May 27, 2018

Pharmacobiomics, liver-microbiome axis, starvation effect on gut microbiota of shrimp,  influence of gut microbiome on the larvae of a lepidopteran pest, microbiota of berries, building a local scientific community in data science and lots of articles for today’s digest.

General microbiome

Pharmacology in the age of the Holobiont – P Norvaisas – Current Opinion in Systems Biology

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production – D Gallagher – Bioresource Technology

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium – N Vardanyan – Environmental Technology

Variation in Electrode Redox Potential Selects for Different Microorganisms Under Cathodic Current Flow From Electrodes in Marine Sediments – BR Lam – Environmental Microbiology

Diurnal patterns of airborne algae in the Hawaiian Islands: a preliminary study – HW Singh – Aerobiologia

Novel human microbe-disease associations inference based on network consistency projection – S Zou – Scientific Reports

Multi-site human microbiome

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans – A Vanhatalo – Free Radical Biology and Medicine

Review: Biodiversity of the Human Oral Mycobiome in Health and Disease – HMHN Bandara – Oral Diseases

 

Human nearly-sterile sites 

Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation – D-L Vu – Clinical Microbiology and Infection

Human gut microbiome

Review: Liver–Microbiome Axis in Health and Disease – TE Adolph – Trends in Immunology

Preprint: Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis. – MM David – bioRxiv

Fecal and Mucosa-Associated Intestinal Microbiota in Patients with Diarrhea-Predominant Irritable Bowel Syndrome – N Maharshak – Digestive Diseases and Sciences

Prevention and treatment of Clostridium difficile associated diarrhea by reconstitution of the microbiota – N Eliakim-Raz – Human Vaccines & Immunotherapeutics

Animal experiments 

Bifidobacterium spp. reshaping in the gut microbiota by low dose of juçara supplementation and hypothalamic insulin resistance in Wistar rats – G Jamar – Journal of Functional Foods

Salvianolic acid B alters the gut microbiota and mitigates colitis severity and associated inflammation – X Wu – Journal of Functional Foods

Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model – X Zhang – Journal of Functional Foods

Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities – W-F Dai – Fish & Shellfish Immunology

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Z Ge – Scientific Reports

Animal microbiome 

Preprint: The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – MT Schwarz – bioRxiv

Plant, root, and soil microbiome

Review: High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota – A pilot study – J Lukša – Food Research International

Microbial functional responses to long-term anthropogenic impact in mangrove soils – L Cabral – Ecotoxicology and Environmental Safety

Foliage application of nitrogen has less influence on soil microbial biomass and community composition than soil application of nitrogen – X Huang – Journal of Soils and Sediments

Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments – Y Chen – Science of The Total Environment

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5 – J Gao – Ecotoxicology and Environmental Safety

Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+‐pumping pyrophosphatase in pepper plants – G Vigani – Environmental Microbiology

Defining plant growth promoting rhizobacteria molecular and biochemical networks in beneficial plant-microbe interactions – A Rosier – Plant and Soil

Roles of Plant-Associated Microbiota in Traditional Herbal Medicine – W Huang – Trends in Plant Science

Spatial structuring of soil microbial communities in commercial apple orchards – G Deakin – Applied Soil Ecology

Effects of root colonization by zinc-solubilizing bacteria on rice plant (Oryza sativa MR219) growth – NMI Othman – Agriculture and Natural Resources

Promising filamentous native fungi isolated from paddy soils for arsenic mitigation in rice grains cultivated under flooded conditions – FR Segura – Journal of Environmental Chemical Engineering

Soil respiration in Chinese tea gardens: autotrophic and heterotrophic respiration – LC Fan – European Journal of Soil Science

Water and extremophile microbiome 

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and ‘Candidatus Methanohalarchaeum thermophilum’, extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. – DY Sorokin – International Journal of Systematic and Evolutionary Microbiology

 

Food microbiology

The Genus Wallemia—From Contamination of Food to Health Threat – J Zajc- Microorganisms

Phages and viruses

Biological species in the viral world – L-M Bobay – PNAS

Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium – K Moon – Scientific Reports

 

Non-microbiology picks

Preprint: Building a local community of practice in scientific programming for Life Scientists – SLR Stevens – bioRxiv

 

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May 26, 2018

We have a big variety of topics covered in today’s posts, from built environment to bat microbiome to biolfilms!

Biofilms

Genomic identification of microbial species adhering to maxillofacial prostheses and susceptibility to different hygiene protocols – Juliana Barchelli, The Journal of Bioadhesion and Biofilm Research

Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses – Wei Ding, The Journal of Bioadhesion and Biofilm Research

Microbial ecology

Keystone taxa as drivers of microbiome structure and functioning – Samiran Banerjee, Nature Reviews Microbiology

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems – Akshit Goya, Physical Review Letters

Pregnancy and early life

Iron supplementation has minor effects on gut microbiota composition in overweight and obese women in early pregnancy – Marloes Dekker Nitert, British Journal of Nutrition

Human respiratory microbiome

The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia – Wenkui Dai, Emerging Microbes & Infections

The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study – Refiloe Masekela, BMC Pulmonary Medicine

Human skin microbiome

Does Lindioil (Indirubin) treatment affect the composition of Malassezia species on psoriatic skin? – Y. K. Lin, British Journal of Dermatology

Shift in skin microbiota of Western European women across aging – Romain Jugé, Journal of Applied Microbiology

Human vaginal microbiome

Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission – Alicia R. Berard, American Journal of Reproductive Immunology

Vaginal microbiome studies in pregnancy must also analyse host factors – S.S. Witkin, BJOG: An International Journal of Obstetrics & Gynaecology

Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case‐control study – Negar Tabatabaei, BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial – Xiaolin Tong, mBio

The role of diet in the aetiopathogenesis of inflammatory bowel disease – Hamed Khalili, Nature Reviews Gastroenterology & Hepatology

Animal experiments

Ethanolamine enhances intestinal functions by altering gut microbiome and mucosal anti-stress capacity in weaned rats – Jian Zhou, British Journal of Nutrition

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Zhongming Ge, Scientific Reports

Evaluation of the impact of glyphosate and its residues in feed on animal health – European Food Safety Authority (EFSA), EFSA Journal

Risks for animal health related to the presence of fumonisins, their modified forms and hidden forms in feed – EFSA Panel on Contaminants in the Food Chain (CONTAM), EFSA Journal

Plateau hypoxia attenuates the metabolic activity of intestinal flora to enhance the bioavailability of nifedipine – Juanhong Zhang, Drug Delivery

Animal microbiome

Fecal Microbiota Composition Changes after a Body Weight Loss Diet in Beagle Dogs – A Salas, Journal of Animal Sciences

The fecal bacterial microbiota of bats; Slovenia – Modest Vengust, PLOS One

Plant, root, and soil microbiome

Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation – Yushan Zhan, Scientific Reports

Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community – Ping-Fu Hou, Scientific Reports

Annual post‐market environmental monitoring report on the cultivation of genetically modified maize MON 810 in 2016 – European Food Safety Authority (EFSA), EFSA Journal

Conserved Responses in a War of Small Molecules between a Plant-Pathogenic Bacterium and Fungi – Joseph E. Spraker, mBio

Pseudomonads contribute to regulation of Pratylenchus penetrans (Nematoda) populations on apple – Tristan T. Watson, Canadian Journal of Microbiology

Water and extremophile microbiome

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm – Jennifer M. Michaud, Nature Communications

Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord – Caroline Utermann, Scientific Reports

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments – Zhichao Zhou, FEMS Microbiology Reviews

Probiotics / prebiotics

Dietary fibers, prebiotics, and exopolysaccharides produced by lactic acid bacteria: potential health benefits with special regard to cholesterol-lowering effects – E. Korcz, Food and Function

Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies – Concetta Panebianco, Microbiome

Built environment

City-scale distribution and dispersal routes of mycobiome in residences – Xinzhao Tong, Microbiome

Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles – Alejandro R. Walker, Biology Direct

Bioinformatics

ASaiM: a Galaxy-based framework to analyze microbiota data – Bérénice Batut, GigaScience

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers – Alexa B. R. McIntyre, Genome Biology

Techniques

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain – Elena A. Oniciuc, Genes

A microbial endocrinology-based simulated small intestinal medium for the evaluation of neurochemical production by gut microbiota – Daniel N Villageliú, FEMS Microbiology Ecology

May 25, 2018

Microbes and climate change, molecules from the microbiota and the gut-brain axis, C. albicans respiration changes lead to differences in macrophage recognition.

Animal experiments

The Gut Microbiota Mediates the Anti-Seizure Effects of the Ketogenic Diet – Christine A Olson – Cell

Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host – Marlies Meisel – Nature

Pre-print: Temporal changes in gut microbiota and signaling molecules of the gut-brain axis in mice fed meat protein diets – Yunting Jie – bioRxiv

Water and extremophile microbiome

Detection and Genetic Characterization of Bacteria of the Genus Pseudomonas from Microbial Communities of Lake Baikal – N L Bel’kova – Russian Journal of Genetics

More microbes

Review: Microbial Function on Climate Change – A Review – Endeshaw Abatenh – Environment Pollution and Climate Change

Pre-print: Inhibition of classical and alternative modes of respiration in C. albicans leads to cell wall remodelling and increased macrophage recognition – Lucian Duvenage – bioRxiv

Microbes in the news

How gut microbes are joining the fight against cancer – Giorgia Guglielmi – Nature

May 24, 2018

Pest gut microbiota indirectly effects plant defenses in corn, evolution of microbial social behavior from shearing in flow environments, a model to predict cytokine responses based on multi-comics data integration.

General microbiome

Shearing in flow environment promotes evolution of social behavior in microbial populations – Gurdip Uppal – eLIFE

Pregnancy and early life

Review: The Neonatal Microbiome and Its Partial Role in Mediating the Association between Birth by Cesarean Section and Adverse Pediatric Outcomes – D Montoya-Williams – Neonatology

Human respiratory microbiome

Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota – Thanit Chalermwatanachai – Scientific Reports

Human oral microbiome

Metagenomic study of bacterial microbiota in persistent endodontic infections using Next‐generation sequencing – G Sánchez-Sanhueza – International Endodontic Journal

Human gut microbiome

Iron Sequestration in Microbiota Biofilms As A Novel Strategy for Treating Inflammatory Bowel Disease – Jean-Paul Motta – Inflammatory Bowel Diseases

Temporal and long‐term gut microbiota variation in allergic disease: A prospective study from infancy to school age – Kotryna Simonyté Sjödin – European Journal of Allergy and Clinical Immunology

Bangladeshi children with acute diarrhea show fecal microbiomes with increased Streptococcus abundance, irrespective of diarrhea etiology – Silas Kieser – Environmental Microbiology

Animal experiments

Effects of a protease and essential oils on growth performance, blood cell profiles, nutrient retention, ileal microbiota, excreta gas emission, and breast meat quality in broiler chicks – J H Park – Poultry Science

Colonic Inhibition of Phosphatase and Tensin Homolog Increases Colitogenic Bacteria, Causing Development of Colitis in Il10-/- Mice – Jonathon Mitchell – Inflammatory Bowel Diseases

Review: Microbial Signatures as a Predictive Tool in IBD—Pearls and Pitfalls – Nadine Waldschmitt – Inflammatory Bowel Diseases

Oral hydroxysafflor yellow A reduces obesity in mice by modulating the gut microbiota and serum metabolism – Juan Liu – Pharmacological Research

Impact of commensal flora on periodontal immune response to lipopolysaccharide – Daiki Fukuhara – Journal of Periodontology

Animal microbiome

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes – Rocky D Patil – Journal of Animal Science

Plant, root, and soil microbiome

Cadmium phytoextraction potential of king grass (Pennisetum sinese Roxb.) and responses of rhizosphere bacterial communities to a cadmium pollution gradient – Li Hu – Environmental Science and Pollution Research

Gut-Associated Bacteria of Helicoverpa zea Indirectly Trigger Plant Defenses in Maize – Jie Wang – Journal of Chemical Ecology

Water and extremophile microbiome

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer – María E Alcamán-Arias – FEMS Microbiology Letters

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands – Catiane Pelissari – Water Research

Pre-print: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines – Andrian P Gajigan – PeerJ

Food microbiology

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry – Naama Massad-Ivanir – Scientific Reports

Probiotics/prebiotics

Survival of Planktonic and Sessile Cells of Lactobacillus rhamnosus and Lactobacillus reuteri upon Exposure to Simulated Fasting-State Gastrointestinal Conditions – Kyle B Klopper – Probiotics and Antimicrobial Proteins

Phages and viruses

Pre-print: A novel oceanic uncultured temperate cyanophage lineage – José Flores-Uribe – bioRxiv

Bioinformatics

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses – Olivier B Bakker – Nature Immunology

More microbes

Pre-print: New sequential touch method for determining bacterial contact transfer rate from finger to surface – Pengcheng Zhao – bioRxiv

Amy’s non-microbiology picks

Restoration of paper artworks with microemulsions confined in hydrogels for safe and efficient removal of adhesive tapes – Nicole Bonelli – PNAS

May 23, 2018

Today’s digest is packed full of awesome gut microbiome studies, a bunch of plant/soil studies, new features to QIIME and other bioinformatics, as well as a good serving of interesting pre-prints, editorials, and doctoral theses. Enjoy!

General microbiome

Microbial micropatches within microbial hotspots – Lisa M. Dann – PLOS ONE

Pregnancy and early life

The matter of the reproductive microbiome – Sam Schoenmakers – Obstetric Medicine

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum – Mie Korslund Wiinblad Crusell – Microbiome

The importance of appropriate initial bacterial colonization of the intestine in newborn, child, and adult health – W Allan Walker – Pediatric Research

Human oral microbiome

Oral health status in historic population: Macroscopic and metagenomic evidence – Claire Willmann – PLOS ONE

The Subgingival Microbiome of Periodontal Pockets With Different Probing Depths in Chronic and Aggressive Periodontitis: A Pilot Study – Meng Shi – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

[Pre-print] Gut microbiota markers in obese adolescent and adult patients: age-dependent differential patterns – Federica Del Chierico – Frontiers in Microbiology

Clinical applications of gut microbiota in cancer biology – Sunny H. Wong – Seminars in Cancer Biology

* Microbiome-Mediated Effects of the Mediterranean Diet on Inflammation – Melisa A Bailey – Advances in Nutrition

** Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury – Benjamin M Howard – Trauma Surgery & Acute Care Open

Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota – Junyue Xing – Nature Communications

Animal experiments

The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets – Wei Jin – Antonie van Leeuwenhoek

Effects of whole-grain rice and wheat on composition of gut microbiota and short-chain fatty acids in rats – Fei Han – Journal of Agriculture and Food Chemistry

Animal microbiome

Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles – Chelsea L. Blankenchip – PeerJ

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – World Journal of Microbiology and Biotechnology

The gut microbiome is associated with behavioural task in honey bees – J. C. Jones – Insectes Sociaux

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Plant, root, and soil microbiome

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems – Anil Somenahally – Soil Biology and Biochemistry

New insights into the effects of support matrix on the removal of organic micro-pollutants and the microbial community in constructed wetlands – Liang Zhang – Environmental Pollution

[Doctoral thesis] Imprint of management on microbial communities in arable soil – Putz, Martina

Study of microbial diversity in plant–microbe interaction system with oil sludge contamination – Dhote, Monika – International Journal of Phytoremediation

Effect of different potassium levels on nitrogen metabolism, nitrogen bacteria and nitrogen archaea bacteria communities in rhizosphere of tobacco plant – WENG Zebin – Acta Tabacaria Sinica

Canola Root–Associated Microbiomes in the Canadian Prairies – Chih-Ying Lay – Frontiers in Microbiology

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves – Leandro Pio de Sousa – Genetics and Molecular Biology

[Review] Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression – Giuliano Bonanomi – Annual Review of Phytopathology

[Pre-print] Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore – Kevin D. Kohl – bioRxiv

[Pre-print] Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California – Sabah Ul-Hasan – bioRxiv

Water and extremophile microbiome 

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community – M.Peces – Water Research

Built environment

[Editorial] Microbiome Yarns: microbiome of the built environment, paranormal microbiology, and the power of single cell genomics – Kenneth Timmis – microbial biotechnology

New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces – Ariel L. Furst – Biochemistry

* [Pre-print] Strain­level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes – Matthew R. Olm – bioRxiv

Probiotics / prebiotics

The effects of probiotics supplementation on metabolic health in pregnant women: An evidence based meta-analysis – Jia Zheng – PLOS ONE

Bioinformatics

[Pre-print / doctoral thesis] Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning – Alneberg, Johannes – DiVA

** Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin – Nicholas A. Bokulich – Microbiome

Techniques

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia – Martina Lardi – High-Throughput

VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens – Yi Zhang – Europe PMC

Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol – Ankur Naqib – Gene Expression Analysis

Ed’s non-microbiology picks 

The Environmental Protection Agency in the Early Trump Administration: Prelude to Regulatory Capture

Perspectives on the Great Amazon Reef: Extension, Biodiversity, and Threats

Fasting boosts stem cells’ regenerative capacity

Eggs not linked to cardiovascular risk, despite conflicting advice

Noninvasive spinal stimulation method enables paralyzed people to regain use of hands, study finds

Cannabidiol significantly reduces seizures in patients with severe form of epilepsy

May 21, 2018

A long update to make up for the past few days, with extra emphasis on Plant/root/soil studies and water studies!

General microbiome

Why do microbes exhibit weak biogeographic patterns? – Kyle M. Meyer, ISME

Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches – Muneer A. Malla, Frontiers in Microbiology

Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration – L. Treu, Bioresource Technology

Microbial ecology

Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi – Alberto Amato, ISME

Cooperation, competition and antibiotic resistance in bacterial colonies – Isabel Frost, ISME

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities – Tyler P. Barnum, ISME

Diversity and Hidden Host Specificity of Chytrids infecting Colonial Volvocacean Algae – Silke Van den Wyngaert, Journal of Eukaryotic Microbiology

Human bone microbiome

Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches – Khalid Johani, Clinical Microbiology and Infection

Human oral microbiome

Bacterial-derived exopolysaccharides enhance antifungal drug tolerance in a cross-kingdom oral biofilm – Dongyeop Kim, ISME

Human vaginal microbiome

Metabolomics as a clinical testing method for the diagnosis of vaginal dysbiosis – Emiley Watson, American Journal of Reproductive Immunology

Human gut microbiome

Design and rationale of the INSYTE study: A randomised, placebo controlled study to test the efficacy of a synbiotic on liver fat, disease biomarkers and intestinal microbiota in non-alcoholic fatty liver disease – Eleonora Scorletti, Contemporary Clinical Trials

Gastrointestinal Disorders Associated with Primary Immunodeficiency Diseases – Stella Hartono, Clinical Reviews in Allergy & Immunology

Impact on the quality of life of an episode of Clostridium difficileinfection in a hospital setting – A. Duburcq, Journal of Epidemiology and Public Health

Animal experiments

Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome – Ece A. Mutlu, Environmental Pollution

Effects of long-term intake of a yogurt fermented with Lactobacillus delbrueckii subsp.bulgaricus 2038 and Streptococcus thermophilus1131 on mice – Yuki Usui, International Immunology

Dietary mung bean protein reduces high-fat diet-induced weight gain by modulating host bile acid metabolism in a gut microbiota-dependent manner – Akiho Nakatani, Biochemical and Biophysical Research Communications

Dietary nitrate modulates gut microbiota profile and prevents the activation of mucosal inflammatory pathways induced by broad-spectrum antibiotics – Bárbara S. Rocha, Free Radical Biology and Medicine

Animal microbiome

Coral bleaching from a single cell perspective – Daniel Aagren Nielsen, ISME

Plant, root, and soil microbiome

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest – Carles Castaño, Forest Ecology and Management

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Intraspecific variation in indirect plant–soil feedbacks influences a wetland plant invasion – Warwick J. Allen, Ecology

Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome – Elisabeth Armada, FEMS Microbiology Ecology

Plant roots redesign the rhizosphere to alter the three‐dimensional physical architecture and water dynamics – Sheikh M. F. Rabbi, New Phytologist

The Invasive Brazilian Pepper Tree (Schinus terebinthifolius) Is Colonized by a Root Microbiome Enriched With Alphaproteobacteria and Unclassified Spartobacteria – Karim Dawkins, Frontiers in Microbiology

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation – Marie-Francoise Noirot-Gros, Frontiers in Microbiology

The Emergence of Endophytic Microbes and Their Biological Promise – Gary Strobel, Journal of Fungi

Changes in soil nitrogen dynamics caused by prescribed fires in dense gorse lands in SW Pyrenees – Leire Múgica, Science of The Total Environment

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Application of biosolids drives the diversity of antibiotic resistance genes in soil and lettuce at harvest – Lu Yang, Soil Biology and Biochemistry

Mycorrhizal Status In Endemic Pipewort: Eriocaulon eurypeplon Körn (Fam: Eriocaulaceae) – Vishal R. Kamble, IOSR Journal of Pharmacy and Biological Sciences

Model formulation of microbial CO2production and efficiency can significantly influence short and long term soil C projections – Ford Ballantyne IV & Sharon A. Billings, ISME

Effect of endophytic fungus Piriformospora indica on yield and some physiological traits of millet (Panicum miliaceum) under water stress – Goudarz Ahmadvand, Crop and Pasture Science

Composition and functional genes analysis of bacterial communities from urban parks of Shanghai, China and their role in ecosystem functionality – Xin Wang, Landscape and Urban Planning

Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest – Lucía Vivanco​, PeerJ

Root-exuded coumarin shapes the root microbiome – Derek S. Lundberg, PNAS

Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities – Jing Tian, Soil Biology and Biochemistry

Distinct nitrogen provisioning from organic amendments in soil as influenced by farming system and water regime – Martina Lori, Frontiers in Microbiology

Biodiversity of urban soils for sustainable cities – C. Guilland, Environmental Chemistry Letters

Predator–prey mass ratio drives microbial activity under dry conditions in Sphagnum peatlands – Monika K. Reczuga, Ecology and Evolution

Organic and Biofertilization on Crop Production in Semiarid Regions – Ayman M. Helmy, The Handbook of Environmental Chemistry

Prevalence of Botrytis cinerea at different phenological stages of table grapes grown in the northern region of South Africa – Patricia C. Carmichael, Scientia Horticulturae

Water and extremophile microbiome

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast – Cene Gostinčar, BMC Genomics

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities – Simone C. Birrer, Science of The Total Environment

Physicochemical drivers of microbial community structure in sediments of Lake Hazen, Nunavut, Canada – Matti O. Ruuskanen, Frontiers in Microbiology

Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane – Jonna E. Teikari, ISME

Seasonal resource conditions favor a summertime increase in North Pacific diatom–diazotroph associations – Christopher L. Follett, ISME

Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning—interplay between nanoflagellates and bacterioplankton – Jinny Wu Yang, ISME

Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight – Qian Liu, ISME

Distributions of phytoplankton carbohydrate, protein and lipid in the world oceans from satellite ocean colour – Shovonlal Roy, ISME

Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments – H J Smith, FEMS Microbiology Ecology

Sediment depth-dependent spatial variations of bacterial communities in mud deposits of the eastern China marginal seas – Yanlu Qiao, Frontiers in Microbiology

Food microbiology

Origin and varietal based proteomic and peptidomic fingerprinting of Theobroma cacao in non-fermented and fermented cocoa beans – Neha Kumari, Food Research International

Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening – Ilhan Cem Duru, International Journal of Food Microbiology

Combined effect of cold atmospheric plasma, intrinsic and extrinsic factors on the microbial behavior in/on (food) model systems during storage – C. Smet, Innovative Food Science & Emerging Technologies

Polyphenols from selected dietary spices and medicinal herbs differentially affect common food-borne pathogenic bacteria and lactic acid bacteria – Chak-Lun Chan, Food Control

Probiotics

Enhanced viability of probiotics (Pediococcus pentosaceusLi05) by encapsulation in microgels doped with inorganic nanoparticles – Mingfei Yao, Food Hydrocolloids

Dysbiosis of microbiome and probiotic treatment in a genetic model of autism spectrum disorders – Tabouy Laure, Brain, Behavior, and Immunity

Bioinformatics

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation – Han Zhang, Nucleic Acids Research

A Multi-Omics Database for Parasitic Nematodes and Trematodes – John Martin, Eukaryotic Genomic Databases

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis – Jasmine Chong, Nucleic Acids Research

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination – Alan J Medlar, Nucleic Acids Research

Techniques

Mutant phenotypes for thousands of bacterial genes of unknown function – Morgan N. Price, Nature

Methods for Generating Microbial Cocultures that Grow in the Absence of Fixed Carbon or Nitrogen – Matthew J. Smith, Synthetic Biology

Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives – C.X. Restrepo-Ortiz, Systematic and Applied Microbiology

Creation of a fibre categories database to quantify different dietary fibres – Stacey Fuller, Journal of Food Composition and Analysis

May 17, 2018

Genome engineering tools for non-model prokaryotes, microgravity and space radiation’s effects on microbes, an analysis of science podcasts.

General microbiome

Taking the technical microbiome into the next decade – Jo De Vrieze – Environmental Microbiology

Pre-print: Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K Fragiadakis – bioRxiv

Human vaginal microbiome

The effect of vaginal microbial communities on colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1): a case–control study – Jacob D Pierson – FEMS Pathogens and Disease

Human urinary microbiome

Lactobacillus and Urine Microbiome in Association with Urinary Tract Infections and Bacterial Vaginosis – Jun-Mo Kim – Urogenital Tract Infection

Human gut microbiome

Combination Antibiotics Improves Disease Activity and Alters Microbial Communities In Children with Ulcerative Colitis – Kattayoun Kordy – Journal of Pediatric Gastroenterology and Nutrition

Animal experiments

Postnatal colonization with human “infant-type” Bifidobacterium species alters behavior of adult gnotobiotic mice – Berkley Luk – PLOS ONE

A gene catalogue of the Sprague-Dawley rat gut metagenome – Hudan Pan – Gigascience

Animal microbiome

Changes in intestinal microbiota of Bufo gargarizans and its association with body weight during metamorphosis – Lihong Chai – Archives of Microbiology

Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome – John M K Roberts – Journal of General Virology

Plant, root, and soil microbiome

Strong associations between plant genotypes and bacterial communities in a natural salt marsh – Gregory P Zogg – Ecology and Evolution

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs – Julian Taffner – mSphere

Rhizosphere hydrophobicity limits root water uptake after drying and subsequent rewetting – Mohsen Zarebanadkouki – Plant and Soil

Crop rotational diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – Ecosphere

Water and extremophile microbiome

A thiotrophic microbial community in an acidic brine lake in Northern Chile – Lorena Escudero – Antonie van Leeuwenhoek

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium – Andrew Hart – PLOS ONE

Microbes in space

Review: Effect of microgravity & space radiation on microbes – Giuliana Senatore – Future Microbiology

Food microbiology

Bacterial community analysis in three types of the fermented seafood, jeotgal, produced in South Korea – Eun-Ji Song – Bioscience, Biotechnology, and Biochemistry

Metabolomics

Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean – Wenshu Kang – BMC Plant Biology

Techniques

Review: Building a genome engineering toolbox in non‐model prokaryotic microbes – Emily Freed – Biotechnology and Bioengineering

Pre-print: Effective soil extraction method for cultivating previously uncultured soil bacteria – Tuan Manh Nguyen – bioRxiv

More microbes

Disentangling complex parasite interactions: Protection against cerebral malaria by one helminth species is jeopardized by co-infection with another – Jessica L Abbate – PLOS Neglected Tropical Diseases

Pre-print: Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells – Shraddha Shitut – bioRxiv

Science, career, and publishing

Pre-print: Science podcasts: analysis of global production and output from 2004 to 2018 – Lewis E MacKenzie – bioRxiv