osman EO, Suggett DJ, Voolstra CR, et al (2020)

Correction to: Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities.

Microbiome, 8(1):24 pii:10.1186/s40168-020-00807-y.

Following publication of the original article [1], the authors reported an error on the legend of of P.damicornis in Fig. 1.

RevDate: 2020-02-22

Kaushal M, Mahuku G, R Swennen (2020)

Metagenomic Insights of the Root Colonizing Microbiome Associated with Symptomatic and Non-Symptomatic Bananas in Fusarium Wilt Infected Fields.

Plants (Basel, Switzerland), 9(2): pii:plants9020263.

Plants tissues are colonized by diverse communities of microorganisms called endophytes. They are key determinants of plant production and health, for example by facilitating nutrient exchanges or limiting disease development. Endophytic communities of banana plants have not been studied until very recently, and their potential role in disease development has not been explored so far. Roots from symptomatic and non-symptomatic banana plants were sampled from fields infected by Fusarium oxysporum f.sp. cubense race 1. The goal was to compare the endophytic microbiota between symptomatic and non-symptomatic plants through high throughput sequencing of 16s rDNA and shotgun metagenome sequencing. The results revealed that the endophytic root microbiome in bananas is dominated by Proteobacteria and Bacteroidetes followed to a lesser extent by Actinobacteria. The development of disease greatly impacted the endophytic microbial communities. For example, Flavobacteriales abundance was correlated with symptom development.

RevDate: 2020-02-22

Ou J, Courtney CM, Steinberger AE, et al (2020)

Nutrition in Necrotizing Enterocolitis and Following Intestinal Resection.

Nutrients, 12(2): pii:nu12020520.

This review aims to discuss the role of nutrition and feeding practices in necrotizing enterocolitis (NEC), NEC prevention, and its complications, including surgical treatment. A thorough PubMed search was performed with a focus on meta-analyses and randomized controlled trials when available. There are several variables in nutrition and the feeding of preterm infants with the intention of preventing necrotizing enterocolitis (NEC). Starting feeds later rather than earlier, advancing feeds slowly and continuous feeds have not been shown to prevent NEC and breast milk remains the only effective prevention strategy. The lack of medical treatment options for NEC often leads to disease progression requiring surgical resection. Following resection, intestinal adaptation occurs, during which villi lengthen and crypts deepen to increase the functional capacity of remaining bowel. The effect of macronutrients on intestinal adaptation has been extensively studied in animal models. Clinically, the length and portion of intestine that is resected may lead to patients requiring parenteral nutrition, which is also reviewed here. There remain significant gaps in knowledge surrounding many of the nutritional aspects of NEC and more research is needed to determine optimal feeding approaches to prevent NEC, particularly in infants younger than 28 weeks and <1000 grams. Additional research is also needed to identify biomarkers reflecting intestinal recovery following NEC diagnosis individualize when feedings should be safely resumed for each patient.

RevDate: 2020-02-22

Žiarovská J, Medo J, Kyseľ M, et al (2020)

Endophytic Bacterial Microbiome Diversity in Early Developmental Stage Plant Tissues of Wheat Varieties.

Plants (Basel, Switzerland), 9(2): pii:plants9020266.

Endophytic bacteria are an important part of different functions in plants that lead to plants' production characteristics as well as their stress response mechanisms. Endophytic bacterial diversity was analyzed in this study to describe 16S rRNA variability and changes in the leaves of drought-tolerant and drought-susceptible wheat when growth under in vitro conditions. A metagenomic analysis was applied and a pilot exploratory study was performed to prove this type of analysis as applicable to tracking endophytic bacterial diversity changes when a drought stress is applied to an in vitro culture of wheat. The study showed that the changes in the bacterial endophytes' variabilities associated preferentially with the drought stress varietal characteristics of the analyzed wheat instead of the applied stress conditions.

RevDate: 2020-02-22

Puengrang P, Suraraksa B, Prommeenate P, et al (2020)

Diverse Microbial Community Profiles of Propionate-Degrading Cultures Derived from Different Sludge Sources of Anaerobic Wastewater Treatment Plants.

Microorganisms, 8(2): pii:microorganisms8020277.

Anaerobic digestion (AD) has been used for wastewater treatment and production of renewable energy or biogas. Propionate accumulation is one of the important problems leading to an unstable system and low methane production. Revealing propionate-degrading microbiome is necessary to gain a better knowledge for alleviation of the problem. Herein, we systematically investigated the propionate-degrading cultures enriched from various anaerobic sludge sources of agro-industrial wastewater treatment plants using 16S rRNA gene sequencing. Different microbial profiles were shown even though the methanogenic activities of all cultures were similar. Interestingly, non-classical propionate-degrading key players Smithella, Syntrophomonas, and Methanosaeta were observed as common prevalent taxa in our enriched cultures. Moreover, different hydrogenotrophic methanogens were found specifically to the different sludge sources. The enriched culture of high salinity sludge showed a distinct microbial profile compared to the others, containing mainly Thermovirga, Anaerolinaceae, Methanosaeta, Syntrophobactor, and Methanospirillum. Our microbiome analysis revealed different propionate-degrading community profiles via mainly the Smithella pathway and offers inside information for microbiome manipulation in AD systems to increase biogas production corresponding to their specific microbial communities.

RevDate: 2020-02-21

Krisko TI, Nicholls HT, Bare CJ, et al (2020)

Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice.

Cell metabolism pii:S1550-4131(20)30013-9 [Epub ahead of print].

Recent studies suggest that a key mechanism whereby the gut microbiome influences energy balance and glucose homeostasis is through the recruitment of brown and beige adipocytes, primary mediators of the adaptive thermogenic response. To test this, we assessed energy expenditure and glucose metabolism in two complementary mouse models of gut microbial deficiency, which were exposed to a broad range of thermal and dietary stresses. Neither ablation of the gut microbiome, nor the substantial microbial perturbations induced by cold ambient temperatures, influenced energy expenditure during cold exposure or high-fat feeding. Nevertheless, we demonstrated a critical role for gut microbial metabolism in maintaining euglycemia through the production of amino acid metabolites that optimized hepatic TCA (tricarboxylic acid) cycle fluxes in support of gluconeogenesis. These results distinguish the dispensability of the gut microbiome for the regulation of energy expenditure from its critical contribution to the maintenance of glucose homeostasis.

RevDate: 2020-02-21

Rossi GA, Fanous H, AA Colin (2020)

Viral strategies predisposing to respiratory bacterial superinfections.

Pediatric pulmonology [Epub ahead of print].

Acute respiratory infections are amongst the leading causes of childhood morbidity and mortality globally. Viruses are the predominant cause of such infections, but mixed etiologies with bacteria has for decades raised the question of the interplay between them in causality and determination of the outcome of such infections. In this review, we examine recent microbiological, biochemical, and immunological advances that contribute to elucidating the mechanisms by which infections by specific viruses enable bacterial infections in the airway, and exacerbate them. We analyze specific domains in which viruses play such facilitating role including enhancement of bacterial adhesion by unmasking cryptic receptors and upregulation of adhesion proteins, disruption of tight junction integrity favoring paracellular transmigration of bacteria and loss of epithelial barrier integrity, increased availability of nutrient, such as mucins and iron, alteration of innate and adaptive immune responses, and disabling defense against bacteria, and lastly, changes in airway microbiome that render the lung more vulnerable to pathogens. Separate exhaustive analysis of each domain focuses on individuals with cystic fibrosis (CF), in whom viruses may play a key role in paving the way for the primary injury that leads to permanence of bacterial pathogens, viruses may then serve as triggers for "CF exacerbations"; these constituting the signature and ultimately the outcome determinants of these patients.

RevDate: 2020-02-21

Lopetuso LR, Ianiro G, Allegretti JR, et al (2020)

Fecal transplantation for ulcerative colitis: current evidence and future applications.

Expert opinion on biological therapy [Epub ahead of print].

IntroductionEstablished evidence suggests that gut microbiota plays a role in ulcerative colitis (UC). Fecal microbiota transplantation (FMT) is clearly recognized as a highly effective treatment for patients with recurrent Clostridium difficile infection, and has been investigated also in patients with UC, with promising results.Areas coveredLiterature review was performed to select publications concerning current evidence on the role of gut microbiota in the pathogenesis of UC, and on the effectiveness of FMT in this disorder.Expert OpinionThe randomized controlled trials published investigating the use of FMT suggested a potential role for FMT in the treatment of mild to moderate UC. However, given several unanswered questions regarding donor selection, dose, route of administration and duration of therapy, this is not yet recommended as a viable therapy option. FMT has allowed for more in depth investigation with regards to the role the gut microbiota may be playing in UC. This knowledge is critical to identifying where FMT may appropriately fit in the UC treatment paradigm. As our understanding of the role the microbiome plays in this chronic disease, FMT, and then eventually defined microbes, will hopefully serve in a complementary role to conventional IBD therapies.

RevDate: 2020-02-21

Adamberg K, Jaagura M, Aaspõllu A, et al (2020)

The composition of faecal microbiota is related to the amount and variety of dietary fibres.

International journal of food sciences and nutrition [Epub ahead of print].

For normal gut and body function, the diet should contain variety of dietary fibres. To elucidate the links between food intake, especially the variety of dietary fibres, faecal microbiota, body mass index and content of blood lipids, 59 healthy subjects on common Estonian diet were enrolled. The dietary records were analysed at nutrient level while seven categories of fibres were characterised to differentiate variety of fibre profiles consumed. The data of the high fibre (HF) intake (>15.1 g/1000 kcal) and the low fibre (LF) intake (<9.4 g/1000 kcal) groups were comparatively evaluated. LF diets associated with Collinsella, Coprococcus and Dorea, and higher consumption of meat and white flour products while HF diet with Roseburia, Bacteroides xylanisolvens and Oxalobacter formigenes, and arabinoxylan and pectin rich cereals and vegetables. Based on the results, modulation of the colon microbiota can be suggested by careful variation and enrichment of dietary fibre sources.

RevDate: 2020-02-21

Wiernikowski JT, MB Bernhardt (2020)

Review of nutritional status, body composition, and effects of antineoplastic drug disposition.

Pediatric blood & cancer [Epub ahead of print].

The overall survival for children with cancer in high income countries is excellent. However, there are many disparities that may negatively affect survival, which are particularly problematic in low income countries, such as nutritional status at diagnosis and throughout therapy. Nutritional status as well as concomitant foods, supplements, and medications may play a role in overall exposure and response to chemotherapy. Emerging science around the microbiome may also play a role and should be further explored as a contributor to disease progression and therapeutic response. This article highlights some of these issues and proposes additional areas of research relevant to nutritional status and pharmacology that are needed in pediatric oncology.

RevDate: 2020-02-21

Callanan J, Stockdale SR, Shkoporov A, et al (2020)

Expansion of known ssRNA phage genomes: From tens to over a thousand.

Science advances, 6(6):eaay5981 pii:aay5981.

The first sequenced genome was that of the 3569-nucleotide single-stranded RNA (ssRNA) bacteriophage MS2. Despite the recent accumulation of vast amounts of DNA and RNA sequence data, only 12 representative ssRNA phage genome sequences are available from the NCBI Genome database (June 2019). The difficulty in detecting RNA phages in metagenomic datasets raises questions as to their abundance, taxonomic structure, and ecological importance. In this study, we iteratively applied profile hidden Markov models to detect conserved ssRNA phage proteins in 82 publicly available metatranscriptomic datasets generated from activated sludge and aquatic environments. We identified 15,611 nonredundant ssRNA phage sequences, including 1015 near-complete genomes. This expansion in the number of known sequences enabled us to complete a phylogenetic assessment of both sequences identified in this study and known ssRNA phage genomes. Our expansion of these viruses from two environments suggests that they have been overlooked within microbiome studies.

RevDate: 2020-02-21

Li X, Kim J, Wu J, et al (2020)

N-Acetyl-cysteine and Mechanisms Involved in Resolution of Chronic Wound Biofilm.

Journal of diabetes research, 2020:9589507.

Chronic wounds are a major global health problem with the presence of biofilm significantly contributing to wound chronicity. Current treatments are ineffective in resolving biofilm and simultaneously killing the bacteria; therefore, effective biofilm-resolving drugs are needed. We have previously shown that, together with α-tocopherol, N-acetyl-cysteine (NAC) significantly improves the healing of biofilm-containing chronic wounds, in a diabetic mouse model we developed, by causing disappearance of the bacteria and breakdown of the extracellular polymeric substance (EPS). We hypothesize that NAC creates a microenvironment that affects bacterial survival and EPS integrity. To test this hypothesis, we developed an in vitro biofilm system using microbiome taken directly from diabetic mouse chronic wounds. For these studies, we chose mice in which chronic wound microbiome was rich in Pseudomonas aeruginosa (97%). We show that NAC at concentrations with pH < pKa causes bacterial cell death and breakdown of EPS. When used before biofilm is formed, NAC leads to bacterial cell death whereas treatment after the biofilm is established NAC causes biofilm dismantling accompanied by bacterial cell death. Mechanistically, we show that NAC can penetrate the bacterial membrane, increase oxidative stress, and halt protein synthesis. We also show that low pH is important for the actions of NAC and that bacterial death occurs independently of the presence of biofilm. In addition, we show that both the acetyl and carboxylic groups play key roles in NAC functions. The results presented here provide insight into the mechanisms by which NAC dismantles biofilm and how it could be used to treat chronic wounds after debridement (NAC applied at the start of culture) or without debridement (NAC applied when biofilm is already formed). This approach can be taken to develop biofilm from microbiome taken directly from human chronic wounds to test molecules that could be effective for the treatment of specific biofilm compositions.

RevDate: 2020-02-21

Liu W, Zhang R, Shu R, et al (2020)

Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing.

BioMed research international, 2020:7828392.

A lot of previous studies have recently reported that the gut microbiota influences the development of colorectal cancer (CRC) in Western countries, but the role of the gut microbiota in Chinese population must be investigated fully. The goal of this study was to determine the role of the gut microbiome in the initiation and development of CRC. We collected fecal samples of 206 Chinese individuals: 59 with polyp (group P), 54 with adenoma (group A), 51 with colorectal cancer (group CC), and 42 healthy controls (group HC).16S ribosomal RNA (rRNA) was used to compare the microbiota community structures among healthy controls, patients with polyp, and those with adenoma or colorectal cancer. Our study proved that intestinal flora, as a specific indicator, showed significant differences in its diversity and composition. Sobs, Chao, and Ace indexes of group CC were significantly lower than those of the healthy control group (CC group: Sobs, Chao, and Ace indexes were 217.3 ± 69, 4265.1 ± 80.7, and 268.6 ± 78.1, respectively; HC group: Sobs, Chao, and Ace indexes were 228.8 ± 44.4, 272.9 ± 58.6, and 271.9 ± 57.2, respectively). When compared with the healthy individuals, the species richness and diversity of intestinal flora in patients with colorectal cancer were significantly reduced: PCA and PCoA both revealed that a significant separation in bacterial community composition between the CC group and HC group (with PCA using the first two principal component scores of PC1 14.73% and PC2 10.34% of the explained variance, respectively; PCoA : PC1 = 14%, PC2 = 9%, PC3 = 6%). Wilcox tests was used to analyze differences between the two groups, it reveals that Firmicutes (P=0.000356), Fusobacteria (P=0.000001), Proteobacteria (P=0.000796), Spirochaetes (P=0.013421), Synergistetes (P=0.005642) were phyla with significantly different distributions between cases and controls. The proportion of microorganism composition is varying at different stages of colon cancer development: Bacteroidetes (52.14%) and Firmicutes (35.88%) were enriched in the healthy individuals; on the phylum level, the abundance of Bacteroidetes (52.14%-53.92%-52.46%-47.06%) and Firmicutes (35.88%-29.73%-24.27%-25.36%) is decreasing with the development of health-polyp-adenomas-CRC, and the abundance of Proteobacteria (9.33%-12.31%-16.51%-22.37%) is increasing. PCA and PCOA analysis showed there was no significant (P < 0.05) difference in species similarity between precancerous and carcinogenic states. However, the composition of the microflora in patients with precancerous lesions (including patients with adenoma and polyp) was proved to have no significant disparity (P < 0.05). Our study provides insights into new angles to dig out potential biomarkers in diagnosis and treatment of colorectal cancer and to provide scientific advice for a healthy lifestyle for the sake of gut microbiota.

RevDate: 2020-02-21

Kong XJ, Liu J, Li J, et al (2020)

Probiotics and oxytocin nasal spray as neuro-social-behavioral interventions for patients with autism spectrum disorders: a pilot randomized controlled trial protocol.

Pilot and feasibility studies, 6:20 pii:557.

Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder characterized by impairments in social interaction and communication. Oxytocin (OXT), as a neuropeptide, plays a role in emotional and social behaviors. Lactobacillus reuteri (L. reuteri) supplementation led to an OXT-dependent behavioral improvement in ASD mouse models. Despite some promising results from animal studies, little is known about the efficacy of supplementation with L. reuteri, alone or with exogenous OXT therapy, on social-behavioral functions in ASD patients. This paper presents a protocol for a pilot randomized controlled trial to evaluate the feasibility of conducting a full trial comparing oral supplementation of L. reuteri probiotics and intranasal OXT spray to placebo on the effect of social and behavioral functions in ASD patients. The study will also capture preliminary estimates of the efficacy of the proposed interventions in ASD patients.

Methods: This pilot trial is a two-staged, randomized, double-blind, placebo-controlled, parallel-group study. Throughout the study (0-24 weeks), 60 patients with ASD will be randomly assigned to receive either oral L. reuteri probiotics or placebo. In the second study stage (13-24 weeks), all participants will receive intranasal OXT spray. As primary outcomes, serum OXT levels will be assayed and social behaviors will be assessed via the Autism Behavior Checklist and the Social Responsiveness Scale which are validated questionnaires, an objective emotional facial matching test, and a new video-based eye-tracking test. Secondary outcomes include the GI-severity-index and Bristol Stool Chart to assess GI function and gut microbiome/short-chain fatty acids. All the outcomes will be assessed at baseline and weeks 12 and 24.

Discussion: This pilot study will provide important information on the feasibility of recruitment, blinding and concealment, treatment administration, tolerability and adherence, specimen collection, outcome assessment, potential adverse effects, and the preliminary efficacy on both primary and secondary outcomes. If successful, this pilot study will inform a larger randomized controlled trial fully powered to examine the efficacies of oral L. reuteri probiotics and/or intranasal OXT spray on social-behavioral improvement in ASD patients.

Trial registration: ClinicalTrials.gov, NCT03337035. Registered 8 November 2017.

RevDate: 2020-02-21

Koninckx PR, Ussia A, Tahlak M, et al (2019)

Infection as a potential cofactor in the genetic-epigenetic pathophysiology of endometriosis: a systematic review.

Facts, views & vision in ObGyn, 11(3):209-216.

Background: The genetic-epigenetic theory postulates that endometriosis is triggered by a cumulative set of genetic-epigenetic (GE) incidents. Pelvic and upper genital tract infection might induce GE incidents and thus play a role in the pathogenesis of endometriosis. Thus, this article aims to review the association of endometriosis with upper genital tract and pelvic infections.

Methods: Pubmed, Scopus and Google Scholar were searched for 'endometriosis AND (infection OR PID OR bacteria OR viruses OR microbiome OR microbiota)', for 'reproductive microbiome' and for 'reproductive microbiome AND endometriosis', respectively. All 384 articles, the first 120 'best match' articles in PubMed for 'reproductive microbiome' and the first 160 hits in Google Scholar for 'reproductive microbiome AND endomytriosis' were hand searched for data describing an association between endometriosis and bacterial, viral or other infections. All 31 articles found were included in this manuscript.

Results: Women with endometriosis have a significantly increased risk of lower genital tract infection, chronic endometritis, severe PID and surgical site infections after hysterectomy. They have more colony forming units of Gardnerella, Streptococcus, Enterococci and Escherichia coli in the endometrium. In the cervix Atopobium is absent, but Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma are increased. They have higher concentrations of Escherichia Coli and higher concentrations of bacterial endotoxins in menstrual blood. A Shigella/Escherichia dominant stool microbiome is more frequent. The peritoneal fluid of women with endometriosis contains higher concentrations of bacterial endotoxins and an increased incidence of mollicutes and of HPV viruses. Endometriosis lesions have a specific bacterial colonisation with more frequently mollicutes (54%) and both high and medium-risk HPV infections (11%). They contain DNA with 96% homology with Shigella. In mice transplanted endometrium changes the gut microbiome while the gut microbiome influences the growth of these endometriosis lesions.

Conclusions: Endometriosis is associated with more upper genital tract and peritoneal infections. These infections might be co-factors causing GE incidents and influencing endometriosis growth.

RevDate: 2020-02-21

Rezasoltani S, Ahmadi Bashirzadeh D, Nazemalhosseini Mojarad E, et al (2020)

Signature of Gut Microbiome by Conventional and Advanced Analysis Techniques: Advantages and Disadvantages.

Middle East journal of digestive diseases, 12(1):5-11.

Gut microbiota is considered as a human organ with its own specific functions and complexity. Development of novel techniques such as shut gun sequencing, metagenomics, and next-generation sequencing (NGS) has enabled bypassing the traditional culturedependent bias and has significantly expanded our understanding of the composition, diversity, and roles of the gut microbiota in human health and diseases. Although amplicon sequencing characterizes the taxonomic composition of the gut microbiome, it is impossible to cover the direct evidence of the microbial biological functions related to the gut microbial community. Hence, the critical next step for gut microbiome studies is shifting from gene/ genome-centric analysis to mechanism-centric techniques by integrating omics data with experimental results. Realizing gut microbial diversity and their bioactive metabolites function will provide insight into the clinical application of gut microbiota in diagnoses and treatments of several diseases. In this review, we focused on explaining the conventional and advanced microbiome analysis techniques regarding gut microbiota investigation with considering the advantages and disadvantages of the platforms.

RevDate: 2020-02-21

Warda AK, de Almeida Bettio PH, Hueston CM, et al (2020)

Oral Administration of Heat-Treated Lactobacilli Modifies the Murine Microbiome and Reduces Citrobacter Induced Colitis.

Frontiers in microbiology, 11:69.

Significant evidence supports a relationship between the gut microbiome, inflammation, host response, and health, including the finding that a number of disorders are associated with disruption of the microbiome. In these disorders, a number of dietary interventions (including prebiotics, live probiotics, or heat-killed microbes) have been proposed to be curative or preventative agents. The use of heat-killed microbes has a number of benefits over living organisms, including reduced infection risk in vulnerable individuals, extended shelf life and the potential for use in combination with antimicrobial agents. We previously reported that murine chow supplemented with 5% ADR-159, a heat-treated fermentate generated by two Lactobacillus strains, altered both behavior and the microbiome of male mice. Now we show that ADR-159 fed female mice also display a similar microbiome shift as determined by 16S rDNA analysis. In particular, we observed a reduction of levels of Turicibacter and Clostridium sensu stricto. These subtle changes in the bacterial component of the microbiome were mirrored by changes in the virome. Extended consumption of the ADR-159 diet had no negative effect on general health and lipocalin 2 levels (LCN2; a proxy for inflammation), but we observed increased IL-17f and decreased IL-12α expression in the colon and decreased short chain fatty acid levels in the ADR-159 fed animals. Four weeks into the diet, half of the animals were dosed with Citrobacter to determine the effect of ADR-159 on infection and on pathogen induced colitis. Overall, our results suggest that while the ADR-159 diet does not prevent Citrobacter infection, it had an effect on Citrobacter-induced inflammation. In contrast to animals fed standard chow, ADR-159 fed animals did not show a reduction of small intestine length and increase of colon crypt depth, which occurred in control mice. These microbiological, histological, and immunological results provide evidence to support the impact of heat-treated microorganisms and their metabolites on the murine microbiome and health.

RevDate: 2020-02-21

Siddik MAB, Fotedar R, Chaklader MR, et al (2019)

Fermented Animal Source Protein as Substitution of Fishmeal on Intestinal Microbiota, Immune-Related Cytokines and Resistance to Vibrio mimicus in Freshwater Crayfish (Cherax cainii).

Frontiers in physiology, 10:1635.

A feeding trial was carried out to evaluate the effects of substitution of fishmeal (FM) by dietary poultry by-product meal, fermented by Lactobacillus casei and Saccharomyces cerevisiae on growth, intestinal health, microbial composition, immune related cytokines and disease resistance of freshwater crayfish, marron (Cherax cainii) against Vibrio mimicus. Two isonitrogenous and isocaloric diets were formulated by replacing FM protein with fermented poultry by-product meal (FPBM) protein at 0% (Control) and 75% (FPBM), and fed marron for 70 days. The results indicated no significant difference (P > 0.05) in final body weights between two groups of marron, whilst intestinal microvilli number per fold was increased in marron fed FPBM than the control. The 16S rRNA sequences revealed an increased number of Lactobacillus and Streptococcus, and decreased number of Aeromonas at genus level in the distal intestine of marron fed FPBM. Marron fed FPBM showed up-regulated expression of IL-8, IL-10, and IL-17F genes in the distal intestine. Significantly (P < 0.05) increased lysozyme and phagocytic activity, and higher survival was found in marron fed FPBM following a bacterial challenge with Vibrio mimicus. Therefore, it is concluded that FPBM is beneficial to marron in terms of microbial community, immune-related cytokines and disease resistance against V. mimicus.

RevDate: 2020-02-21

Onojighofia Tobore T (2020)

Towards a Comprehensive Theory of Obesity and a Healthy Diet: The Causal Role of Oxidative Stress in Food Addiction and Obesity.

Behavioural brain research pii:S0166-4328(19)31562-1 [Epub ahead of print].

BACKGROUND: Obesity is a major public health problem whose prevalence has been rapidly increasing in the United States (U.S), and globally. It is one of the leading causes of preventable deaths globally and contributes to the development of many diseases.

METHODS: The search was limited to studies published in English and other languages involving both animal and human subjects. Articles selected included preclinical studies, randomized clinical trials (RCTs), observational studies, meta-analyses, narrative and systemic reviews providing primary quantitative data with a measure of obesity or food addiction as an outcome. Over 5,000 articles were found in the first round of search which was filtered to 506 articles.

RESULTS: Oxidative stress plays a critical role in food addiction and is both a cause and mediator of obesity. Reactive oxygen species and oxidative stress play a direct role in adipogenesis and modulate all factors involved in obesity including genetics, sleep, gut microbiome, insulin, ghrelin, inflammation, adipokines, leptin, stress, HPA axis, and the hypothalamus.

CONCLUSIONS: The idea of thinking of combating obesity from the lens of calorie count, low carbohydrate, high or low-fat, vegetarian, vegan, plant-based, or animal-based diet is fundamentally wrong. The best way to look at obesity is through the framework of systemic redox homeostasis. Since redox homeostasis is tilted towards increased reactive oxygen species production, and excessive antioxidant intake can result in oxidative stress, an antioxidant and prooxidant food ratio of 2:3 per meal is the ideal nutritional ratio for good health and ideal weight. A ratio of 3:4 is ideal for obese individuals. Regular physical activity, good sleep quality, stress-relieving activities including yoga and meditation, maternal prenatal diet and oxidative stress promoting disease conditions are also important modulators of oxidative stress and obesity.

RevDate: 2020-02-21

Heidenreich PA, P Mamic (2020)

Is Our Diet Turning Our Gut Microbiome Against Us?.

Journal of the American College of Cardiology, 75(7):773-775.

RevDate: 2020-02-21

Miyake S, Soh M, Azman MN, et al (2020)

Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov.

Antonie van Leeuwenhoek pii:10.1007/s10482-020-01391-9 [Epub ahead of print].

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes), most notably Tenacibaculum maritimum. The impact of tenacibaculosis on the fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissues of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farmed fish. The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One isolated strain, TLL-A2T, shares 98.7% 16S rRNA gene identity with Tenacibaculum mesophilum DSM 13764T. The genome of strain TLL-A2T was sequenced and compared to that of T. mesophilum DSM 13764T. Analysis of average nucleotide identity and comparative genome analysis revealed only 92% identity between T. mesophilum DSM 13764T and strain TLL-A2T and differences between the two strains in predicted carbohydrate activating enzymes respectively. Phenotypic comparison between strain TLL-A2T and T. mesophilum DSM 13764T indicated additional differences, such as growth response at different salt concentrations. Based on molecular and phenotypic differences, strain TLL-A2T (=DSM 106434T, KCTC 62393T) is proposed as the type strain of Tenacibaculum singaporense sp. nov.

RevDate: 2020-02-21

Sanglard LP, Schmitz-Esser S, Gray KA, et al (2020)

Vaginal microbiota diverges in sows with low and high reproductive performance after porcine reproductive and respiratory syndrome vaccination.

Scientific reports, 10(1):3046 pii:10.1038/s41598-020-59955-8.

Previous studies have demonstrated evidence for a relationship between the vaginal microbiome and reproductive performance, suggesting the vaginal microbiota may serve as a tool to predict farrowing outcomes in commercial pigs. In this study, we compared the vaginal microbiome in sows with low and high farrowing performance and used it to classify animals with contrasting reproductive outcomes in commercial sows following immune challenge with porcine respiratory and reproductive syndrome (PRRS) vaccination. Eighteen microbes were differentially abundant (q-value < 0.05) between the Low and High farrowing performance groups. Among them, Campylobacter, Bacteroides, Porphyromonas, Lachnospiraceae unclassified, Prevotella, and Phascolarctobacterium were also selected in the discriminant and linear regression analyses, and could be used as potential biomarkers for reproductive outcomes. The correct classification rate in the two groups was 100%. In conclusion, this study demonstrates that vaginal microbiota collected after PRRS vaccination could be potentially used to classify sows into having low or high farrowing performance in commercial herds.

RevDate: 2020-02-21

Vogel G (2020)

Microbiome researcher accused of sexual misconduct.

Science (New York, N.Y.), 367(6480):837-838.

RevDate: 2020-02-21

Greathouse KL, White JR, Vargas AJ, et al (2020)

Author Correction: Interaction between the microbiome and TP53 in human lung cancer.

Genome biology, 21(1):41 pii:10.1186/s13059-020-01961-0.

Following publication of the original paper [1], the authors submitted a new Additional file 5 to replace the one containing formatting issues. The updated Additional file 5 is published in this correction.

RevDate: 2020-02-21

Voronina OL, Ryzhova NN, Kunda MS, et al (2020)

Characteristics of the Airway Microbiome of Cystic Fibrosis Patients.

Biochemistry. Biokhimiia, 85(1):1-10.

Microbiota as an integral component of human body is actively investigated, including by massively parallel sequencing. However, microbiomes of lungs and sinuses have become the object of scientific attention only in the last decade. For patients with cystic fibrosis, monitoring the state of respiratory tract microorganisms is essential for maintaining lung function. Here, we studied the role of sinuses and polyps in the formation of respiratory tract microbiome. We identified Proteobacteria in the sinuses and samples from the lower respiratory tract (even in childhood). In some cases, they were accompanied by potentially dangerous basidiomycetes. The presence of polyps did not affect formation of the sinus microbiome. Proteobacteria are decisive in reducing the biodiversity of lung and sinus microbiomes, which correlated with the worsening of the lung function indicators. Soft mutations in the CFTR gene contribute to the formation of safer microbiome even in heterozygotes with class I mutations.

RevDate: 2020-02-21

Zhang J, Zhao J, Jin H, et al (2020)

Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage.

Gut microbes [Epub ahead of print].

The challenging conditions encountered during long sea voyages increase the risk of health-threatening physiological and psychological stress for sailors compared with land-based workers. However, how the intestinal microbiota responds to a long sea voyage and whether there is a feasible approach for protecting gut health during sea voyage are still unexplored. Here, we designed a 30-d longitudinal study including a placebo group (n = 42) and a probiotic group (n = 40) and used shotgun metagenomic sequencing to explore the impacts of sea voyage on the intestinal microbiome of sailors. By comparing the intestinal microbiome of subjects in the placebo group at baseline (d 0) and at the end of the sea voyage (d 30), we observed an alteration in the intestinal microbiome during the long sea voyage based on the microbial structure; the results revealed an increase in the species Streptococcus gordonii and Klebsiella pneumoniae as well as a decrease in some functional features. However, the change in the microbial structure of sailors in the probiotic group between d 0 and d 30 was limited, which indicated a maintenance effect of probiotics on intestinal microbiome homeostasis. At the metagenomic strain level, a generally positive correlation was observed between probiotics and the strains belonging to Bifidobacterium longum and Bifidobacterium animalis, whereas a common negative correlation was observed between probiotics and Clostridium leptum; this result revealed the potential mechanism of maintaining intestinal microbiome homeostasis by probiotics. The present study provided a feasible approach for protecting gut health during a long sea voyage.

RevDate: 2020-02-21

Jeong DY, Daily J, Lee G, et al (2020)

Short-term fermented soybeans with Bacillus amyloliquefaciens potentiated insulin secretion capacity and improving gut microbiome diversity and intestinal integrity to alleviate type 2 diabetic symptoms.

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

We determined that consuming chungkookjang fermented by Bacillus subtilis(BS) or Bacillus amyloliquefaciens(BA) alleviated hyperglycemia in partially pancreatectomized(Px) rats, an Asian type 2 diabetic(T2D) animal model. Px rats had deteriorated glucose metabolism with decreased glucose-stimulated insulin secretion and insulin sensitivity. Insulin secretion capacity was improved in the ascending order of the Px-control, positive-control(3 mg metformin/kg bw), BS(4.5% BS diet), BA(4.5% BA diet), and normal-control(sham-operated rats). BA and BS increased β-cell mass and decreased malondialdehyde contents and TNF-α expression in the islets. BA increased hepatic PPAR-α and PPAR-β similar to the positive-control. Bacillales, Lactobacillales, and Verrucomicrobiales(Akkermentia muciniphila) increased and Enterobacteriales decreased in the BA and BS compared to the Px-control. BA prevented the decrease in villi area and number of goblet cells in intestinal tissues. In conclusion, BA improved glucose regulation by potentiating insulin secretion and reducing insulin resistance while maintaining gut mucin contents by improving gut microbiota in lean T2D rats.

RevDate: 2020-02-18

Nilsson PM, Korduner J, M Magnusson (2020)

Metabolically Healthy Obesity (MHO)-New Research Directions for Personalised Medicine in Cardiovascular Prevention.

Current hypertension reports, 22(2):18 pii:10.1007/s11906-020-1027-7.

PURPOSE OF REVIEW: To discuss new findings on the heterogeneity of obesity and associated risks.

RECENT FINDINGS: Obesity is a public health problem of immense importance on a global scale. However, epidemiological findings and clinical studies have revealed that obesity is a heterogeneous phenotype and that not all obese subjects run the same risk for complications. Current research has tried to describe so-called metabolically healthy obesity (MHO), defined by lack of risk factors included in the metabolic syndrome. These subjects will not escape long-term complications, but mortality risk is not increased. However, a new definition of MHO has recently been proposed, based on the lack of hospitalisation for somatic disease for decades in middle life. MHO subjects defined in this way are characterised by being "fat and fit" and also run a lower risk of long-term complications. If MHO could be better understood, this could contribute to a more diverse clinical approach to obesity based on personalised medicine.

RevDate: 2020-02-20

Moreau CS (2020)

Symbioses among ants and microbes.

Current opinion in insect science, 39:1-5 pii:S2214-5745(20)30016-X [Epub ahead of print].

Ants have been shown to engage in symbiosis across the tree of life, although our knowledge is far from complete. These interactions range from mutualistic to parasitic with several instances of manipulation of host behavior. Nutrient contributions in these symbioses include both farming for food and nitrogen recycling by gut-associated microbes. Interestingly, the ants that are mostly likely to host diverse and likely functional gut microbial communities are those that feed on extreme diets. Although we do see many instances of symbiosis between ants and microbes, there are also examples of species without a functional gut microbiome. Symbiosis among microbes and eukaryotic hosts is common and often considered a hallmark of multicellular evolution [1]. This is true among many of the over 13000 species of ants, although symbiosis between ants and microbes are not ubiquitous. These microbial-ant symbiotic interactions span the tree of life and include microbial eukaryotes, fungi, viruses, and bacteria. These interactions range from pathogenic to mutualistic, with many relationships still not well understood. Although our knowledge of the diversity of these microbes in ants is growing rapidly, and in some cases we know the function and interaction with the host, we still have much to learn about - the little things that run the little things that run the world!

RevDate: 2020-02-20

Kim EK, Lee KA, Hyeon DY, et al (2020)

Bacterial Nucleoside Catabolism Controls Quorum Sensing and Commensal-to-Pathogen Transition in the Drosophila Gut.

Cell host & microbe pii:S1931-3128(20)30066-4 [Epub ahead of print].

Although the gut microbiome is generally symbiotic or commensal, some microbiome members become pathogenic under certain circumstances. However, the factors driving this pathogenic switch are largely unknown. Pathogenic bacteria can generate uracil that triggers host dual oxidase (DUOX) to produce antimicrobial reactive oxygen species (ROS). We show that pathogens generate uracil and ribose upon nucleoside catabolism of gut luminal uridine, which triggers not only host defenses but also inter-bacterial communication and pathogenesis in Drosophila. Uridine-derived uracil triggers DUOX-dependent ROS generation, whereas ribose induces bacterial quorum sensing (QS) and virulence gene expression. Genes implicated in nucleotide metabolism are found in pathogens but not commensal bacteria, and their genetic ablation blocks QS and the commensal-to-pathogen transition in vivo. Furthermore, commensal bacteria lack functional nucleoside catabolism, which is required to achieve gut-microbe symbiosis, but can become pathogenic by enabling nucleotide catabolism. These findings reveal molecular mechanisms governing the commensal-to-pathogen transition in different contexts of host-microbe interactions.

RevDate: 2020-02-20

Jha AR, Shmalberg J, Tanprasertsuk J, et al (2020)

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach.

PloS one, 15(2):e0227289 pii:PONE-D-19-23510.

The role of gut microbiomes as important regulators of mammalian health is increasingly recognized, although feline and canine gut microbiomes remain poorly characterized. In this proof-of-concept study, we assessed the utility of a direct-to-consumer approach to executing pet microbiome studies. We characterized the gut microbiomes of 238 pets (46 cats and 192 dogs) by generating ~11 million merged reads that were mapped to the V4 region of 16S ribosomal RNA gene at a sequencing depth of 45,806 (±22,325) reads per sample. Analyses of these reads revealed that both feline and canine gut microbiomes are dominated by three major phyla, namely Firmicutes, Proteobacteria, and Bacteroides and that alpha diversity is higher in the feline gut. In addition to interspecies differences between the feline and canine gut, we also detected appreciable intraspecies bacterial variation within the canine population. While the dogs in this dataset could be assigned to three distinct clusters based on their gut microbiome, no clustering was observed within the feline population. Integration of additional data obtained from survey questionnaires revealed that geography and body weight may be associated with canine gut microbiome composition. Furthermore, we found that both the inter and intraspecies differences are more pronounced at finer taxonomic levels, indicating that strain-level investigations may be necessary in the future. This study demonstrates that the direct-to-consumer approach overcomes existing limitations in pet microbiome research, for example, it allows collection of large numbers of pet samples. The direct-to-consumer approach has proven successful in human genomics as well as human microbiomics and this study demonstrates that by building partnerships with an engaged general public this approach can also propel the field of pet microbiomics forward.

RevDate: 2020-02-20

Bowers SJ, Vargas F, González A, et al (2020)

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome.

PloS one, 15(2):e0229001 pii:PONE-D-19-35357.

It has been established in recent years that the gut microbiome plays a role in health and disease, potentially via alterations in metabolites that influence host physiology. Although sleep disruption and gut dysbiosis have been associated with many of the same diseases, studies investigating the gut microbiome in the context of sleep disruption have yielded inconsistent results, and have not assessed the fecal metabolome. We exposed mice to five days of sleep disruption followed by four days of ad libitum recovery sleep, and assessed the fecal microbiome and fecal metabolome at multiple timepoints using 16S rRNA gene amplicons and untargeted LC-MS/MS mass spectrometry. We found global shifts in both the microbiome and metabolome in the sleep-disrupted group on the second day of recovery sleep, when most sleep parameters had recovered to baseline levels. We observed an increase in the Firmicutes:Bacteroidetes ratio, along with decreases in the genus Lactobacillus, phylum Actinobacteria, and genus Bifidobacterium in sleep-disrupted mice compared to control mice. The latter two taxa remained low at the fourth day post-sleep disruption. We also identified multiple classes of fecal metabolites that were differentially abundant in sleep-disrupted mice, some of which are physiologically relevant and commonly influenced by the microbiome. This included bile acids, and inference of microbial functional gene content suggested reduced levels of the microbial bile salt hydrolase gene in sleep-disrupted mice. Overall, this study adds to the evidence base linking disrupted sleep to the gut microbiome and expands it to the fecal metabolome, identifying sleep disruption-sensitive bacterial taxa and classes of metabolites that may serve as therapeutic targets to improve health after poor sleep.

RevDate: 2020-02-20

Chen P, Zhao M, Tang F, et al (2020)

The effect of plant compartments on the Broussonetia papyrifera-associated fungal and bacterial communities.

Applied microbiology and biotechnology pii:10.1007/s00253-020-10466-6 [Epub ahead of print].

Plants associate with numerous microbes, but little is known about how microbiome components, especially fungi, adapt to specific plant compartments. The adaptability of microbial function to the plant compartment is also not clear especially for woody species. Here, we characterized the bacterial and fungal communities in root endosphere, stems, and rhizospheres of 33 Broussonetia papyrifera seedlings, based on amplification of 16S and ITS rRNA. Results showed that the α-diversity indexes of the bacterial community were significantly different in different plant compartments and they significantly increased from stem to root endosphere to the rhizosphere, whereas those of the fungal community were similar (p > 0.05). However, the result of constrained PCoA (CPCoA) and analysis of similarity (ANOSIM) showed that both bacterial and fungal compositions were significantly affected by plant compartments (p < 0.01). In detail, the operational taxonomic units (OTUs) distribution of the bacterial community was significantly different, but 249 of 252 fungal OTUs were shared in different plant compartments. Both the bacterial and fungal compositions were significantly influenced by plant compartments, based on the result on phyla, core OTUs, and indicator OTUs level. Further, 40 of 42 enriched KEGG pathways involving the bacteria also differed significantly among plant compartments (p < 0.01). This study provides an understanding of the influence of plant compartments on the microbiome and confirms that the disperse limitation of fungal OTUs across different plant compartments is smaller. This study sheds light on how the microbial community adapts to and thrives in different plant compartments.

RevDate: 2020-02-20

Wang Q, Lu H, Zhang L, et al (2020)

Peri-implant mucositis sites with suppuration have higher microbial risk than sites without suppuration.

Journal of periodontology [Epub ahead of print].

OBJECTIVE: The aims of the present study were to compare the microbial differences between peri-implant mucositis sites with or without suppuration, and to construct a classification model with microbiota.

METHODS: Twenty-four implants with peri-implant mucositis were divided into suppuration (SUP) group and non-suppuration (Non-SUP) group. Clinical assessments of bleeding index (BI), probing depth (PD), suppuration following probing (SUP) were recorded. Submucosal samples were collected from mesiobuccal sites and distobuccal sites, and analyzed by 16S rRNA gene sequencing. Generalized linear mixed model was used to adjust intraindividual correlation.

RESULTS: It was demonstrated that the microbial richness was lower in SUP group. The relative abundance of some pathogenic taxa, such as Fusobacterium, Tannerella, and Peptostreptococcus, were significantly higher in SUP group than Non-SUP group. In addition, SUP group had less Gram-positive bacteria, aerobic bacteria, and more metabolic pathway related to life activity. The classification model constructed with 12 genera got a 100% accuracy in identifying sites with or without suppuration.

CONCLUSIONS: The results from this study demonstrate a higher pathogenicity of microbiome at peri-implant mucositis sites with suppuration than without suppuration, which supports suppuration as a clinical indicator for higher microbial risk. This article is protected by copyright. All rights reserved.

RevDate: 2020-02-20

Grosse CS, Christophersen CT, Devine A, et al (2020)

The role of a plant-based diet in the pathogenesis, etiology and management of the Inflammatory Bowel Diseases.

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

Introduction: Inflammatory Bowel Disease (IBD) carries a significant burden on an individual's quality-of-life and on the healthcare system. The majority of patients use dietary modifications to manage their symptoms, despite limited research to support these changes. There is emerging data that a plant-based diet will be of benefit to IBD patients.Areas covered: A literature review on the pathogenesis and potential benefits of dietary management of IBD.Expert opinion: A Westernized diet has been associated with IBD risk and relapse; hence a plant-based diet may be of benefit to IBD patients through reducing inflammation and restoring symbiosis. Dietary therapy can be an important adjunct therapy, however, better quality studies are still required.

RevDate: 2020-02-20

Bresalier RS, RS Chapkin (2020)

Human Microbiome in Health and Disease: The Good, the Bad, and the Bugly.

RevDate: 2020-02-20

Tabrett A, MW Horton (2020)

The influence of host genetics on the microbiome.

F1000Research, 9:.

It is well understood that genetic differences among hosts contribute to variation in pathogen susceptibility and the ability to associate with symbionts. However, it remains unclear just how influential host genes are in shaping the overall microbiome. Studies of both animal and plant microbial communities indicate that host genes impact species richness and the abundances of individual taxa. Analyses of beta diversity (that is, overall similarity), on the other hand, often conclude that hosts play a minor role in shaping microbial communities. In this review, we discuss recent attempts to identify the factors that shape host microbial communities and whether our understanding of these communities is affected by the traits chosen to represent them.

RevDate: 2020-02-20

Brown JJ, Mihaljevic JR, Des Marteaux L, et al (2020)

Metacommunity theory for transmission of heritable symbionts within insect communities.

Ecology and evolution, 10(3):1703-1721 pii:ECE35754.

Microbial organisms are ubiquitous in nature and often form communities closely associated with their host, referred to as the microbiome. The microbiome has strong influence on species interactions, but microbiome studies rarely take interactions between hosts into account, and network interaction studies rarely consider microbiomes. Here, we propose to use metacommunity theory as a framework to unify research on microbiomes and host communities by considering host insects and their microbes as discretely defined "communities of communities" linked by dispersal (transmission) through biotic interactions. We provide an overview of the effects of heritable symbiotic bacteria on their insect hosts and how those effects subsequently influence host interactions, thereby altering the host community. We suggest multiple scenarios for integrating the microbiome into metacommunity ecology and demonstrate ways in which to employ and parameterize models of symbiont transmission to quantitatively assess metacommunity processes in host-associated microbial systems. Successfully incorporating microbiota into community-level studies is a crucial step for understanding the importance of the microbiome to host species and their interactions.

RevDate: 2020-02-20

Carey RM, Rajasekaran K, Seckar T, et al (2020)

The virome of HPV-positive tonsil squamous cell carcinoma and neck metastasis.

Oncotarget, 11(3):282-293 pii:27436.

Oropharyngeal squamous cell carcinoma (OPSCC) represents the most common HPV-related malignancy in the United States with increasing incidence. There is heterogeneity between the behavior and response to treatment of HPV-positive oropharyngeal squamous cell carcinoma that may be linked to the tumor virome. In this prospective study, a pan-pathogen microarray (PathoChip) was used to determine the virome of early stage, p16-positive OPSCC and neck metastasis treated with transoral robotic surgery (TORS) and neck dissection. The virome findings of primary tumors and neck lymph nodes were correlated with clinical data to determine if specific organisms were associated with clinical outcomes. A total of 114 patients were enrolled in the study. Double-stranded DNA viruses, specifically Papillomaviridae, showed the highest hybridization signal (viral copies) across all viral families in the primary and positive lymph node samples. High hybridization signals were also detected for signatures of Baculoviridae, Reoviridae, Siphoviridae, Myoviridae, and Polydnaviridae in most of the cancer specimens, including the lymph nodes without cancer present. Across all HPV signatures, HPV16 and 18 had the highest average hybridization signal index and prevalence. To our knowledge, this is the first study that has identified the viral signatures of OPSCC tumors. This will serve as a foundation for future research investigating the role of the virome in OPSCC. Further investigation into the OPSCC microbiome and its variations may allow for improved appreciation of the impact of microbial dysbiosis on risk stratification, oncologic outcomes, and treatment response which has been shown in other cancer sites.

RevDate: 2020-02-20

Gude S, Pinçe E, Taute KM, et al (2020)

Bacterial coexistence driven by motility and spatial competition.

Nature pii:10.1038/s41586-020-2033-2 [Epub ahead of print].

Elucidating elementary mechanisms that underlie bacterial diversity is central to ecology1,2 and microbiome research3. Bacteria are known to coexist by metabolic specialization4, cooperation5 and cyclic warfare6-8. Many species are also motile9, which is studied in terms of mechanism10,11, benefit12,13, strategy14,15, evolution16,17 and ecology18,19. Indeed, bacteria often compete for nutrient patches that become available periodically or by random disturbances2,20,21. However, the role of bacterial motility in coexistence remains unexplored experimentally. Here we show that-for mixed bacterial populations that colonize nutrient patches-either population outcompetes the other when low in relative abundance. This inversion of the competitive hierarchy is caused by active segregation and spatial exclusion within the patch: a small fast-moving population can outcompete a large fast-growing population by impeding its migration into the patch, while a small fast-growing population can outcompete a large fast-moving population by expelling it from the initial contact area. The resulting spatial segregation is lost for weak growth-migration trade-offs and a lack of virgin space, but is robust to population ratio, density and chemotactic ability, and is observed in both laboratory and wild strains. These findings show that motility differences and their trade-offs with growth are sufficient to promote diversity, and suggest previously undescribed roles for motility in niche formation and collective expulsion-containment strategies beyond individual search and survival.

RevDate: 2020-02-20

Darcy JL, Washburne AD, Robeson MS, et al (2020)

A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome.

The ISME journal pii:10.1038/s41396-020-0613-7 [Epub ahead of print].

Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example, species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e., nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the datasets we analyzed showed statistically significant phylogenetic overdispersion.

RevDate: 2020-02-20

Helmersen K, HV Aamot (2020)

DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing.

Scientific reports, 10(1):2985 pii:10.1038/s41598-020-59957-6.

Identification of bacteria causing tissue infections can be comprehensive and, in the cases of non- or slow-growing bacteria, near impossible with conventional methods. Performing shotgun metagenomic sequencing on bacterial DNA extracted directly from the infected tissue may improve time to diagnosis and targeted treatment considerably. However, infected tissue consists mainly of human DNA (hDNA) which hampers bacterial identification. In this proof of concept study, we present a modified version of the Ultra-Deep Microbiome Prep kit for DNA extraction procedure, removing additional human DNA. Tissue biopsies from 3 patients with orthopedic implant-related infections containing varying degrees of Staphylococcus aureus were included. Subsequent DNA shotgun metagenomic sequencing using Oxford Nanopore Technologies' (ONT) MinION platform and ONTs EPI2ME WIMP and ARMA bioinformatic workflows for microbe and antibiotic resistance genes identification, respectively. The modified DNA extraction protocol led to an additional ~10-fold reduction of human DNA while preserving S. aureus DNA. Including the DNA sequencing and bioinformatics analyses, the presented protocol has the potential of identifying the infection-causing pathogen in infected tissue within 7 hours after biopsy. However, due to low number of S. aureus reads, positive identification of antibiotic resistance genes was not possible.

RevDate: 2020-02-20

Moretó M, Miró L, Amat C, et al (2020)

Dietary supplementation with spray-dried porcine plasma has prebiotic effects on gut microbiota in mice.

Scientific reports, 10(1):2926 pii:10.1038/s41598-020-59756-z.

In animal models of inflammation and in farm animals, dietary inclusion of spray-dried porcine plasma (SDP) reduces mucosal inflammation. Here, we study whether these effects could be mediated by changes in the intestinal microbiota and if these changes are similar to those induced by oral antibiotics. Weaned 21-day-old C57BL/6 mice were divided into 3 groups: the CTL group, fed the control diet; the COL group, administered low doses of neomycin and colistin; and the SDP group, supplemented with 8% SDP. After 14 days, analysis of the fecal microbiome showed that the microbiota profiles induced by SDP and the antibiotics were very different, thus, SDP has prebiotic rather than antibiotic effects. At the phylum level, SDP stimulated the presence of Firmicutes, considerably increasing the lactobacilli population. It also enhanced the growth of species involved in regulatory T-lymphocyte homeostasis and restoration of the mucosal barrier, as well as species negatively correlated with expression of pro-inflammatory cytokines. At the mucosal level, expression of toll-like receptors Tlr2, Tlr4 and Tlr9, and mucous-related genes Muc2 and Tff3 with regulatory and barrier stability functions, were increased. SDP also increased expression of Il-10 and Tgf-β, as well as markers of macrophages and dendritic cells eventually promoting an immune-tolerant environment.

RevDate: 2020-02-20

Hernandez-Sanabria E, Heiremans E, Calatayud Arroyo M, et al (2020)

Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation.

NPJ biofilms and microbiomes, 6(1):9 pii:10.1038/s41522-020-0119-0.

Celecoxib has been effective in the prevention and treatment of chronic inflammatory disorders through inhibition of altered cyclooxygenase-2 (COX-2) pathways. Despite the benefits, continuous administration may increase risk of cardiovascular events. Understanding microbiome-drug-host interactions is fundamental for improving drug disposition and safety responses of colon-targeted formulations, but little information is available on the bidirectional interaction between individual microbiomes and celecoxib. Here, we conducted in vitro batch incubations of human faecal microbiota to obtain a mechanistic proof-of-concept of the short-term impact of celecoxib on activity and composition of colon bacterial communities. Celecoxib-exposed microbiota shifted metabolic activity and community composition, whereas total transcriptionally active bacterial population was not significantly changed. Butyrate production decreased by 50% in a donor-dependent manner, suggesting that celecoxib impacts in vitro fermentation. Microbiota-derived acetate has been associated with inhibition of cancer markers and our results suggest uptake of acetate for bacterial functions when celecoxib was supplied, which potentially favoured bacterial competition for acetyl-CoA. We further assessed whether colon microbiota modulates anti-inflammatory efficacy of celecoxib using a simplified inflammation model, and a novel in vitro simulation of the enterohepatic metabolism. Celecoxib was responsible for only 5% of the variance in bacterial community composition but celecoxib-exposed microbiota preserved barrier function and decreased concentrations of IL-8 and CXCL16 in a donor-dependent manner in our two models simulating gut inflammatory milieu. Our results suggest that celecoxib-microbiome-host interactions may not only elicit adaptations in community composition but also in microbiota functionality, and these may need to be considered for guaranteeing efficient COX-2 inhibition.

RevDate: 2020-02-20

Takahashi S, Luo Y, Ranjit S, et al (2020)

Bile Acid Sequestration Reverses Liver Injury and Prevents Progression of NASH in Western Diet-Fed Mice.

The Journal of biological chemistry pii:RA119.011913 [Epub ahead of print].

Non-alcoholic fatty liver disease (NAFLD) is a rapidly rising problem in the 21st century and is a leading cause of chronic liver disease that can lead to end-stage liver diseases, including cirrhosis and hepatocellular cancer. Despite this rising epidemic, no pharmacological treatment has yet been established to treat this disease. The rapidly increasing prevalence of NAFLD and its aggressive form, nonalcoholic steatohepatitis (NASH), requires novel therapeutic approaches to prevent disease progression. Alterations in microbiome dynamics and dysbiosis play an important role in liver disease, and these may represent targetable pathways to treat liver disorders. Improving microbiome properties or restoring normal bile acid metabolism may prevent or slow the progression of liver diseases such as NASH. Importantly, aberrant systemic circulation of bile acids can greatly disrupt metabolic homeostasis. Bile acid sequestrants (BAS) are orally administered polymers that bind bile acids in the intestine forming nonabsorbable complexes. BAS interrupts intestinal reabsorption of bile acids, decreasing in their circulating levels. We determined that treatment with the bile acid sequestrant sevelamer reversed the liver injury and prevented the progression of NASH, including steatosis, inflammation, and fibrosis in a western diet-induced NASH mouse model. Metabolomics and microbiome analysis revealed that this beneficial effect is associated with changes in the microbiota population and bile acid composition, including reversing microbiota complexity in cecum by increasing Lactobacillus and decreased Desulfovibrio. The net effect of these changes was improvement in liver function and markers of liver injury, and the positive effects of reversal of insulin resistance.

RevDate: 2020-02-20

Meslier V, Laiola M, Roager HM, et al (2020)

Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake.

Gut pii:gutjnl-2019-320438 [Epub ahead of print].

OBJECTIVES: This study aimed to explore the effects of an isocaloric Mediterranean diet (MD) intervention on metabolic health, gut microbiome and systemic metabolome in subjects with lifestyle risk factors for metabolic disease.

DESIGN: Eighty-two healthy overweight and obese subjects with a habitually low intake of fruit and vegetables and a sedentary lifestyle participated in a parallel 8-week randomised controlled trial. Forty-three participants consumed an MD tailored to their habitual energy intakes (MedD), and 39 maintained their regular diets (ConD). Dietary adherence, metabolic parameters, gut microbiome and systemic metabolome were monitored over the study period.

RESULTS: Increased MD adherence in the MedD group successfully reprogrammed subjects' intake of fibre and animal proteins. Compliance was confirmed by lowered levels of carnitine in plasma and urine. Significant reductions in plasma cholesterol (primary outcome) and faecal bile acids occurred in the MedD compared with the ConD group. Shotgun metagenomics showed gut microbiome changes that reflected individual MD adherence and increase in gene richness in participants who reduced systemic inflammation over the intervention. The MD intervention led to increased levels of the fibre-degrading Faecalibacterium prausnitzii and of genes for microbial carbohydrate degradation linked to butyrate metabolism. The dietary changes in the MedD group led to increased urinary urolithins, faecal bile acid degradation and insulin sensitivity that co-varied with specific microbial taxa.

CONCLUSION: Switching subjects to an MD while maintaining their energy intake reduced their blood cholesterol and caused multiple changes in their microbiome and metabolome that are relevant in future strategies for the improvement of metabolic health.

RevDate: 2020-02-20

Brial F, Alzaid F, Sonomura K, et al (2020)

The Natural Metabolite 4-Cresol Improves Glucose Homeostasis and Enhances β-Cell Function.

Cell reports pii:S2211-1247(20)30091-7 [Epub ahead of print].

Exposure to natural metabolites contributes to the risk of cardiometabolic diseases (CMDs). Through metabolome profiling, we identify the inverse correlation between serum concentrations of 4-cresol and type 2 diabetes. The chronic administration of non-toxic doses of 4-cresol in complementary preclinical models of CMD reduces adiposity, glucose intolerance, and liver triglycerides, enhances insulin secretion in vivo, stimulates islet density and size, and pancreatic β-cell proliferation, and increases vascularization, suggesting activated islet enlargement. In vivo insulin sensitivity is not affected by 4-cresol. The incubation of mouse isolated islets with 4-cresol results in enhanced insulin secretion, insulin content, and β-cell proliferation of a magnitude similar to that induced by GLP-1. In both CMD models and isolated islets, 4-cresol is associated with the downregulated expression of the kinase DYRK1A, which may mediate its biological effects. Our findings identify 4-cresol as an effective regulator of β-cell function, which opens up perspectives for therapeutic applications in syndromes of insulin deficiency.

RevDate: 2020-02-20

Barcik W, Boutin RCT, Sokolowska M, et al (2020)

The Role of Lung and Gut Microbiota in the Pathology of Asthma.

Immunity, 52(2):241-255.

Asthma is a common chronic respiratory disease affecting more than 300 million people worldwide. Clinical features of asthma and its immunological and molecular etiology vary significantly among patients. An understanding of the complexities of asthma has evolved to the point where precision medicine approaches, including microbiome analysis, are being increasingly recognized as an important part of disease management. Lung and gut microbiota play several important roles in the development, regulation, and maintenance of healthy immune responses. Dysbiosis and subsequent dysregulation of microbiota-related immunological processes affect the onset of the disease, its clinical characteristics, and responses to treatment. Bacteria and viruses are the most extensively studied microorganisms relating to asthma pathogenesis, but other microbes, including fungi and even archaea, can potently influence airway inflammation. This review focuses on recently discovered connections between lung and gut microbiota, including bacteria, fungi, viruses, and archaea, and their influence on asthma.

RevDate: 2020-02-20

Lewin-Epstein O, L Hadany (2020)

Host-microbiome coevolution can promote cooperation in a rock-paper-scissors dynamics.

Proceedings. Biological sciences, 287(1920):20192754.

Cooperation is a fundamental behaviour observed in all forms of life. The evolution of cooperation has been widely studied, but almost all theories focused on the cooperating individual and its genes. We suggest a different approach, taking into account the microbes carried by the interacting individuals. Accumulating evidence reveals that microbes can affect their host's well-being and behaviour, yet hosts can evolve mechanisms to resist the manipulations of their microbes. We thus propose that coevolution of microbes with their hosts may favour microbes that induce their host to cooperate. Using computational modelling, we show that microbe-induced cooperation can evolve and be maintained in a wide range of conditions, including when facing hosts' resistance to the microbial effect. We find that host-microbe coevolution leads the population to a rock-paper-scissors dynamics that enables maintenance of cooperation in a polymorphic state. Our results suggest a mechanism for the evolution and maintenance of cooperation that may be relevant to a wide variety of organisms, including cases that are difficult to explain by current theories. This study provides a new perspective on the coevolution of hosts and their microbiome, emphasizing the potential role of microbes in shaping their host's behaviour.

RevDate: 2020-02-20

Bor B, Collins AJ, Murugkar PP, et al (2020)

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts.

Journal of dental research [Epub ahead of print].

Oral microbiome research has moved from asking "Who's there?" to "What are they doing?" Understanding what microbes "do" involves multiple approaches, including obtaining genomic information and examining the interspecies interactions. Recently we isolated a human oral Saccharibacteria (TM7) bacterium, HMT-952, strain TM7x, which is an ultrasmall parasite of the oral bacterium Actinomyces odontolyticus. The host-parasite interactions, such as phage-bacterium or Saccharibacteria-host bacterium, are understudied areas with large potential for insight. The Saccharibacteria phylum is a member of Candidate Phyla Radiation, a large lineage previously devoid of cultivated members. However, expanding our understanding of Saccharibacteria-host interactions requires examining multiple phylogenetically distinct Saccharibacteria-host pairs. Here we report the isolation of 3 additional Saccharibacteria species from the human oral cavity in binary coculture with their bacterial hosts. They were obtained by filtering ultrasmall Saccharibacteria cells free of other larger bacteria and inoculating them into cultures of potential host bacteria. The binary cocultures obtained could be stably passaged and studied. Complete closed genomes were obtained and allowed full genome analyses. All have small genomes (<1 Mb) characteristic of parasitic species and dramatically limited de novo synthetic pathway capabilities but include either restriction modification or CRISPR-Cas systems as part of an innate defense against foreign DNA. High levels of gene synteny exist among Saccharibacteria species. Having isolates growing in coculture with their hosts allowed time course studies of growth and parasite-host interactions by phase contrast, fluorescence in situ hybridization, and scanning electron microscopy. The cells of the 4 oral Saccharibacteria species are ultrasmall and could be seen attached to their larger Actinobacteria hosts. Parasite attachment appears to lead to host cell death and lysis. The successful cultivation of Saccharibacteria species has significantly expanded our understanding of these ultrasmall Candidate Phyla Radiation bacteria.

RevDate: 2020-02-20

Ebersole J, Kirakodu S, Chen J, et al (2020)

Oral Microbiome and Gingival Transcriptome Profiles of Ligature-Induced Periodontitis.

Journal of dental research [Epub ahead of print].

This investigation evaluated the relationship of the oral microbiome and gingival transcriptome in health and periodontitis in nonhuman primates (Macaca mulatta). Subgingival plaque samples and gingival biopsies were collected from healthy sites and at sites undergoing ligature-induced periodontitis. Microbial samples were analyzed with 16S amplicon sequencing to identify bacterial profiles in young (3 to 7 y) and adult (12 to 23 y) animals. The gingival transcriptome was determined with a microarray analysis and focused on the expression level of 452 genes that are associated with the development of inflammation and innate and adaptive immune responses. Of the 396 total operational taxonomic units (OTUs) identified across the samples, 81.8% were detected in the young group and 99.5% in the adult group. Nevertheless, 58 of the OTUs composed 88% of the signal in adults, and 49 OTUs covered 91% of the OTU readouts in the young group. Correlation analyses between the microbiome members and specific gingival genes showed a high number of significant bacteria-gene correlations in the young healthy tissues, which decreased by 75% in diseased tissues. In contrast, these correlations increased by 2.5-fold in diseased versus healthy tissues of adult animals. Complexes of bacteria were delineated that related to specific sets of immune genes, differing in health and disease and in the young versus adult animals. The correlated gene profiles demonstrated selected pathway overrepresentation related to particular bacterial complexes. These results provide novel insights into microbiome changes with disease and the relationship of these changes to specific gene profiles and likely biologic activities occurring in healthy and diseased gingival tissues in this human-like periodontitis model.

RevDate: 2020-02-20

Kawasaki K, Ohya K, Omatsu T, et al (2020)

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana.

Microorganisms, 8(2): pii:microorganisms8020265.

The grasscutter (also known as the greater cane rat; Thryonomys swinderianus) is a large rodent native to West Africa that is currently under domestication process for meat production. However, little is known about the physiology of this species. In the present study, aiming to provide information about gut microbiota of the grasscutter and better understand its physiology, we investigated the intestinal microbiota of grasscutters and compared it with that of other livestock (cattle, goat, rabbit, and sheep) using 16S rRNA metagenomics analysis. Similar to the other herbivorous animals, bacteria classified as Bacteroidales, Clostridiales, Ruminococcaceae, and Lachnospiraceae were abundant in the microbiome of grasscutters. However, Prevotella and Treponema bacteria, which have fiber fermentation ability, were especially abundant in grasscutters, where the relative abundance of these genera was higher than that in the other animals. The presence of these genera might confer grasscutters the ability to easily breakdown dietary fibers. Diets for grasscutters should be made from ingredients not consumed by humans to avoid competition for resources and the ability to digest fibers may allow the use of fiber-rich feed materials not used by humans. Our findings serve as reference and support future studies on changes in the gut microbiota of the grasscutter as domestication progresses in order to establish appropriate feeding methods and captivity conditions.

RevDate: 2020-02-20

Benedetti F, Cocchi F, Latinovic OS, et al (2020)

Role of Mycoplasma Chaperone DnaK in Cellular Transformation.

International journal of molecular sciences, 21(4): pii:ijms21041311.

Studies of the human microbiome have elucidated an array of complex interactions between prokaryotes and their hosts. However, precise bacterial pathogen-cancer relationships remain largely elusive, although several bacteria, particularly those establishing persistent intra-cellular infections, like mycoplasmas, can alter host cell cycles, affect apoptotic pathways, and stimulate the production of inflammatory substances linked to DNA damage, thus potentially promoting abnormal cell growth and transformation. Consistent with this idea, in vivo experiments in several chemically induced or genetically deficient mouse models showed that germ-free conditions reduce colonic tumor formation. We demonstrate that mycoplasma DnaK, a chaperone protein belonging to the Heath shock protein (Hsp)-70 family, binds Poly-(ADP-ribose) Polymerase (PARP)-1, a protein that plays a critical role in the pathways involved in recognition of DNA damage and repair, and reduces its catalytic activity. It also binds USP10, a key p53 regulator, reducing p53 stability and anti-cancer functions. Finally, we showed that bystander, uninfected cells take up exogenous DnaK-suggesting a possible paracrine function in promoting cellular transformation, over and above direct mycoplasma infection. We propose that mycoplasmas, and perhaps certain other bacteria with closely related DnaK, may have oncogenic activity, mediated through the inhibition of DNA repair and p53 functions, and may be involved in the initiation of some cancers but not necessarily involved nor necessarily even be present in later stages.

RevDate: 2020-02-20

Liu K, Zhang Y, Li Q, et al (2020)

Ethnic Differences Shape the Alpha but Not Beta Diversity of Gut Microbiota from School Children in the Absence of Environmental Differences.

Microorganisms, 8(2): pii:microorganisms8020254.

Although the human gut microbiome is shaped by factors such as diet, environment, and genetic background, most studies investigating the relationship between ethnicity and microbiota have compared groups living in separate geographical locations. To isolate the effects of ethnicity on microbial diversity by minimizing environmental differences, we selected 143 school children from Han, Tibetan, and Hui populations from the same town on the Qinghai-Tibetan Plateau for fecal microbiome 16S rDNA sequencing. We characterized the diversity, identified signature taxa, and performed correlation analysis between diet and community composition. Firmicutes (47.61%) and Bacteroidetes (38.05%) were dominant phyla among the three ethnic groups; seven genera showed significant differences in relative abundance. Tibetan populations had a higher relative abundance of Oscillibacter and Barnesiella, compared with Han and Hui populations. Alpha diversity analyses (observed species, ACE, and Shannon indices) showed that the Tibetan population had the highest diversity compared to the Hui and Han groups, whereas beta diversity analysis revealed no significant differences between groups. The consumption of grains, milk, eggs, and fruits were positively correlated with specific taxa. Under similar environments and diet, ethnic background significantly contributed to differences in alpha diversity but not beta diversity of gut microbiota.

RevDate: 2020-02-19

Bersani FS, Mellon SH, Lindqvist D, et al (2020)

Novel Pharmacological Targets for Combat PTSD-Metabolism, Inflammation, The Gut Microbiome, and Mitochondrial Dysfunction.

Military medicine, 185(Supplement_1):311-318.

INTRODUCTION: Current pharmacological treatments of post-traumatic stress disorder (PTSD) have limited efficacy. Although the diagnosis is based on psychopathological criteria, it is frequently accompanied by somatic comorbidities and perhaps "accelerated biological aging," suggesting widespread physical concomitants. Such physiological comorbidities may affect core PTSD symptoms but are rarely the focus of therapeutic trials.

METHODS: To elucidate the potential involvement of metabolism, inflammation, and mitochondrial function in PTSD, we integrate findings and mechanistic models from the DOD-sponsored "Systems Biology of PTSD Study" with previous data on these topics.

RESULTS: Data implicate inter-linked dysregulations in metabolism, inflammation, mitochondrial function, and perhaps the gut microbiome in PTSD. Several inadequately tested targets of pharmacological intervention are proposed, including insulin sensitizers, lipid regulators, anti-inflammatories, and mitochondrial biogenesis modulators.

CONCLUSIONS: Systemic pathologies that are intricately involved in brain functioning and behavior may not only contribute to somatic comorbidities in PTSD, but may represent novel targets for treating core psychiatric symptoms.

RevDate: 2020-02-19

Ozkul C, Yalinay M, T Karakan (2020)

Structural changes in gut microbiome after Ramadan fasting: a pilot study.

Beneficial microbes [Epub ahead of print].

It has been largely accepted that dietary changes have an effect on gut microbial composition. In this pilot study we hypothesised that Ramadan fasting, which can be considered as a type of time-restricted feeding may lead to changes in gut microbial composition and diversity. A total of 9 adult subjects were included in the study. Stool samples were collected before (baseline) and at the end of the Ramadan fasting (after 29 days). Following the construction of an 16S rRNA amplicon library, the V4 region was sequenced using the Illumina Miseq platform. Microbial community analysis was performed using the QIIME program. A total of 27,521 operational taxonomic units (OTUs) with a 97% similarity were determined in all of the samples. Microbial richness was significantly increased after Ramadan according to observed OTU results (P=0.016). No significant difference was found in terms of Shannon index or phylogenetic diversity metrics of alpha diversity. Microbial community structure was significantly different between baseline and after Ramadan samples according to unweighted UniFrac analysis (P=0.025). LEfSe analysis revealed that Butyricicoccus, Bacteroides, Faecalibacterium, Roseburia, Allobaculum, Eubacterium, Dialister and Erysipelotrichi were significantly enriched genera after the end of Ramadan fasting. According to random forest analysis, the bacterial species most affected by the Ramadan fasting was Butyricicoccus pullicaecorum. Despite this is a pilot study with a limited sample size; our results clearly revealed that Ramadan fasting, which represents an intermittent fasting regime, leads to compositional changes in the gut microbiota.

RevDate: 2020-02-19

Swanson KS, de Vos WM, Martens EC, et al (2020)

Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review.

Beneficial microbes [Epub ahead of print].

The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest. Research and collective initiatives to determine the composition and diversity of the human gut microbiota have increased over the past decade due to great advances in high-throughput technologies, particularly the 16S ribosomal RNA (rRNA) sequencing. Here we reviewed the application of 16S rRNA-based molecular technologies, both community wide (sequencing and phylogenetic microarrays) and targeted methodologies (quantitative PCR, fluorescent in situ hybridisation) to study the effect of chicory inulin-type fructans, NDOs and specific added fibres, such as resistant starches, on the human intestinal microbiota. Overall, such technologies facilitated the monitoring of microbiota shifts due to prebiotic/fibre consumption, though there are limited community-wide sequencing studies so far. Molecular studies confirmed the selective bifidogenic effect of fructans and galactooligosaccharides (GOS) in human intervention studies. Fructans only occasionally decreased relative abundance of Bacteroidetes or stimulated other groups. The sequencing studies for various resistant starches, polydextrose and beta-glucan showed broader effects with more and different types of gut microbial species being enhanced, often including phylotypes of Ruminococcaceae. There was substantial variation in terms of magnitude of response and in individual responses to a specific fibre or NDO which may be due to numerous factors, such as initial presence and relative abundance of a microbial type, diet, genetics of the host, and intervention parameters, such as intervention duration and fibre dose. The field will clearly benefit from a more systematic approach that will support defining the impact of prebiotics and fibres on the gut microbiome, identify biomarkers that link gut microbes to health, and address the personalised response of an individual's microbiota to prebiotics and dietary fibres.

RevDate: 2020-02-19

Mehmood MA, Zhao H, Cheng J, et al (2020)

Sclerotia of a phytopathogenic fungus restrict microbial diversity and improve soil health by suppressing other pathogens and enriching beneficial microorganisms.

Journal of environmental management, 259:109857.

Sclerotinia sclerotiorum, a notorious soil-borne pathogen of various important crops, produces numerous sclerotia to oversummer in the soil. Considering that sclerotia may also be attacked by other microbes in the soil, we hypothesized that sclerotia in soil may affect the community of soil microbes directly and/or indirectly. In this study, we inoculated sclerotia of S. sclerotiorum in soil collected from the field to observe changes in microbial diversity over three months using 16S rRNA and ITS2 sequencing techniques. Alpha diversity indices exhibited a decline in the diversity of microbial communities, while permanova results confirmed a significant difference in the microbial communities of sclerotia-amended and non-amended soil samples. In sclerotia-amended soil, fungal diversity showed enrichment of antagonists such as Clonostachys, Trichoderma, and Talaromyces and a drastic reduction in the plant pathogenic microbes compared to the non-amended soil. Sclerotia not only activated the antagonists but also enhanced the abundance of plant growth-promoting bacteria, such as Chitinophaga, Burkholderia, and Dyella. Moreover, the presence of sclerotia curtailed the growth of several notorious plant pathogenic fungi belonging to various genera such as Fusarium, Colletotrichum, Cladosporium, Athelia, Alternaria, and Macrophomina. Thus, we conclude that S. sclerotiorum when dormant in soil can reduce the diversity of soil microbes, including suppressing plant pathogens and enriching beneficial microbes. To the best of our knowledge, this is the first time a plant pathogen has been found in soil that can significantly suppress other pathogens. Our findings may provide novel cues to understand the ecology of crop pathogens in soil and maintaining soil conditions that could be beneficial for constructing a healthy soil microorganism community required for mitigating soil-borne diseases.

RevDate: 2020-02-19

Christian N, Sedio BE, Florez-Buitrago X, et al (2020)

Host affinity of endophytic fungi and the potential for reciprocal interactions involving host secondary chemistry.

American journal of botany [Epub ahead of print].

PREMISE: Interactions between fungal endophytes and their host plants present useful systems for identifying important factors affecting assembly of host-associated microbiomes. Here we investigated the role of secondary chemistry in mediating host affinity of asymptomatic foliar endophytic fungi using Psychotria spp. and Theobroma cacao (cacao) as hosts.

METHODS: First, we surveyed endophytic communities in Psychotria species in a natural common garden using culture-based methods. Then we compared differences in endophytic community composition with differences in foliar secondary chemistry in the same host species, determined by liquid chromatography-tandem mass spectrometry. Finally, we tested how inoculation with live and heat-killed endophytes affected the cacao chemical profile.

RESULTS: Despite sharing a common environment and source pool for endophyte spores, different Psychotria host species harbored strikingly different endophytic communities that reflected intrinsic differences in their leaf chemical profiles. In T. cacao, inoculation with live and heat-killed endophytes produced distinct cacao chemical profiles not found in uninoculated plants or pure fungal cultures, suggesting that endophytes, like pathogens, induce changes in secondary chemical profiles of their host plant.

CONCLUSIONS: Collectively our results suggest at least two potential processes: (1) Plant secondary chemistry influences assembly and composition of fungal endophytic communities, and (2) host colonization by endophytes subsequently induces changes in the host chemical landscape. We propose a series of testable predictions based on the possibility that reciprocal chemical interactions are a general property of plant-endophyte interactions.

RevDate: 2020-02-19

Erban T, Klimov P, Molva V, et al (2020)

Whole genomic sequencing and sex-dependent abundance estimation of Cardinium sp., a common and hyperabundant bacterial endosymbiont of the American house dust mite, Dermatophagoides farinae.

Experimental & applied acarology pii:10.1007/s10493-020-00475-5 [Epub ahead of print].

The two common species of house dust mites (HDMs), Dermatophagoides farinae and D. pteronyssinus, are major sources of allergens in human dwellings worldwide. Many allergens from HDMs have been described, but their extracts vary in immunogens. Mite strains may differ in their microbiomes, which affect mite allergen expression and contents of bacterial endotoxins. Some bacteria, such as the intracellular symbiont Cardinium, can affect both the sex ratio and biochemical pathways of mites, resulting in abundance variations of mite allergens/immunogens. Here, we investigated the bacterial microbiomes of D. farinae and D. pteronyssinus males and females using barcode 16S rDNA sequencing, qPCR, and genomic data analysis. We found a single species of Cardinium associated with D. farinae strains from the USA, China and Europe. Cardinium had high abundance relative to other bacterial taxa and represented 99% of all bacterial DNA reads from female mites from the USA. Cardinium was also abundant with respect to the number of host cells-we estimated 10.4-11.8 cells of Cardinium per single female mite cell. In a European D. farinae strain, Cardinium was more prevalent in females than in males (representing 92 and 67% of all bacterial taxa in females and males, respectively). In contrast, D. pteronyssinus lacked any Cardinium species, and the microbiomes of male and female mites were similar. We produced a Cardinium genome assembly (1.48 Mb; GenBank: PRJNA555788, GCA_007559345.1) associated with D. farinae. The ascertained ubiquity and abundance of Cardinium strongly suggest that this intracellular bacterium plays an important biological role in D. farinae.

RevDate: 2020-02-19

Kapitansky O, Giladi E, Jaljuli I, et al (2020)

Microbiota changes associated with ADNP deficiencies: rapid indicators for NAP (CP201) treatment of the ADNP syndrome and beyond.

Journal of neural transmission (Vienna, Austria : 1996) pii:10.1007/s00702-020-02155-5 [Epub ahead of print].

Activity-dependent neuroprotective protein (ADNP) and its protein snippet NAP (drug candidate CP201) regulate synapse formation and cognitive as well as behavioral functions, in part, through microtubule interaction. Given potential interactions between the microbiome and brain function, we now investigated the potential effects of the ADNP-deficient genotype, mimicking the ADNP syndrome on microbiota composition in the Adnp+/- mouse model. We have discovered a surprising robust sexually dichotomized Adnp genotype effect and correction by NAP (CP201) as follows. Most of the commensal bacterial microbiota tested were affected by the Adnp genotype and corrected by NAP treatment in a male sex-dependent manner. The following list includes all the bacterial groups tested-labeled in bold are male Adnp-genotype increased and corrected (decreased) by NAP. (1) Eubacteriaceae (EubV3), (2) Enterobacteriaceae (Entero), (3) Enterococcus genus (gEncocc), (4) Lactobacillus group (Lacto), (5) Bifidobacterium genus (BIF), (6) Bacteroides/Prevotella species (Bac), (7) Clostridium coccoides group (Coer), (8) Clostridium leptum group (Cluster IV, sgClep), and (9) Mouse intestinal Bacteroides (MIB). No similarities were found between males and females regarding sex- and genotype-dependent microbiota distributions. Furthermore, a female Adnp+/- genotype associated decrease (contrasting male increase) was observed in the Lactobacillus group (Lacto). Significant correlations were discovered between specific bacterial group loads and open-field behavior as well as social recognition behaviors. In summary, we discovered ADNP deficiency associated changes in commensal gut microbiota compositions, a sex-dependent biomarker for the ADNP syndrome and beyond. Strikingly, we discovered rapidly detected NAP (CP201) treatment-dependent biomarkers within the gut microbiota.

RevDate: 2020-02-19

Hufnagl K, Pali-Schöll I, Roth-Walter F, et al (2020)

Dysbiosis of the gut and lung microbiome has a role in asthma.

Seminars in immunopathology pii:10.1007/s00281-019-00775-y [Epub ahead of print].

Worldwide 300 million children and adults are affected by asthma. The development of asthma is influenced by environmental and other exogenous factors synergizing with genetic predisposition, and shaping the lung microbiome especially during birth and in very early life. The healthy lung microbial composition is characterized by a prevalence of bacteria belonging to the phyla Bacteroidetes, Actinobacteria, and Firmicutes. However, viral respiratory infections are associated with an abundance of Proteobacteria with genera Haemophilus and Moraxella in young children and adult asthmatics. This dysbiosis supports the activation of inflammatory pathways and contributes to bronchoconstriction and bronchial hyperresponsiveness. Exogenous factors can affect the natural lung microbiota composition positively (farming environment) or negatively (allergens, air pollutants). It is evident that also gut microbiota dysbiosis has a high influence on asthma pathogenesis. Antibiotics, antiulcer medications, and other drugs severely impair gut as well as lung microbiota. Resulting dysbiosis and reduced microbial diversity dysregulate the bidirectional crosstalk across the gut-lung axis, resulting in hypersensitivity and hyperreactivity to respiratory and food allergens. Efforts are undertaken to reconstitute the microbiota and immune balance by probiotics and engineered bacteria, but results from human studies do not yet support their efficacy in asthma prevention or treatment. Overall, dysbiosis of gut and lung seem to be critical causes of the increased emergence of asthma.

RevDate: 2020-02-19

Dworsky-Fried Z, Kerr BJ, AMW Taylor (2020)

Microbes, microglia, and pain.

Neurobiology of pain (Cambridge, Mass.), 7:100045 pii:100045.

Globally, it is estimated that one in five people suffer from chronic pain, with prevalence increasing with age. The pathophysiology of chronic pain encompasses complex sensory, immune, and inflammatory interactions within both the central and peripheral nervous systems. Microglia, the resident macrophages of the central nervous system (CNS), are critically involved in the initiation and persistence of chronic pain. Microglia respond to local signals from the CNS but are also modulated by signals from the gastrointestinal tract. Emerging data from preclinical and clinical studies suggest that communication between the gut microbiome, the community of bacteria residing within the gut, and microglia is involved in producing chronic pain. Targeted strategies that manipulate or restore the gut microbiome have been shown to reduce microglial activation and alleviate symptoms associated with inflammation. These data indicate that manipulations of the gut microbiome in chronic pain patients might be a viable strategy in improving pain outcomes. Herein, we discuss the evidence for a connection between microglia and the gut microbiome and explore the mechanisms by which commensal bacteria might influence microglial reactivity to drive chronic pain.

RevDate: 2020-02-19

Bai S, G Hou (2020)

Microbial communities on fish eggs from Acanthopagrus schlegelii and Halichoeres nigrescens at the XuWen coral reef in the Gulf of Tonkin.

PeerJ, 8:e8517 pii:8517.

Coral reefs are an important part of the ocean ecosystem and are a vital spawning ground for marine fish. Microorganisms are abundant in this environment and play a key role in the growth and development of host species. Many studies have investigated the microbial communities of fish with a focus on the intestinal microbiome of laboratory-reared adult fish. Little is known about the relationship between fish eggs and their microorganisms, especially as microbial communities relate to wild fish eggs in coral reefs. In this study, we analyzed the microbial communities of two species of coral fish eggs, Acanthopagrus schlegelii and Halichoeres nigrescens, using 16S rRNA gene amplicon sequencing technology. Pseudomonas, Archromobacter, and Serratia were the main bacterial genera associated with these fish eggs and are known to be bacteria with potentially pathogenic and spoilage effects. The microbial community structures of Acanthopagrus schlegelii and Halichoeres nigrescens eggs were separated based on the 30 most abundant operational taxonomic units (OTUs). Principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) further confirmed that the microbial communities of coral fish eggs differ by species, which may be due to host selection. A functional prediction of the microbial communities indicated that most of the microbial communities were chemoheterotrophic and involved in nitrogen cycling. Our results showed that the microbial communities of coral fish eggs were distinct by species and that key microorganisms were potentially pathogenic, leading to the spoilage of fish eggs, high mortality, and low incubation rates. This study provided new insights for understanding the relationship between microorganisms and wild fish eggs.

RevDate: 2020-02-19

Wang Y, Wang H, Cheng H, et al (2020)

Niche differentiation in the rhizosphere and endosphere fungal microbiome of wild Paris polyphylla Sm.

PeerJ, 8:e8510 pii:8510.

Background: The plant microbiome is one of the key determinants of plant health and metabolite production. The plant microbiome affects the plant's absorption of nutrient elements, improves plant tolerance to negative environmental factors, increases the accumulation of active components, and alters tissue texture. The microbial community is also important for the accumulation of secondary metabolites by plants. However, there are few studies on the niche differentiation of endophytic microorganisms of plants, especially at different elevations.

Methods: We investigated the effects of altitude on the community composition of endophytic fungal communities and the differentiation of endophytic microorganisms among different niches in Paris polyphylla Sm. The rhizosphere soil, roots, rhizomes and leaves of wild-type P. polyphylla Sm. at different altitudes were sampled, and the fungal communities of all samples were analyzed by internal transcribed spacer one amplification sequencing.

Results: The results showed that in rhizosphere soil, the number of operational taxonomic units (OTUs) that could be classified or identified decreased significantly with increasing altitude, whereas in the endosphere of plants, the total number of OTUs was higher at intermediate altitudes than other altitudes. Furthermore, the structural variability in the rhizosphere fungal community was significantly lower than that in the endophytic communities. In addition, our results confirmed the presence of niche differentiation among members of the endophytic microbial community. Finally, we also determined that the predominant genus of mycobiota in the rhizome was Cadophora. This study provides insight into the relationships between the endosphere microbiome and plants and can guide the artificial cultivation of this plant.

RevDate: 2020-02-19

Peng Q, Chen Y, Ding L, et al (2020)

Early-life intestinal microbiome in Trachemys scripta elegans analyzed using 16S rRNA sequencing.

PeerJ, 8:e8501 pii:8501.

During the early-life period, the hatchlings of red-eared slider turtles (Trachemys scripta elegans) rely on their own post-hatching internal yolk for several days before beginning to feed. The gut microbiome is critical for the adaptation of organisms to new environments, but, to date, how the microbiome taxa are assembled during early life of the turtle is unknown. In this study, the intestinal microbiome of red-eared slider hatchlings (fed on commercial particle food) was systematically analyzed at four different growth stages (0 d, 10 d, 20 d, 30 d) by a high-throughput sequencing approach. Results showed that the dominant phyla were Firmicutes (58.23%) and Proteobacteria (41.42%) at 0-day, Firmicutes (92.94%) at 10-day, Firmicutes (67.08%) and Bacteroidetes (27.17%) at 20-day, and Firmicutes (56.46%), Bacteroidetes (22.55%) and Proteobacteria (20.66%) at 30-day post-hatching. Members of the Bacteroidaceae family were absent in 0-day and 10-day turtles, but dominated in 20-day and 30-day turtles. The abundance of Clostridium also showed the highest value in 10-day turtles. The richness of the intestinal microbiomes was lower at 0-day and 30-day than that at 10-day and 20-day, while the diversity was higher at 10-day and 30-day than that at 0-day and 20-day. The results endowed the turtles with an ability to enhance their tolerance to the environment.

RevDate: 2020-02-19

Klimenko NS, Tyakht AV, Toshchakov SV, et al (2020)

Co-occurrence patterns of bacteria within microbiome of Moscow subway.

Computational and structural biotechnology journal, 18:314-322 pii:S2001-0370(19)30410-6.

Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers. Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New-York City subway microbiome. Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, "shotgun" metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology and urban design.

RevDate: 2020-02-19

Santos A, van Aerle R, Barrientos L, et al (2020)

Computational methods for 16S metabarcoding studies using Nanopore sequencing data.

Computational and structural biotechnology journal, 18:296-305 pii:S2001-0370(19)30374-5.

Assessment of bacterial diversity through sequencing of 16S ribosomal RNA (16S rRNA) genes has been an approach widely used in environmental microbiology, particularly since the advent of high-throughput sequencing technologies. An additional innovation introduced by these technologies was the need of developing new strategies to manage and investigate the massive amount of sequencing data generated. This situation stimulated the rapid expansion of the field of bioinformatics with the release of new tools to be applied to the downstream analysis and interpretation of sequencing data mainly generated using Illumina technology. In recent years, a third generation of sequencing technologies has been developed and have been applied in parallel and complementarily to the former sequencing strategies. In particular, Oxford Nanopore Technologies (ONT) introduced nanopore sequencing which has become very popular among molecular ecologists. Nanopore technology offers a low price, portability and fast sequencing throughput. This powerful technology has been recently tested for 16S rRNA analyses showing promising results. However, compared with previous technologies, there is a scarcity of bioinformatic tools and protocols designed specifically for the analysis of Nanopore 16S sequences. Due its notable characteristics, researchers have recently started performing assessments regarding the suitability MinION on 16S rRNA sequencing studies, and have obtained remarkable results. Here we present a review of the state-of-the-art of MinION technology applied to microbiome studies, the current possible application and main challenges for its use on 16S rRNA metabarcoding.

RevDate: 2020-02-19

Chen X, Krug L, Yang H, et al (2020)

Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars.

Computational and structural biotechnology journal, 18:287-295 pii:S2001-0370(19)30250-8.

Seed endophytes of crop plants have recently received increased attention due to their implications in plant health and the potential to be included in agro-biotechnological applications. While previous studies indicated that plants from the Solanaceae family harbor a highly diverse seed microbiome, genotype-specific effects on the community composition and structure remained largely unexplored. The present study revealed Enterobacteriaceae-dominated seed-endophytic communities in four Nicotiana tabacum L. cultivars originating from Brazil, China, and the USA. When the dissimilarity of bacterial communities was assessed, none of the cultivars showed significant differences in microbial community composition. Various unusual endophyte signatures were represented by Spirochaetaceae family members and the genera Mycobacterium, Clostridium, and Staphylococcus. The bacterial fraction shared by all cultivars was dominated by members of the phyla Proteobacteria and Firmicutes. In total, 29 OTUs were present in all investigated cultivars and accounted for 65.5% of the combined core microbiome reads. Cultivars from the same breeding line were shown to share a higher number of common OTUs than more distant lines. Moreover, the Chinese cultivar Yunyan 87 contained the highest number (33 taxa) of unique signatures. Our results indicate that a distinct proportion of the seed microbiome of N. tabacum remained unaffected by breeding approaches of the last century, while a substantial proportion co-diverged with the plant genotype. Moreover, they provide the basis to identify plant-specific endophytes that could be addressed for upcoming biotechnological approaches in agriculture.

RevDate: 2020-02-19

Łaniewski P, Ilhan ZE, MM Herbst-Kralovetz (2020)

The microbiome and gynaecological cancer development, prevention and therapy.

Nature reviews. Urology pii:10.1038/s41585-020-0286-z [Epub ahead of print].

The female reproductive tract (FRT), similar to other mucosal sites, harbours a site-specific microbiome, which has an essential role in maintaining health and homeostasis. In the majority of women of reproductive age, the microbiota of the lower FRT (vagina and cervix) microenvironment is dominated by Lactobacillus species, which benefit the host through symbiotic relationships. By contrast, the upper FRT (uterus, Fallopian tubes and ovaries) might be sterile in healthy individuals or contain a low-biomass microbiome with a diverse mixture of microorganisms. When dysbiosis occurs, altered immune and metabolic signalling can affect hallmarks of cancer, including chronic inflammation, epithelial barrier breach, changes in cellular proliferation and apoptosis, genome instability, angiogenesis and metabolic dysregulation. These pathophysiological changes might lead to gynaecological cancer. Emerging evidence shows that genital dysbiosis and/or specific bacteria might have an active role in the development and/or progression and metastasis of gynaecological malignancies, such as cervical, endometrial and ovarian cancers, through direct and indirect mechanisms, including modulation of oestrogen metabolism. Cancer therapies might also alter microbiota at sites throughout the body. Reciprocally, microbiota composition can influence the efficacy and toxic effects of cancer therapies, as well as quality of life following cancer treatment. Modulation of the microbiome via probiotics or microbiota transplant might prove useful in improving responsiveness to cancer treatment and quality of life. Elucidating these complex host-microbiome interactions, including the crosstalk between distal and local sites, will translate into interventions for prevention, therapeutic efficacy and toxic effects to enhance health outcomes for women with gynaecological cancers.

RevDate: 2020-02-19

Lokmer A, Aflalo S, Amougou N, et al (2020)

Response of the human gut and saliva microbiome to urbanization in Cameroon.

Scientific reports, 10(1):2856 pii:10.1038/s41598-020-59849-9.

Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.

RevDate: 2020-02-19

Kim DJ, Yang J, Seo H, et al (2020)

Colorectal cancer diagnostic model utilizing metagenomic and metabolomic data of stool microbial extracellular vesicles.

Scientific reports, 10(1):2860 pii:10.1038/s41598-020-59529-8.

Colorectal cancer (CRC) is the most common type cancers in the world. CRC occurs sporadically in the majority of cases, indicating the predominant cause of the disease are environmental factors. Diet-induced changes in gut-microbiome are recently supposed to contribute on epidemics of CRC. This study was aimed to investigate the association of metagenomics and metabolomics in gut extracellular vesicles (EVs) of CRC and healthy subjects. A total of 40 healthy volunteers and 32 patients with CRC were enrolled in this study. Metagenomic profiling by sequencing 16 S rDNA was performed for assessing microbial codiversity. We explored the small molecule metabolites using gas chromatography-time-of-flight mass spectrometry. In total, stool EVs were prepared from 40 healthy volunteers and 32 patients with CRC. Metagenomic profiling demonstrated that bacterial phyla, particularly of Firmicutes and Proteobacteria, were significantly altered in patients with colorectal cancer. Through metabolomics profiling, we determined seven amino acids, four carboxylic acids, and four fatty acids; including short-chain to long chain fatty acids that altered in the disease group. Binary logistic regression was further tested to evaluate the diagnostic performance. In summary, the present findings suggest that gut flora dysbiosis may result in alternation of amino acid metabolism, which may be correlated with the pathogenesis of CRC.

RevDate: 2020-02-19

Madhusoodanan J (2020)

News Feature: Editing the microbiome.

Proceedings of the National Academy of Sciences of the United States of America, 117(7):3345-3348.

RevDate: 2020-02-19

Groves HT, Higham SL, Moffatt MF, et al (2020)

Respiratory Viral Infection Alters the Gut Microbiota by Inducing Inappetence.

mBio, 11(1): pii:mBio.03236-19.

Respiratory viral infections are extremely common, but their impacts on the composition and function of the gut microbiota are poorly understood. We previously observed a significant change in the gut microbiota after viral lung infection. Here, we show that weight loss during respiratory syncytial virus (RSV) or influenza virus infection was due to decreased food consumption, and that the fasting of mice altered gut microbiota composition independently of infection. While the acute phase tumor necrosis factor alpha (TNF-α) response drove early weight loss and inappetence during RSV infection, this was not sufficient to induce changes in the gut microbiota. However, the depletion of CD8+ cells increased food intake and prevented weight loss, resulting in a reversal of the gut microbiota changes normally observed during RSV infection. Viral infection also led to changes in the fecal gut metabolome, with a significant shift in lipid metabolism. Sphingolipids, polyunsaturated fatty acids (PUFAs), and the short-chain fatty acid (SCFA) valerate were all increased in abundance in the fecal metabolome following RSV infection. Whether this and the impact of infection-induced anorexia on the gut microbiota are part of a protective anti-inflammatory response during respiratory viral infections remains to be determined.IMPORTANCE The gut microbiota has an important role in health and disease: gut bacteria can generate metabolites that alter the function of immune cells systemically. Understanding the factors that can lead to changes in the gut microbiome may help to inform therapeutic interventions. This is the first study to systematically dissect the pathway of events from viral lung infection to changes in gut microbiota. We show that the cellular immune response to viral lung infection induces inappetence, which in turn alters the gut microbiome and metabolome. Strikingly, there was an increase in lipids that have been associated with the resolution of disease. This opens up new paths of investigation: first, what is the (presumably secreted) factor made by the T cells that can induce inappetence? Second, is inappetence an adaptation that accelerates recovery from infection, and if so, does the microbiome play a role in this?

RevDate: 2020-02-19

Kim M, Vogtmann E, Ahlquist DA, et al (2020)

Fecal Metabolomic Signatures in Colorectal Adenoma Patients Are Associated with Gut Microbiota and Early Events of Colorectal Cancer Pathogenesis.

mBio, 11(1): pii:mBio.03186-19.

Colorectal adenomas are precancerous lesions of colorectal cancer (CRC) that offer a means of viewing the events key to early CRC development. A number of studies have investigated the changes and roles of gut microbiota in adenoma and carcinoma development, highlighting its impact on carcinogenesis. However, there has been less of a focus on the gut metabolome, which mediates interactions between the host and gut microbes. Here, we investigated metabolomic profiles of stool samples from patients with advanced adenoma (n = 102), matched controls (n = 102), and patients with CRC (n = 36). We found that several classes of bioactive lipids, including polyunsaturated fatty acids, secondary bile acids, and sphingolipids, were elevated in the adenoma patients compared to the controls. Most such metabolites showed directionally consistent changes in the CRC patients, suggesting that those changes may represent early events of carcinogenesis. We also examined gut microbiome-metabolome associations using gut microbiota profiles in these patients. We found remarkably strong overall associations between the microbiome and metabolome data and catalogued a list of robustly correlated pairs of bacterial taxa and metabolomic features which included signatures of adenoma. Our findings highlight the importance of gut metabolites, and potentially their interplay with gut microbes, in the early events of CRC pathogenesis.IMPORTANCE Colorectal adenomas are precursors of CRC. Recently, the gut microbiota, i.e., the collection of microbes residing in our gut, has been recognized as a key player in CRC development. There have been a number of gut microbiota profiling studies for colorectal adenoma and CRC; however, fewer studies have considered the gut metabolome, which serves as the chemical interface between the host and gut microbiota. Here, we conducted a gut metabolome profiling study of colorectal adenoma and CRC and analyzed the metabolomic profiles together with paired microbiota composition profiles. We found several chemical signatures of colorectal adenoma that were associated with some gut microbes and potentially indicative of future CRC. This study highlights potential early-driver metabolites in CRC pathogenesis and guides further targeted experiments and thus provides an important stepping stone toward developing better CRC prevention strategies.

RevDate: 2020-02-19

Röttjers L, K Faust (2020)

manta: a Clustering Algorithm for Weighted Ecological Networks.

mSystems, 5(1): pii:5/1/e00903-19.

Microbial network inference and analysis have become successful approaches to extract biological hypotheses from microbial sequencing data. Network clustering is a crucial step in this analysis. Here, we present a novel heuristic network clustering algorithm, manta, which clusters nodes in weighted networks. In contrast to existing algorithms, manta exploits negative edges while differentiating between weak and strong cluster assignments. For this reason, manta can tackle gradients and is able to avoid clustering problematic nodes. In addition, manta assesses the robustness of cluster assignment, which makes it more robust to noisy data than most existing tools. On noise-free synthetic data, manta equals or outperforms existing algorithms, while it identifies biologically relevant subcompositions in real-world data sets. On a cheese rind data set, manta identifies groups of taxa that correspond to intermediate moisture content in the rinds, while on an ocean data set, the algorithm identifies a cluster of organisms that were reduced in abundance during a transition period but did not correlate strongly to biochemical parameters that changed during the transition period. These case studies demonstrate the power of manta as a tool that identifies biologically informative groups within microbial networks.IMPORTANCE manta comes with unique strengths, such as the abilities to identify nodes that represent an intermediate between clusters, to exploit negative edges, and to assess the robustness of cluster membership. manta does not require parameter tuning, is straightforward to install and run, and can be easily combined with existing microbial network inference tools.

RevDate: 2020-02-19

Liechty Z, Santos-Medellín C, Edwards J, et al (2020)

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters.

mSystems, 5(1): pii:5/1/e00897-19.

Rice cultivation worldwide accounts for ∼7 to 17% of global methane emissions. Methane cycling in rice paddies is a microbial process not only involving methane producers (methanogens) and methane metabolizers (methanotrophs) but also other microbial taxa that affect upstream processes related to methane metabolism. Rice cultivars vary in their rates of methane emissions, but the influence of rice genotypes on methane cycling microbiota has been poorly characterized. Here, we profiled the rhizosphere, rhizoplane, and endosphere microbiomes of a high-methane-emitting cultivar (Sabine) and a low-methane-emitting cultivar (CLXL745) throughout the growing season to identify variations in the archaeal and bacterial communities relating to methane emissions. The rhizosphere of the high-emitting cultivar was enriched in methanogens compared to that in the low emitter, whereas the relative abundances of methanotrophs between the cultivars were not significantly different. Further analysis of cultivar-sensitive taxa identified families enriched in the high emitter that are associated with methanogenesis-related processes. The high emitter had greater relative abundances of sulfate-reducing and iron-reducing taxa which peak earlier in the season than methanogens and are necessary to lower soil oxidation reduction potential before methanogenesis can occur. The high emitter also had a greater abundance of fermentative taxa which produce methanogenesis precursors (acetate, CO2, and H2). Furthermore, the high emitter was enriched in taxa related to acetogenesis which compete with methanogens for CO2 and H2 These taxa were enriched in a spatio-specific manner and reveal a complex network of microbial interactions on which plant genotype-dependent factors can act to affect methanogenesis and methane emissions.IMPORTANCE Rice cultivation is a major source of anthropogenic emissions of methane, a greenhouse gas with a potentially severe impact on climate change. Emission variation between rice cultivars suggests the feasibility of breeding low-emission rice, but there is a limited understanding of how genotypes affect the microbiota involved in methane cycling. Here, we show that the root microbiome of the high-emitting cultivar is enriched both in methanogens and in taxa associated with fermentation, iron, and sulfate reduction and acetogenesis, processes that support methanogenesis. Understanding how cultivars affect microbes with methanogenesis-related functions is vital for understanding the genetic basis for methane emission in rice and can aid in the development of breeding programs that reduce the environmental impact of rice cultivation.

RevDate: 2020-02-19

Tarallo S, Ferrero G, Gallo G, et al (2020)

Correction for Tarallo et al., "Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples".

mSystems, 5(1): pii:5/1/e00072-20.

RevDate: 2020-02-19

Kumar-Sharma A, Debusk WT, Stepanov I, et al (2020)

Oral microbiome profiling in smokers with and without head and neck cancer reveals variations between health and disease.

Cancer prevention research (Philadelphia, Pa.) pii:1940-6207.CAPR-19-0459 [Epub ahead of print].

While smoking is inextricably linked to Oral/Head and Neck Cancer (HNSCC), only a small fraction of smokers develop HNSCC. Thus, we have sought to identify other factors which may influence the development of HNSCC in smokers including microbiology. To determine microbial associations with HNSCC among tobacco users, we characterized oral microbiome composition in smokers with and without HNSCC. 16S rRNA MiSeq sequencing was used to examine the oral mucosa microbiome of 27 smokers with (cases) and 24 without HNSCC (controls). In addition, we correlated previously reported levels of DNA damage with the microbiome data. Smokers with HNSCC showed lower microbiome richness compared to controls (p=0.012). Beta-diversity analyses assessed as UniFrac (weighted and unweighted) and Bray-Curtis distances, showed significant differences in oral mucosal microbiome signatures between cases and controls (r2=0.03, p=0.03) and higher inter-individual microbiome heterogeneity in the former (q<=0.01). Higher relative abundance of Stenotrophomonas and Comamonadaceae and predicted bacterial pathways mainly involved in xenobiotic and amine degradation were found in cases compared to controls. The latter, in contrast, exhibited higher abundance of common oral commensals and predicted sugar degradation pathways. Lastly, levels of DNA damage in the oral cavity were correlated with the microbiome profiles above. Oral microbiome traits differ in smokers with and without HNSCC, potentially informing the risk of eventual HNSCC and shedding light into possible microbially-mediated mechanisms of disease. These findings present data which may be useful in screening efforts for HNSCC among smokers who are unable to quit.

RevDate: 2020-02-19

Ibekwe AM, Ors S, Ferreira JFS, et al (2020)

Functional relationships between aboveground and belowground spinach (Spinacia oleracea L., cv. Racoon) microbiomes impacted by salinity and drought.

The Science of the total environment, 717:137207 pii:S0048-9697(20)30717-8 [Epub ahead of print].

Salinity is a major problem facing agriculture in arid and semiarid regions of the world. This problem may vary among seasons affecting both above- and belowground plant microbiomes. However, very few studies have been conducted to examine the influence of salinity and drought on microbiomes and on their functional relationships. The objective for the study was to examine the effects of salinity and drought on above- and belowground spinach microbiomes and evaluate seasonal changes in their bacterial community composition and diversity. Furthermore, potential consequences for community functioning were assessed based on 16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on results obtained with Piphillin. The experiment was repeated three times from early fall to late spring in sand tanks planted with spinach (Spinacia oleracea L., cv. Racoon) grown with saline water of different concentrations and provided at different amounts. Proteobacteria, Cyanobacteria, and Bacteroidetes accounted for 77.1% of taxa detected in the rhizosphere; Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil, while Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria accounted for 55.35% of taxa detected in the phyllosphere. Salinity significantly affected root microbiome beta-diversity according to weighted abundances (p = 0.032) but had no significant effect on the relative abundances of microbial taxa (p = 0.568). Pathways and functional genes analysis of soil, rhizosphere, and phyllosphere showed that the most abundant functional genes were mapped to membrane transport, DNA repair and recombination, signal transduction, purine metabolism, translation-related protein processing, oxidative phosphorylation, bacterial motility protein secretion, and membrane receptor proteins. Monoterpenoid biosynthesis was the most significantly enriched pathway in rhizosphere samples when compared to the soil samples. Overall, the predictive abundances indicate that, functionally, the rhizosphere bacteria had the highest gene abundances and that salinity and drought affected the above- and belowground microbiomes differently.

RevDate: 2020-02-19

Fitzgerald PJ (2020)

Neurodining: Common dietary factors may be substrates in novel biosynthetic pathways for monoaminergic neurotransmitters.

Medical hypotheses, 138:109618 pii:S0306-9877(19)31479-3 [Epub ahead of print].

It is not established that there are multiple endogenous mechanisms for synthesizing each of the three major monoamine neurotransmitters: serotonin, norepinephrine, and dopamine. Having multiple biosynthetic pathways for each of these important signaling molecules would provide greater assurance that they are available in sufficient quantities for their various physiological roles in the body. This paper puts forth the hypothesis that a number of common dietary factors-including sucrose and glucose, fats, plant components, and even ethanol-are substrates in novel biosynthetic pathways for the monoamines. A major aspect of this hypothesis is that in a range of multicellular organisms, D-glucose in particular may participate in novel biosynthetic pathways for the monoamines, where this sugar has already been linked with synthesis of the neurotransmitters acetylcholine, glutamate, and GABA through the tricarboxylic acid cycle. Another major aspect of the hypothesis is that phenol or polyphenol molecules, found in various plants, may combine with particular fats or even ethanol to form dopamine, which can then be converted to norepinephrine through the already established step involving the enzyme dopamine beta-hydroxylase. If such a biosynthetic pathway exists for converting ethanol to dopamine in humans, it could be a major factor in substance abuse, including early onset alcoholism. Further, if the above biosynthetic pathways exist in a range of organisms, they may be associated with appetitive processes regulating consumption of particular dietary factors, such as fruits and vegetables, to maintain internal "set points" of, for example, elevated noradrenergic signaling. In this scenario, exposure to psychological stress, which could eventually deplete neurotransmitters such as norepinephrine, may result in craving for sucrose, fats, or alcohol to help replenish the depleted cellular levels of this signaling molecule. An alternative to the overall biosynthetic hypothesis put forth here is that animal cells do not possess these pathways, but the animal microbiome harbors bacteria that do carry out these reactions and helps supply the body with monoamines and other signaling molecules.

RevDate: 2020-02-19

Milajerdi A, Sadeghi O, Siadat SD, et al (2020)

A randomized controlled trial investigating the effect of a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols on the intestinal microbiome and inflammation in patients with ulcerative colitis: study protocol for a randomized controlled trial.

Trials, 21(1):201 pii:10.1186/s13063-020-4108-7.

BACKGROUND: No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis.

METHODS AND ANALYSIS: This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n = 15) or to continue their usual diet as control (n = 15), for 4 weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-α (TNF-α) and IL-1β will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18).

DISCUSSION: Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.

RevDate: 2020-02-19

Poudel P, Levesque CL, Samuel R, et al (2020)

Dietary inclusion of Peptiva, a peptide-based feed additive, can accelerate the maturation of the fecal bacterial microbiome in weaned pigs.

BMC veterinary research, 16(1):60 pii:10.1186/s12917-020-02282-x.

BACKGROUND: Weaning is one of the most critical transition stages of the swine production cycle, as the piglet gut physiology and microbiome need to rapidly adapt to changes in diet and environmental conditions. Based on their potential for producing a vast array of bioactive molecules, peptide formulations represent a largely untapped source of compounds that could be developed into feed additives to benefit animal health and nutrition. In this context, a commercial-scale nursery trial was performed to evaluate the impact of low inclusion of a peptide-based feed additive (Peptiva, Vitech Bio-Chem Corporation) on the performance and fecal microbiome of weaned pigs.

RESULTS: While no significant differences in body weight, daily gain, daily feed intake nor gain:feed were observed between control and treatment animals (P > 0.05), an effect of Peptiva on the fecal bacterial composition of weaned pigs was observed. The first main observation was that the fecal bacterial profiles from pigs fed Control-Phase II and Control Phase III diets were found to be very distinct, suggesting that a transition or succession stage had occurred between the two phases. Lactobacilli, represented by four main OTUs (Ssd-00002, Ssd-00019, Ssd-00025, and Ssd-00053), were more abundant at the end of Phase II (P < 0.05), while Streptococci, mostly represented by OTUs Ssd-00039 and Ssd-00048, were in higher abundance at the end of Phase III (P < 0.05). Secondly, the fecal bacterial composition from pigs fed Peptiva Phase II diets showed similarities to both Control-Phase II and Control Phase III samples, while there was no difference in fecal bacterial composition between Control-Phase III and Peptiva Phase III samples. For instance, OTUs Ssd-00019,and Ssd-00053 were in lower abundance in Peptiva Phase II samples compared to Control Phase II (P < 0.05), but no significant difference was observed in the abundance of these two OTUs when comparing Peptiva Phase II to Control Phase III (P > 0.05).

CONCLUSIONS: Together, these results suggest that Peptiva can modulate the composition of the swine microbiome during a specific window of the nursery stage, potentially by accelerating its maturation.

RevDate: 2020-02-19

Das M, Ghosh TS, IB Jeffery (2020)

IPCO: Inference of Pathways from Co-variance analysis.

BMC bioinformatics, 21(1):62 pii:10.1186/s12859-020-3404-2.

BACKGROUND: Key aspects of microbiome research are the accurate identification of taxa and the profiling of their functionality. Amplicon profiling based on the 16S ribosomal DNA sequence is a ubiquitous technique to identify and profile the abundance of the various taxa. However, it does not provide information on their encoded functionality. Predictive tools that can accurately extrapolate the functional information of a microbiome based on taxonomic profile composition are essential. At present, the applicability of these tools is limited due to requirement of reference genomes from known species. We present IPCO (Inference of Pathways from Co-variance analysis), a new method of inferring functionality for 16S-based microbiome profiles independent of reference genomes. IPCO utilises the biological co-variance observed between paired taxonomic and functional profiles and co-varies it with the queried dataset.

RESULTS: IPCO outperforms other established methods both in terms of sample and feature profile prediction. Validation results confirmed that IPCO can replicate observed biological associations between shotgun and metabolite profiles. Comparative analysis of predicted functionality profiles with other popular 16S-based functional prediction tools showed significantly lower performances with predicted functionality showing little to no correlation with paired shotgun features across samples.

CONCLUSIONS: IPCO can infer functionality from 16S datasets and significantly outperforms existing tools. IPCO is implemented in R and available from https://github.com/IPCO-Rlibrary/IPCO.

RevDate: 2020-02-19

Ossowicki A, Tracanna V, Petrus MLC, et al (2020)

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat.

Proceedings. Biological sciences, 287(1921):20192527.

In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.

RevDate: 2020-02-19

Romano-Armada N, Yañez-Yazlle MF, Irazusta VP, et al (2020)

Potential of Bioremediation and PGP Traits in Streptomyces as Strategies for Bio-Reclamation of Salt-Affected Soils for Agriculture.

Pathogens (Basel, Switzerland), 9(2): pii:pathogens9020117.

Environmental limitations influence food production and distribution, adding up to global problems like world hunger. Conditions caused by climate change require global efforts to be improved, but others like soil degradation demand local management. For many years, saline soils were not a problem; indeed, natural salinity shaped different biomes around the world. However, overall saline soils present adverse conditions for plant growth, which then translate into limitations for agriculture. Shortage on the surface of productive land, either due to depletion of arable land or to soil degradation, represents a threat to the growing worldwide population. Hence, the need to use degraded land leads scientists to think of recovery alternatives. In the case of salt-affected soils (naturally occurring or human-made), which are traditionally washed or amended with calcium salts, bio-reclamation via microbiome presents itself as an innovative and environmentally friendly option. Due to their low pathogenicity, endurance to adverse environmental conditions, and production of a wide variety of secondary metabolic compounds, members of the genus Streptomyces are good candidates for bio-reclamation of salt-affected soils. Thus, plant growth promotion and soil bioremediation strategies combine to overcome biotic and abiotic stressors, providing green management options for agriculture in the near future.

RevDate: 2020-02-19

Piersigilli F, Van Grambezen B, Hocq C, et al (2020)

Nutrients and Microbiota in Lung Diseases of Prematurity: The Placenta-Gut-Lung Triangle.

Nutrients, 12(2): pii:nu12020469.

Cardiorespiratory function is not only the foremost determinant of life after premature birth, but also a major factor of long-term outcomes. However, the path from placental disconnection to nutritional autonomy is enduring and challenging for the preterm infant and, at each step, will have profound influences on respiratory physiology and disease. Fluid and energy intake, specific nutrients such as amino-acids, lipids and vitamins, and their ways of administration -parenteral or enteral-have direct implications on lung tissue composition and cellular functions, thus affect lung development and homeostasis and contributing to acute and chronic respiratory disorders. In addition, metabolomic signatures have recently emerged as biomarkers of bronchopulmonary dysplasia and other neonatal diseases, suggesting a profound implication of specific metabolites such as amino-acids, acylcarnitine and fatty acids in lung injury and repair, inflammation and immune modulation. Recent advances have highlighted the profound influence of the microbiome on many short- and long-term outcomes in the preterm infant. Lung and intestinal microbiomes are deeply intricated, and nutrition plays a prominent role in their establishment and regulation. There is an emerging evidence that human milk prevents bronchopulmonary dysplasia in premature infants, potentially through microbiome composition and/or inflammation modulation. Restoring antibiotic therapy-mediated microbiome disruption is another potentially beneficial action of human milk, which can be in part emulated by pre- and probiotics and supplements. This review will explore the many facets of the gut-lung axis and its pathophysiology in acute and chronic respiratory disorders of the prematurely born infant, and explore established and innovative nutritional approaches for prevention and treatment.

RevDate: 2020-02-18

O'Hara E, Neves ALA, Song Y, et al (2020)

The Role of the Gut Microbiome in Cattle Production and Health: Driver or Passenger?.

Annual review of animal biosciences, 8:199-220.

Ruminant production systems face significant challenges currently, driven by heightened awareness of their negative environmental impact and the rapidly rising global population. Recent findings have underscored how the composition and function of the rumen microbiome are associated with economically valuable traits, including feed efficiency and methane emission. Although omics-based technological advances in the last decade have revolutionized our understanding of host-associated microbial communities, there remains incongruence over the correct approach for analysis of large omic data sets. A global approach that examines host/microbiome interactions in both the rumen and the lower digestive tract is required to harness the full potential of the gastrointestinal microbiome for sustainable ruminant production. This review highlights how the ruminant animal production community may identify and exploit the causal relationships between the gut microbiome and host traits of interest for a practical application of omic data to animal health and production.

RevDate: 2020-02-18

Duar RM, Kyle D, RM Tribe (2020)

Reintroducing Bifidobacterium infantis to the Cesarean-born neonate: an ecologically sound alternative to "vaginal seeding".

FEMS microbiology letters pii:5739918 [Epub ahead of print].

There is a burgeoning literature highlighting differences in long term health outcomes of babies born by caesarean section (C-section) versus vaginal delivery. This has led to the suggestion that infants born by C-section may benefit from vaginal swabbing/seeding. In this opinion piece, we discuss from an ecological and evolutionary perspective that it is gut-adapted, not vagina-adapted, microbes that are likely to take up residence in the infant gut and have the most beneficial impact on the developing neonate. Further, we caution the practice of 'vaginal seeding' in that it may be potentially unsafe and also give parents and health professionals a false sense of action that the infant microbiome has been restored following C-section. Instead, we argue that restoring B. longum subps. infantis, an infant gut symbiont that has uniquely evolved to colonize the infant gut in the presence of human breastmilk, is a safe and ecologically-sound approach to restoring the microbiome of infants with demonstrated success in clinical trials.


RJR Experience and Expertise


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


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


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


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


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


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


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


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

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

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

Research Gate page for R J Robbins

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

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

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RJR Picks from Around the Web (updated 11 MAY 2018 )