February 19, 2018

Events and jobs

Research Technician I – University at Buffalo

General microbiome

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation – Ji Lu, bioRxiv

Oncologists tap the microbiome in bid to improve immunotherapy outcomes – Asher Mullard, Nature Reviews Drug Discovery

Nasal microbiome

Establishment of the Nasal Microbiota in the first 18 Months of Life – Correlation with Early Onset Rhinitis and Wheezing – Le Duc Huy Ta, Journal of Allergy and Clinical Immunology

The nasal microbiome in chronic rhinosinusitis: analyzing the effects of atopy and bacterial functional pathways in 111 patients – Mahboobeh Mahdavinia, Journal of Allergy and Clinical Immunology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela S. A. Goltsman, bioRxiv

Human vaginal microbiome

Microbiota changes impact on sexually transmitted infections and the development of pelvic inflammatory disease – Nathalie Loeper, Microbes and Infection

Human gut microbiome

Efficacy of Bifidobacterium breve Fermented Milk in Maintaining Remission of Ulcerative Colitis – Katsuyoshi Matsuoka, Digestive Diseases and Sciences

Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review – Simon D. Goldenberg, Infectious Diseases and Therapy

Fecal Microbiota Transplant for Refractory Clostridium difficile Infection Interrupts 25-Year History of Recurrent Urinary Tract Infections – Tiffany Wang, Open Forum Infectious Diseases

Fecal microbiota transplantation for severe complicated C. difficile colitis in a patient with acquired immunodeficiency syndrome – P. Martínez-Ayala, Revista de Gastroenterología de México

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD – Robert P Hirten, bioRxiv

The impact of a helminth-modified microbiome on host immunity – Tara P. Brosschot &
Lisa A. Reynolds, Mucosal Immunology

Depression and obesity: evidence of shared biological mechanisms – Yuri Milaneschi, Molecular Psychiatry

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation – Juliana Durack, Nature Communications

Roux-en-Y Gastric-Bypass and sleeve gastrectomy induces specific shifts of the gut microbiota without altering the metabolism of bile acids in the intestinal lumen – Henri Duboc, International Journal of Obesity

Effects of ewe’s milk yogurt (whole and semi-skimmed) and cow’s milk yogurt on inflammation markers and gut microbiota of subjects with borderline-high plasma cholesterol levels: a crossover study – Noemí Redondo, European Journal of Nutrition

Impact of food additives on the gut-brain axis – Mary K. Holder, Physiology & Behavior

Gut microbiota injury in allogeneic haematopoietic stem cell transplantation – Yusuke Shono, Nature Reviews Cancer

Microbiota: Pathobiont peacekeepers – Kirsty Minton, Nature Reviews Immunology

Gut Microbiomics—A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation – Amy Zhang, Journal of Heredity

Oral microbiome

Host defense against oral microbiota by bone-damaging T cells – Masayuki Tsukasaki, Nature Communications

Beyond Streptococcus mutans: clinical implications of the evolving dental caries aetiological paradigms and its associated microbiome – N. Philip, BDJ

Animal experiments

The Divergence in Bacterial Components Associated with Bactrocera dorsalis across Developmental Stages – Xiaofeng Zhao, Frontiers in Microbiology

Microbiota in fermented feed and swine gut – Cheng Wang, Applied Microbiology and Biotechnology

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract – Carl J. Yeoman, Scientific Reports

Animal microbiome

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure – Kieran A. Bates, Nature Communications

The effect of cadmium exposure on diversity of intestinal microbial community of Rana chensinensis tadpoles – Danyang Mu, Ecotoxicology and Environmental Safety

A new cell extraction method reveals hemolymph microbiome of three aquatic invertebrates – Xinxu Zhang, Applied Microbiology and Biotechnology

The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition – Ting Jia, Scientific Reports

Plant, root, and soil microbiome

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health – Jia Zhao, PLOS One

Water and extremophile microbiome

Seasonal dynamics of tetracycline resistance gene transport in the Sumas River agricultural watershed of British Columbia, Canada – Patricia L. Keen, Science of The Total Environment

Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde – Ana Paula Semedo-Aguiar, bioRxiv

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities – Adam C. Mumford, Applied and Environmental Microbiology

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation – Bing Li, Applied and Environmental Microbiology

Properties of bacterial communities attached to artificial substrates in a hypereutrophic urban river – Xianlei Cai, AMB Express

Food microbiology

Nitrogen removal enhancement using lactic acid fermentation products from food waste as external carbon sources: performance and microbial communities – Jialing Tang, Bioresource Technology

Probiotics/Prebiotics

Advances in Probiotic Regulation of Bone and Mineral Metabolism – Laura R. McCabe, Calcified Tissue International

Prebiotics as functional food ingredients preventing diet-related diseases – A. Florowska, Food and Function

A prebiotic mixture improved Lactobacillus acidophilus and Bifidobacterium animalisgastrointestinal in vitro resistance in petit-suisse – Marina Padilha, Food and Function

Bioinformatics

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses – Tomáš Větrovský, Bioinformatics

Techniques

Use of Rectal Swab Samples for Analysis of the Intestinal Microbiome in Children – Nan Zhang, Chinese Medical Journal

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February 11, 2018

General microbiome

How the microbiome challenges our concept of self – Tobias Rees, PloS Biology

Human gut microbiome

Inflammatory bowel disease and Clostridium difficile infection: contrasting views of international clinical professionals – Andreas Stallmach, Zeitschrift für Gastroenterologie

Digestibility of sulfated polysaccharide from the brown seaweed Ascophyllum nodosum and its effect on the human gut microbiota in vitro – Ligen Chen, International Journal of Biological Macromolecules

Microbiome-based mechanisms hypothesized to initiate obesity-associated rheumatoid arthritis – Y. Luo, Obesity Reviews

Tissue macrophages as mediators of a healthy relationship with gut commensal microbiota – Brenda Naemi Nakagaki, Cellular Immunology

Fecal microbiota transplantation for recurrent Clostridium difficile infection in a patient with ulcerative colitis – Kosaku Nanki, Intestinal Research

Efficacy and safety of the adalimumab biosimilar Exemptia as induction therapy in moderate-to-severe ulcerative colitis – Vandana Midha, Intestinal Research

Sensing Bacterial-Induced DNA Damaging Effects via Natural Killer Group 2 Member D Immune Receptor: From Dysbiosis to Autoimmunity and Carcinogenesis – J. Luis Espinoza, Frontiers in Immunology

Environmental Exposures and Neuropsychiatric Disorders: What Role Does the Gut–Immune–Brain Axis Play? – Shannon Delaney, Current Environmental Health Reports

Human nearly-sterile sites

Identification and Characterization of Blood and Neutrophil-Associated Microbiomes in Patients with Severe Acute Pancreatitis Using Next-Generation Sequencing – Qiurong Li, Frontiers in Cellular and Infectious Microbiology

Animal experiments

Effects of levan-type fructan on growth performance, nutrient digestibility, diarrhoea scores, faecal shedding of total lactic acid bacteria and coliform bacteria, and faecal gas emission in weaning pigs – Xin Jian Lei, Journal of the Science of Food and Agriculture

Dietary proline supplementation alters colonic luminal microbiota and bacterial metabolite composition between days 45 and 70 of pregnancy in Huanjiang mini-pigs – Yujiao Ji, Journal of Animal Science and Biotechnology

Effects of the Artificial Sweetener Neotame on the Gut Microbiome and Fecal Metabolites in Mice – Liang Chi, Molecules

Animal microbiomes

Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges – Guofang Feng, Marine Biotechnology

Community structure, dispersal ability and functional profiling of microbiome existing in fat body and ovary of the brown planthopper, Nilaparvata lugens – Jian-Hua Zhang, Insect Science

Plant, root, and soil microbiome

Influence of biochar aged in acidic soil on ecosystem engineers and two tropical agricultural plants – Ihuoma N. Anyanwu, Ecotoxicology and Environmental Safety

Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems –  Juan Ling, Frontiers in Microbiology

Dibutyl phthalate alters the metabolic pathways of microbes in black soils – Weihui Xu, Scientific Reports

Native soils with their microbiotas elicit a state of alert in tomato plants – Matteo Chialva, New Phytologist

Water and extremophile microbiome

A probabilistic approach to assess antibiotic resistance development risks in environmental compartments and its application to an intensive aquaculture production scenario – Andreu Rico, Environmental Pollution

Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific) – Julia Endresen Storesund, Antonie van Leeuwenhoek

Enhancing methane production from lignocellulosic biomass by combined steam-explosion pretreatment and bioaugmentation with cellulolytic bacterium Caldicellulosiruptor bescii – Daniel Girma Mulat, Biotechnology for Biofuels

Microbial ecology

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle – K. Dimitri Kits, Nature Letters

Microbes in the news

Safety blunders expose lab staff to potentially lethal diseases in UK – The Guardian

This UV Lamp Could Prevent the Flu Virus From Spreading in Public Places –  Amanda Macmillan, Time

December 30, 2017

Enjoy your daily dose of (mostly human gut) microbiome literature!

General microbiome

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes – Nicole Gerardo, BMC Biology

The Dark Side of IFN-γ: Its Role in Promoting Cancer Immunoevasion – Marija Mojic, International Journal of Molecular Sciences

Two-stage pretreatment of excess sludge for electricity generation in microbial fuel cell – Yi Zhang, Environmental Technology

Human respiratory microbiome

Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial – Carmen Gonzalez-Martinez, BMC Biology

Human skin microbiome

Characterization of the facial microbiome in twins discordant for rosacea – Asifa K. Zaidi, Experimental Dermatology

Human oral microbiome

Oral health in geroscience: animal models and the aging oral cavity – Jonathan Y. An, GeroScience

Extracellular matrix Influence in Streptococcus mutans gene expression in a cariogenic biofilm – Elkin Jahir Florez Salamanca, Molecular Oral Microbiology

Human gut microbiome

The Microbiome–Gut–Behavior Axis: Crosstalk Between the Gut Microbiome and Oligodendrocytes Modulates Behavioral Responses – Achilles Ntranos, Neurotherapeutics

Antibiotics Associated Disorders and Postbiotics Induced Rescue in Gut Health – Debarati Paul, Current Pharmaceutical Design

We are not alone in our body: insights into the involvement of microbiota in the etiopathogenesis and pharmacology of mental illness –  Claudia Pisanu, Current Drug Metabolism

Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003 – Francesca Bottacini, BMC Genomics

Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis – Michael A. Henson, BMC Systems Biology

Gut microbiota: Fibre restores healthy gut microbiota – Alan Morris, Nature Reviews Endocrinology

The human microbiome in evolution – Emily R. Davenport, BMC Biology

Clinical characteristics and long-term prognosis of elderly onset ulcerative colitis – Eun Mi Song, Gastroenterology and Hepatology

Environmental contributions to gastrointestinal and liver cancer in the Asia–Pacific region – Kwang-Pil Ko, Gastroenterology and Hepatology

Effect of oral tobacco use and smoking on outcomes of Crohn’s disease in India – Umang Arora, Gastroenterology and Hepatology

Irritable bowel syndrome in Asia: Pathogenesis, natural history, epidemiology, and management – Kok-Ann Gwee, Gastroenterology and Hepatology

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial – Nina Kimer, Gastroenterology and Hepatology

The role of the microbiome and the use of probiotics in gastrointestinal disorders in adults in the Asia-Pacific region – background and recommendations of a regional consensus meeting – Uday C Ghoshal, Gastroenterology and Hepatology

Animal experiments

Inclusion of Bacillus amyloliquefaciensstrain TOA5001 in the diet of broilers suppresses the symptoms of coccidiosis by modulating intestinal microbiota – Takamitsu Tsukahara, Animal Science Journal

Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases – Yu Wang, Theriogenology

Replacement of alfalfa hay (Medicago sativa L.) with subabul (Leucaena leucocephala) leaf meal in diets of Najdi goats: effect on digestion activity of rumen microorganisms – Tahereh Mohammadabadi, Tropical Animal Health and Production

Animal microbiome

Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing – Kathrin Engel, Microbial Ecology

Plant, root, and soil microbiome

Changes of microbial population and N-cycling function genes with depth in three Chinese paddy soils – Huanhuan Wang, PLOS One

Water and extremophile microbiome

Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome – Sophie S Abby, bioRxiv

Microbes in the news

Artificial intelligence identifies bacteria images quickly, accurately – Greg Slabodkin, Health Data Management

Microbes on the market

Assembly Biosciences, Inc. (ASMB) Reaches $45.08 After 7.00% Up Move; GEOX SPA (GXSBF) Shorts Raised By 18.36% – Stephen Andrade, Herald KS

December 22, 2017

As the end of this year approaches, we have a post filled with plant/soil microbiome papers, as well as a few interesting food microbiology papers — enjoy!

General microbiome

A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis – Romain Savary, ISME

Pregnancy and early life

Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan, Acta Obstetricia et Gynecologica Scandinavica

Liver microbiome

Environmental peer pressure: CD4+ T cell help in tolerance and transplantation – Dana Tedesco, Liver Transplantation

Skin microbiome

Food allergy and atopic dermatitis: Prediction, progression, and prevention – Carla Mastrorilli, Pediatric Allergy and Immunology

Respiratory microbiome

The Lung Microbiome in Idiopathic Pulmonary Fibrosis: A Promising Approach for Targeted Therapies – Fastrès Aline, International Journal of Molecular Sciences

Allergy – European Journal of Allergy and Clinical Immunology

Plant, root, and soil microbiome

Microbial and organic matter patterns in a prescribed burned and thinned managed forest ecosystem – Dessy A. Owiti, Ecosphere

Microbial Interactions and Perspectives for Bioremediation of Pesticides in the Soils – Ratna Prabha, Plant-Microbe Interactions in Agro-Ecological Perspectives

Fungi: An Effective Tool for Bioremediation – Sachin Gupta, Plant-Microbe Interactions in Agro-Ecological Perspectives

Arbuscular Mycorrhizal Fungi Improve Tolerance of Agricultural Plants to Cope Abiotic Stress Conditions – Pablo Cornejo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Assessment of bacterial communities of black soybean grown in fields – Akifumi Sugiyama, Communicative & Integrative Biology

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community – S. Hortal, Scientific Reports

Trichoderma and Its Potential Applications – Monika Jangir, Plant-Microbe Interactions in Agro-Ecological Perspectives

Bacterial Rhizoremediation of Petroleum Hydrocarbons (PHC) – Jai Godheja, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential of Beneficial Bacteria as Eco-friendly Options for Chemical-Free Alternative Agriculture – Ch. Srinivasarao, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential Microbiological Approaches for the Remediation of Heavy Metal-Contaminated Soils – R. Krishnamoorthy, Plant-Microbe Interactions in Agro-Ecological Perspectives

Commercial Microbial Products: Exploiting Beneficial Plant-Microbe Interaction – Pallavi, Plant-Microbe Interactions in Agro-Ecological Perspectives

Interaction Between Beneficial Bacteria and Sugarcane – Guilherme Grodzki Oliveira Figueiredo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential for Developing Low-Input Sustainable Agriculture in the Tropical Andes by Making Use of Native Microbial Resources – Luis Andrés Yarzábal, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant-Microbe Interactions in the Rhizosphere: Mechanisms and Their Ecological Benefits – Kulandaivelu Velmourougane, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant Interaction with Methylotrophic Communities – Manish Kumar, Plant-Microbe Interactions in Agro-Ecological Perspectives

Toward an Integrated Resource Management: Harnessing Trichoderma for Sustainable Intensification in Agriculture – Sumita Pal, Plant-Microbe Interactions in Agro-Ecological Perspectives,

Harnessing the Plant Microbiome: A Key Towards Sustainable Agriculture – Sanjana Kaul, Plant-Microbe Interactions in Agro-Ecological Perspectives

Rhizoremediation of Environmental Contaminants Using Microbial Communities – Ashish A. Prabhu, Plant-Microbe Interactions in Agro-Ecological Perspectives

Role of Plant Growth-Promoting Rhizobacteria for Improving Crop Productivity in Sustainable Agriculture – Abhijeet S. Kashyap, Plant-Microbe Interactions in Agro-Ecological Perspectives

Molecular evidence strongly supports deadwood-inhabiting fungi exhibiting unexpected tree species preferences in temperate forests – Witoon Purahong, ISME

Animal microbiome

Rare symbionts may contribute to the resilience of coral–algal assemblages – Maren Ziegler, ISME

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton – Anny Cárdenas, ISME

Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs – Bram Flahou, ISME

Water and extremophile microbiome

Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates – Jürgen F H Strassert, ISME

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters – Vincent Hervé, ISME

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment – Kohei Ino, ISME

Food microbiome

Evaluation of the use of malic acid decarboxylase-deficient starter culture in NaCl-free cucumber fermentations to reduce bloater incidence – Y. Zhai, Journal of Applied Microbiology

Effect of phenolic compounds on the growth of selected probiotic and pathogenic bacteria – R. Pacheco-Ordaz, Letters in Applied Microbiology

Recent advances in the microencapsulation of omega-3 oil and probiotic bacteria through complex coacervation: A review – Divya Eratte, Trends in Food Science & Technology

Q fever and prevalence of Coxiella burnetii in milk – Andreana Pexara, Trends in Food Science & Technology

Microbes and art

Bioessays Cover Art

 

November 17, 2017

Jobs and events

Lab Assistant – Microbiology, Dublin Ohio

General microbiome

Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications? – Chantal Villeneuve, Microbes and Infection

Human gut microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour, Microbiome

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks – Anubhav Das, Scientific Reports

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut – Natalya Yutin, Nature Microbiology

Fecal Transplantation for Treatment of Clostridium Difficile Infection in Elderly and Debilitated Patients – Tali Friedman-Korn, Digestive Diseases and Sciences

Myocardial infarction and gut microbiota: an incidental connection – Sepideh ZununiVahed, Pharmacological Research

Anxiety, Depression, and the Microbiome: A Role for Gut Peptides – Gilliard Lach, Neurotherapeutics

The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location – John P. Haran, Journal of Medical Microbiology

Human nearly-sterile sites

Risk of Subsequent Sepsis within 90 Days of a Previous Hospital Stay by Type of Antibiotic Exposure – James Baggs, Clinical Infectious Diseases

Human vaginal microbiome

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women – Supriya D. Mehta, Scientific Reports

Animal experiments

The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure – Eun Sung Jung, PLOS ONE

Acute Administration of the Nonpathogenic, Saprophytic Bacterium, Mycobacterium vaccae, Induces Activation of Serotonergic Neurons in the Dorsal Raphe Nucleus and Antidepressant-Like Behavior in Association with Mild Hypothermia – Philip H. Siebler, Cellular and Molecular Neurobiology

Maternal High Fat Diet and its Consequence on the Gut Microbiome: A Rat Model – Phyllis E. Mann, Gut Microbes

Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice – Alessandra Bragonzi, International Journal of Molecular Sciences

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis – Marion Darnaud, Gastroenterology

Animal microbiome

Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil – Andressa Zelenski de Lara Pinto, PLOS ONE

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li, PLOS ONE

Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study – Veronika Jílková, Soil Biology and Biochemistry

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola – Aubree J. Hill, EcoHealth

Plant, root, and soil microbiome

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils – Xian Xiao, Molecular Ecology

Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils – Gabriel Sigmund, Journal of Hazardous Materials

Epiphytic Bacteria Alter Floral Scent Emissions – Carola Helletsgruber, Journal of Chemical Ecology

In vitro bacterization of banana (Musa spp.) with native endophytic and rhizospheric bacterial isolates: Novel ways to combat Fusarium wilt – M. Kavino, European Journal of Plant Pathology

Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn, PeerJ

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert – Cristina Montiel-González, PeerJ

Entomopathogenic Fungi as Dual Control Agents against Both the Pest Myzus persicae and Phytopathogen Botrytis cinerea – Hwi-Geon Yun, Mycobiology

Glycomyces rhizosphaerae sp. nov., isolated from the root and rhizosphere soil of wheat (Triticum aestivum L.) – Wenchao Li, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation – G. Llorens-Blanch, Waste Management

Iron Chloride Flocculation of Bacteriophages from Seawater – Bonnie T. Poulos, Bacteriophages

Multi-Level Contact Oxidation Process Performance When Treating Automobile Painting Wastewater: Pollutant Removal Efficiency and Microbial Community Structures – Yufang Zhu, Water

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments – Brodie Sutcliffe, Microbial Ecology

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization? – Dave R. Clark, Global Ecology and Biogeography

Diversity of microbiota found in coffee processing wastewater treatment plant – Josiane Ferreira Pires, World Journal of Microbiology and Biotechnology

Food microbiology

Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions – M. Oliveira, Letters in Applied Microbiology

Bioinformatics

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities – Weizhi Song, PeerJ

Techniques

Significance estimation for large scale metabolomics annotations by spectral matching – Kerstin Scheubert, Nature

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) – Mette Myrmel, PLOS ONE

Developing selective media for quantification of multispecies biofilms following antibiotic treatment – Eva Vandeplassche, PLOS ONE

Microbes in the news

Microbiology: Bacteria disarm host-defence proteins – John D. MacMicking, Nature News and Views

Probiotics: Health boost or waste of cash? – Anne Allred, 5-ON-YOUR-SIDE

Cygnus Open for Business; Crew Unloading New Bacteria, Plant and Tech Studies – Mark Garcia, NASA blog

Bacteria Hysteria

Your supermarket is filled with germs — here are 7 facts that will make you dread grocery shopping –  Joanna Fantozzi, Insider

November 12, 2017

General microbiome

Rapid colonization of artificial endolithic uninhabited habitats – Charles S. Cockell, International Journal of Astrobiology

A bacterial pioneer produces cellulase complexes that persist through community succession – Sebastian Kolinko, Nature Microbiology

Endoglucanase and Xylanase Production by Chryseobacterium Species Isolated from Decaying Biomass – Asisipho Nkohla, Polish Journal of Environmental Studies

Human gut microbiome

Extended screening costs associated with selecting donors for fecal microbiota transplantation for treatment of metabolic syndrome-associated diseases – Laura J Craven, Open Forum Infectious Diseases

Fecal microbiota signatures of adult patients with different types of short bowel syndrome – Yuhua Huang, Gastroenterology

Association Between Small Intestinal Bacterial Overgrowth by Glucose Breath Test and Coronary Artery Disease – Andre Fialho, Digestive Diseases and Sciences

Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions – Jiayan Li, Microbial Ecology

Animal experiments

Transcriptomics-driven lipidomics (TDL) identifies the microbiome-regulated targets of ileal lipid metabolism – Anirikh Chakrabarti, npj Systems Biology and Applications

Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis – Yuan Tian, The Journal of Nutritional Biochemistry

Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish – Victor Schmidt, mSystems

Effect of partially replacing a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows – E. Castillo-Lopez, Journal of Applied Microbiology

How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota – Alyssa Bost, Molecular Ecology

Gut microbiomes and reproductive isolation in Drosophila – Philip T. Leftwich, PNAS

Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages – Shenzheng Zeng, PeerJ

Animal microbiome

FVD: The fish-associated virus database – Yaxin Chen, Infection, Genetics and Evolution

Bats host diverse parvoviruses as possible origin of mammalian dependoparvoviruses and source for bat–swine interspecies transmission –  Susanna K. P. Lau, Journal of General Virology

Forest canopy, water level, and biopesticide interact to determine oviposition habitat selection in Aedes albopictus – Christopher A. Binckley, Journal of Vector Ecology

Ecological characterization of Aedes aegyptilarval habitats (Diptera: Culicidae) in artificial water containers in Girardot, Colombia – Diana C. Garcia-Sánchez, Journal of Vector Ecology

Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water – Renata Medina-Silva, Antonie van Leeuwenhoek

Plant, root, and soil microbiome

Changes in the soil bacterial community along a pedogenic gradient – Manuel Sánchez-Marañón, Scientific Reports

 

Rhizosphere activity and atmospheric methane concentrations drive variations of methane fluxes in a temperate forest soil – Jens-Arne Subke, Soil Biology and Biochemistry

The Impact of the Diurnal Cycle on the Microbial Transcriptome in the Rhizosphere of Barley – Divyashri Baraniya, Microbial Ecology

The temperature sensitivity of soil organic matter decomposition is constrained by microbial access to substrates – Gabriel Y.K. Moinet, Soil Biology and Biochemistry

Application of Aspergillus aculeatus to rice roots reduces Cd concentration in grain – Yan Xie, Plant and Soil

Screening Bacillus species as biological control agents of Gaeumannomyces graminis var. tritici on wheat – Lirong Yang, Biological Control

Soil geochemical factors regulate Cd accumulation by metal hyperaccumulating Noccaea caerulescens (J. Presl & C. Presl) F.K. Mey in field-contaminated soils – Carla E. Rosenfeld, Science of The Total Environment

Antibiotics in the Soil: Sources, Environmental Issues, and Bioremediation – Umesh B. Jagtap, Antibiotics and Antibiotics Resistance Genes in Soils

Water and extremophile microbiome

Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach – Paula M. Tribelli, Journal of Industrial Microbiology & Biotechnology

Potential Role of Halophile in Crude Glycerol Based Biorefinery – Noopur Singh, Biorefining of Biomass to Biofuels

Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein – Chen Wang, PLOS one

Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp. – Jake V. Bailey, mBio

Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation – Jonathan Botha, Extremophiles

Prospects of Solvent Tolerance in Butanol Fermenting Bacteria – Shuvashish Behera, Biorefining of Biomass to Biofuels

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead – Susanna M. Blunt, Science of the Total Environment

Effect of TiO2 and CeO2 nanoparticles on the metabolic activity of surficial sediment microbial communities based on oxygen microelectrodes and high-throughput sequencing – Lingzhan Miao, Water Research

Performance and microbial communities in a combined bioelectrochemical and sulfur autotrophic denitrification system at low temperature – Dan Chen, Chemosphere

Ongoing biodegradation of Deepwater Horizon oil in beach sands: Insights from tracing petroleum carbon into microbial biomass – Joel T. Bostic, Marine Pollution Bulletin

Antibiotic degradation and microbial community structures during acidification and methanogenesis of swine manure containing chlortetracycline or oxytetracycline – Fubin Yin, Bioresource Technology

Metagenomics profiling for assessing microbial diversity in both active and closed landfills – Mohamad Yusof Zainun, Science of The Total Environment

Development of a microbial community-based index of biotic integrity (MC-IBI) for the assessment of ecological status of rivers in the Taihu Basin, China – Lihua Niu, Ecological Indicators

Microbial community response to silver nanoparticles and Ag+in nitrifying activated sludge revealed by ion semiconductor sequencing – Carley A. Gwin, Science of The Total Environment

Anaerobic co-digestion of pig manure and food waste; effects on digestate biosafety, dewaterability, and microbial community dynamics – C. Dennehy, Waste Management

Evaluating the impacts of triclosan on wastewater treatment performance during startup and acclimation – R. M. Holzem, Water Science and Technology

Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage – Bhargavi Ramanathan, Frontiers in Microbiology

Live Faecalibacterium prausnitzii induces greater TLR2 and TLR2/6 activation than the dead bacterium in an apical anaerobic co-culture system – Eva Maier, Cellular Microbiology

Food microbiome

A mathematical model to predict early quality attributes in hake during storage at low temperature – C. Vilas, Journal of Food Engineering

Chemical, Physiochemical, and Microstructural Properties, and Probiotic Survivability of Fermented Goat Milk Using Polymerized Whey Protein and Starter Culture Kefir Mild 01 – Hao Wang, Food Microbiology & Safety

Re-evaluation of mono- and di-glycerides of fatty acids (E 471) as food additives – EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS), European Food Safety Authority

Opportunities and hurdles of edible insects for food and feed – D. Dobermann, Nutrition Bulletin

Re-evaluation of alginic acid and its sodium, potassium, ammonium and calcium salts (E 400–E 404) as food additives – EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS), European Food Safety Authority

The SALAMANDER project: SALivAry bioMarkers of mediterraneAN Diet associated with long-tERm protection against type 2 diabetes – G. B. Proctor, Nutrition Bulletin

Polyphenols and health: Interactions between fibre, plant polyphenols and the gut microbiota – C. A. Edwards, Nutrition Bulletin

Techniques

Optimization of Culture Conditions for the Production of Halophilic Protease by Newly Isolated Bacillus sonorensis – S. Sankaralingam, American-Eurasian Journal of Agricultural & Environmental Science

November 5, 2017

 

A shorter digest today, but includes a lot of human gut microbiome studies and a cool study on microbes used to treat snake bites!

General microbiome

Comparison of two Jatropha species (Euphorbiaceae) used popularly to treat snakebites in Northeastern Brazil: Chemical profile, inhibitory activity against Bothrops erythromelas venom and antibacterial activity – Juliana Félix-Silva, Journal of Ethnopharmacology

Multi-site human microbiome

A slippery slope: On the origin, role and physiology of mucus – Farhan Taherali, Advanced Drug Delivery Reviews

Human gut microbiome

Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial –  Peter Holger Johnsen, The Lancet Gastroenterology & Hepatology

Estrogens and Female Liver Health – Karen L. Chen, Steroids

Safety and Efficacy of Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection in Patients With Cancer Treated With Cytotoxic Chemotherapy: A Single-Institution Retrospective Case Series – Mehrdad Hefazi, Mayo Clinic Proceedings

Gut Microbiota and Cancer Patients: A Broad-Ranging Relationship – Giovanni Cammarota, Mayo Clinic Proceedings

Gut microbiota and hypertension: From pathogenesis to new therapeutic strategies – Yongbo Kang, Clinics and Research in Hepatology and Gastroenterology

Preface to “Gut microbiome in health and disease” – Maikel P. Peppelenbosch, Best Practice & Research Clinical Gastroenterology

Results of the implementation of a multidisciplinary programme of faecal microbiota transplantation by colonoscopy for the treatment of recurrent Clostridium difficile infection – Antonio López-Sanromán, Gastroenterología y Hepatología (English Edition)

Animal experiments

Alterations in ruminal bacterial populations at induction and recovery from diet-induced milk fat depression in dairy cows – D.W. Pitta, Journal of Dairy Science

Chronic chlorpyrifos exposure elicits diet-specific effects on metabolism and the gut microbiome in rats – Bing Fang, Food and Chemical Toxicology

Housing influences tissue cytokine levels and the fecal bacterial community structure in rats – Padmaja Shastri, Journal of Functional Foods

An intact gut microbiota may be required for lactoferrin-driven immunomodulation in rats – Yongping Wen, Journal of Functional Foods

Untargeted metabolomic profiling of urine in Wistar rats reveals enhanced bioavailability of soy isoflavones post short-term consumption of noni (Morinda citrifolia) juice – José-Manuel Fallas-Ramirez, Journal of Functional Foods

Plant, root, and soil microbiome

Long and short term effects of solarization on soil microbiome and agricultural production – Housam Kanaan, Applied Soil Ecology

Water and extremophile microbiome

Microbial communities involved in biogas production exhibit high resilience to heat shocks – Abendroth Christian, Bioresource Technology

Food microbiome

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins, Food Research International

Microbial ecology along the processing of Spanish olives darkened by oxidation – Eduardo Medina, Food Control

Co-fermentation of onion and whey: A promising synbiotic combination – Federica Tinello, Journal of Functional Foods

Diverse yeasts for diverse fermented beverages and foods – Chris Todd Hittinger, Current Opinion in Biotechnology

Techniques

Microbiome measurement: Possibilities and pitfalls – Djawad Radjabzadeh, Best Practice & Research Clinical Gastroenterology

High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration – DongFeng Yan, Biological Conservation

Commensal Koch’s postulates: establishing causation in human microbiota research – B Anne Neville, Current Opinion in Microbiology

Microbes in the news

Disease outbreak at Marine Corps boot camp abates in San Diego – Carl Prine, The San Diego Union-Tribune