Category Archives: General Microbiome

October 15, 2017

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General microbiome

Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces – Christel Schmeisser, Functional Metagenomics: Tools and Applications

Prediction analysis for microbiome sequencing data – Tao Wang, arxiv

Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria – Jiujun Cheng, Functional Metagenomics: Tools and Applications

Moulds associated with contaminated ocular and injectable drugs: FDA recalls, epidemiology considerations, drug shortages, and aseptic processing – Donald G. Ahearn, Medical Mycology

Human skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs – Bo Zeng, Frontiers in Microbiology

Human vaginal microbiome

Role of Molecular Biology in Diagnosis and Characterization of Vulvo-Vaginitis in Clinical Practice – Donders G.G.G., Gynecologic and Obstetric Investigation

Human gut microbiome

A Review of the Oesophageal Microbiome in Health and Disease – Dervla Kelly, Methods in Microbiology

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients – Ryo Inoue, Journal of Clinical Biochemistry and Nutrition

Human oral microbiome

The Effect of Supragingival Biofilm Re-development on the Subgingival Microbiota in Chronic Periodontitis – Fátima Aparecida Rocha Resende Hartenbach, Archives of Oral Biology

Animal experiments

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch, PNAS

Comparative study of probiotic effects of Lactobacillusand Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice – Rostyslav V. Bubnov, The EPMA Journal

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: methane production and microbial community in CSTR process – Xuemei Wang, Bioresource Technology

Animal microbiome

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites – Lavanya Reddivari, mSystems

Hymenobacter cavernae sp. nov., isolated from a karst cave – Hai-Zhen Zhu, International Journal of Systematic and Evolutionary Microbiology

Plant, root, and soil microbiome

Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment – Tongchu Deng, International Journal of Systematic and Evolutionary Microbiology

Deinococcus taklimakanensis sp. nov., isolated from desert soil –  Zuobing Liu, International Journal of Systematic and Evolutionary Microbiology

Improvement of the catalytic characteristics of a salt-tolerant GH10 xylanase from Streptomyce rochei L10904 – Qin Li, International Journal of Biological Macromolecules

Trees harness the power of microbes to survive climate change – Jennifer A. Lau, PNAS

Exploring the earthworm gut as model for soil microbial ecology – Fatima Hussain, MBL

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

The intimate talk between plants and microorganisms at the leaf surface – Wendy Aragón, Journal of Experimental Botany

Metagenomics of Plant Microbiomes – G. Brader, Functional Metagenomics: Tools and Applications

Effects of different soil remediation methods on inhibition of lead absorption and growth and quality of Dianthus superbus L. – Xiaoyu Yang, Environmental Science and Pollution Research

Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens – Telsa Willsey, Frontiers in Plant Science

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

Switchgrass Yield, Nutrient Uptake, And Rhizosphere Microbial Community Composition As Affected By Cultivar And Soil Fertility – Anne Sawyer, University of Minnesota Digital Conservancy

Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China – Yongxing Cui, Soil Biology and Biochemistry

Soil microbiota respond to green manure in organic vineyards – Claudia M. O. Longa, Journal of Applied Microbiology

Water and extremophile microbiome

Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia – Yana Ryzhmanova, International Journal of Systematic and Evolutionary Microbiology

100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions – Vladimir S. Cheptsov, Extremophiles

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities – Laura Selbmann, Extremophiles

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations – Almudena Rivadeneyra, Extremophiles

Biosurfactant production by haloalkaliphilic Bacillusstrains isolated from Red Sea, Egypt – Khouloud M.Barakat, The Egyptian Journal of Aquatic Research

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide – Yuguang Wang, Bioresource Technology

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Waste microbes

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion – Chunhui Zhao, Bioresource Technology

Antibiotic resistance genes and associated microbial community conditions in aging landfill systems – Dong Wu, Environmental Science and Technology

Bioinformatics

Bioinformatics in Microbiome Analysis – Yuhan Hao, Methods in Microbiology

Techniques

Enhancing Metagenomic Approaches Through Synthetic Biology – Luana de Fátima Alves, Functional Metagenomics: Tools and Applications

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes – Marcela Hernández, Functional Metagenomics: Tools and Applications

The P/N (Positive-to-Negative Links) Ratio in Complex Networks—A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma, Microbial Ecology

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach – Alinne L. R. Santana-Pereira, Functional Metagenomics: Tools and Applications

Emerging whole-cell modeling principles and methods – Arthur P. Goldberg, arxiv

Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli – Anna Lewin, Functional Metagenomics: Tools and Applications

Microbes in the news

AST: The Linchpin of Antimicrobial Stewardship – James Lewis, ModernMedicine Network

The Black Death Rages In Madagascar –  Julianna LeMieux, American Council on Science and Health

Report: 17 New Species Of Bacteria Found Every Day In World’s Rainforest Cafés – The Onion (Satire)

October 14, 2017

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The marine sponge microbiome, bacterial communication mediated by hydrogen sulfide, a gnotobiotic pig model to study interactions between a defined gut community and antibiotics, probiotics, and rotavirus.

General microbiome

Evolutionary contribution to coexistence of competitors in microbial food webs – Teppo Hiltunen – Proceedings of the Royal Society Biological Sciences

Pregnancy and early life

Effects of Therapeutic Hypothermia on the Gut Microbiota and Metabolome of Infants suffering Hypoxic-Ischemic Encephalopathy at birth – C Watkins – The International Journal of Biochemistry and Cell Biology

Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose? – O Sakwinska – Beneficial Microbes

Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy – J S Y Low – Beneficial Microbes

Human oral microbiome

Exopolysaccharides regulate calcium flow in cariogenic biofilms – Monika Astasov-Frauenhoffer – PLOS ONE

Human gut microbiome

The Gut Microbiome Feelings of the Brain: A Perspective for Non-Microbiologists – Aaron Lerner – Microorganisms

The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study – K Adamberg – Beneficial Microbes

Review: Our gut microbiota: a long walk to homeostasis – L M T Dicks – Beneficial Microbes

Animal experiments

Flavanol-Rich Cocoa Powder Interacts with Lactobacillus rhamnossus LGG to Alter the Antibody Response to Infection with the Parasitic Nematode Ascaris suum – Saebyeol Jang – Nutrients

Effect of antibiotic, probiotic, and human rotavirus infection on colonisation dynamics of defined commensal microbiota in a gnotobiotic pig model – H C Huang – Beneficial Microbes

Animal microbiome

Pre-print: An RNA Virome associated to the Golden Orb-weaver Spider Nephila clavipes – Humberto J Debat – bioRxiv

The sponge microbiome project – Lucas Moutinho-Silva – Gigascience

Water and extremophile microbiome

Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline – Luis Linares-Otoya – Marine Drugs

Bioinformatics

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data – Fanny Berglund – Microbiome

More microbes

Pre-print: Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria – Xiaowei Jiang – bioRxiv

Pre-print: H2S mediates interbacterial communication through the air reverting intrinsic antibiotic resistance – Daniel Thomas-Lopez – bioRxiv

Pre-print: Interplay between antibiotic efficacy and drug-induced lysis underlies enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

Microbes in the news

How switches work in bacteria – EurekAlert

Opinion: Microbiology Needs More Math – Mikhail Tikhonov – The Scientist

Fluctuating environments can help cooperating bacteria – Science Daily

How to study the inside of a humpback whale’s blowhole? Drones, of course – Teresa Welsh – The Sacramento Bee

Scientists Generate 3D Map of Gut Microbiome – Genetic Engineering and Biotechnology News

Microbes on the market

Research Foundation Calls for Canadian Proposals to Study Dietary Interactions with Microbiota – PR Newswire

October 10, 2017

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Effects of amino acid supplements on metabolic health, a discussion of the broader risks and benefits of microbiome research, a book chapter evaluating microbiome statistical analysis tools.

Events and jobs

Assistant Professor in Microbiology, Tenure Track – Department of Microbiology & Immunology, University of British Columbia

General microbiome

Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research – Daria Shamarina – Microbiome

Pregnancy and early life

Review: Early microbiota, antibiotics and health – Alicja M Nogacka – Cellular and Molecular Life Sciences

Human gut microbiome

Amino acid supplements and metabolic health: a potential interplay between intestinal microbiota and systems control – Francesco Bifari – Genes & Nutrition

Microbial dysbiosis in spouses of ulcerative colitis patients: Any clues to disease pathogenesis? – Dario Sorrentino – World Journal of Gastroenterology

Phages and viruses

Pre-print: Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – Alexander Harms – bioRxiv

Bioinformatics

Book Chapter: Processing and Analyzing Human Microbiome Data – Xuan Zhu – Statistical Human Genetics

Interpretation of microbiota-based diagnostics by explaining individual classifier decisions – A Eck – BMC Bioinformatics

Techniques

Pre-print: Umbilical cord blood diagnostics for early onset sepsis in premature infants: detection of bacterial DNA and systemic inflammatory response – Leena B Mithal – bioRxiv

Pre-print: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs – Robert C Edgar – PeerJ

Microbes in the news

Bacteria with synthetic gene circuit self-assemble to build working device with gold nanoparticles – Phys Org

New test identifies antibiotic-resistant bacteria in 30 minutes – The Statesman

Microbes on the market

Summit Highlights Microbiome Preservation During Ridinilazole Treatment in Exploratory Phase 2 Clinical Trial at ID Week 2017 – Globe Newswire

October 8, 2017

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General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

The fecal microbiome of ALS patients – David Brenner, Neurobiology of Aging

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – Christopher L. Hager, Digestive and Liver Disease

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

Scientists are trying to figure out how to keep bacteria from running rampant on space missions –  Claire Maldarelli, Popular Science

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

October 7, 2017

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Events and jobs

Director of the Microbiome Research Laboratory – UT Southwestern

DOCTORAL STUDENT OR POSTDOCTORAL RESEARCHER –  Faculty of Veterinary Medicine, University of Helsinki – Application deadline: Nov 5, 2017

 

General microbiome

Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production – Y Boltyanskaya – Antonie van Leeuwenhoek

Biochemical Features of Beneficial Microbes: Foundations for Therapeutic Microbiology. – MA Engevik – Microbiology Spectrum

 

Pregnancy and early life

Immunological tolerance, pregnancy and pre-eclampsia: the roles of semen microbes and the father – LC Kenny – bioRxiv

 

Human respiratory microbiome

Long-term effects of inhaled corticosteroids on sputum bacterial and viral loads in COPD. – M Contoli – The European Respiratory Journal

 

 

Human gut microbiome

Bifidobacteria and the infant gut: an example of co-evolution and natural selection. – F Turroni – Cellular and Molecular Life Sciences

Inflammatory bactericidal lectin RegIIIβ: Friend or Foe for the host? – T Miki – Gut Microbes

Review: Host-microbiota interplay in mediating immune disorders. – KM Felix – Annals of the New York Academy of Sciences

Review: Probiotics for the prevention of Hirschsprung-associated enterocolitis: a systematic review and meta-analysis. – H Nakamura – Pediatric Surgery International

 

Animal experiments 

Can intestinal microbiota be associated with non-intestinal cancers? – C Jacqueline – Scientific Reports

Gnotobiotics: getting a grip on the microbiome boom – S Mallapaty – Lab Animal

Nanoparticle curcumin ameliorates experimental colitis via modulation of gut microbiota and induction of regulatory T cells. – M Ohno – PLoS One

 

Animal microbiome 

Comparative analysis of microbial communities associated with bacteriomes, reproductive organs and eggs of the cicada Subpsaltria yangi. – D Wang – Archives of Microbiology

Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats. – H Shen – Microbiology Open

Elucidating the microbial community associated with the protein preference of sludge degrading worms – S de Valk – Environmental Technology

 

Plant, root and soil microbiome

Mycorrhizal fungi show regular community compositions in natural ecosystems. – E Verbruggen – The ISME Journal

Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays – J Vacheron – Molecular Plant-Microbe Interactions

Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development. – SC Castle – Oecologica

 

Water microbiome and extremophile 

Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. – D Kalenitchenko – The ISME Journal

Importance of free-living and particle-associated bacteria for the growth of the harmful dinoflagellate Prorocentrum minimum: evidence in culture stages – BS  Park – Marine and Freshwater Research

Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. – R Rathour – Genome Announcements

 

Built environment 

Managing the excessive proliferation of glycogen accumulating organisms in industrial activated sludge by nitrogen supplementation: A FISH-NanoSIMS approach – CA Onetto – Systematic and Applied Microbiology

 

 

Phages and viruses

Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. – G Freer – Current Medicinal Chemistry

 

Techniques

Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing – P Schwendner – Microbiome

 

Microbes in the news

Puppies Linked To Bacterial Infection Outbreak Across 12 States – Forbes

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

Episode Review: VICE’s ‘Post-Truth News and Microbiome’ – The Hoya

Second grade handwashing experiment leads to big decrease in bacteria, illness – EurekAlert

Validating microbiome claims:Including the latest DNA techniques-Formulation Summit – Cosmetics Design Europe

Macromolecules: Weapons in the Fight Against Antibiotic Resistance  – American Veterinarian

Scientists are trying to figure out how to keep bacteria from running rampant on space missions – Popular Science

Bacteria can spread antibiotic resistance through soil – Phys.org

October 6, 2017

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Events and jobs

Clinical Laboratory Technologist IV (SL-1), Microbiology Laboratory – Stony Brook University Hospital – Posting End Date: Nov 2, 2017, 11:59:00 PM

Assistant Professor in Microbiology – Emporia State University – Deadline- open until filled

Assistant Professor in Virology and Microbiome Research – Auburn University, Alabama – Deadline- open until filled

Faculty Position in Microbial Environmental Metagenomics and Bioinformatics – University of Kansas – Initial review of applications: Nov 14, 2017

 

General microbiome

A mechanism for prime-realignment during influenza A virus replication – J Oymans – bioRxiv

 

 

Human vaginal microbiome

Microbiome: Detecting diversity – C Humphries – Nature

 

Human gut microbiome

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome. – DA Medina – International Journal of Molecular Sciences

Synthetic biology and the gut microbiome. – J Dou – Biotechnology Journal

The Gut and Its Microbiome as Related to Central Nervous System Functioning and Psychological Well-being: Introduction to the Special Issue of Psychosomatic Medicine. – EA Mayer – Psychosomatic Medicine

Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease. – CE Rosen – BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology.

 

Animal experiments 

Colonic thioguanine pro-drug: investigation of microbiome and novel host metabolism. – T Florin – Gut Microbes

The gastric microbiome, its interaction with Helicobacter pylori, and its potential role in the progression to stomach cancer – JM Noto – PLoS Pathogens

Review: Microbiota, cirrhosis, and the emerging oral-gut-liver axis. – C Acharya – JCI Insight

 

Animal microbiome 

Interactions of pathogenic and commensal strains of Mannheimia haemolytica with differentiated bovine airway epithelial cells grown at an air-liquid interface – D Cozens – bioRxiv

Ixodes scapularis does not harbor a stable midgut microbiome – BD Ross – bioRxiv

 

Plant, root and soil microbiome

Protists are an integral part of the Arabidopsis thaliana microbiome. – M Sapp – Environmental Microbiology

Fusarium verticillioides: Advancements in Understanding the Toxicity, Virulence, and Niche Adaptations of a Model Mycotoxigenic Pathogen of Maize. – AA Blacutt – Phytopathology

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities – ER Hester – bioRxiv

Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. – J Almario – Proceedings of the National Academy of Sciences of the United States of America

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration. – CP Ward – Nature Communications

Changes in the abundance and structure of bacterial communities in the greenhouse tomato cultivation system under long-term fertilization treatments – X Zhang – Applied Soil Ecology

 

 

Phages and viruses

Evolution: Zapping viral RNAs – SP Goff – Nature

 

Techniques

Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System. – JF Chignell – Microbial Ecology

Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology. – L Bircher – Microbial Biotechnology

On the Reproduction Number of a Gut Microbiota Model. – C Barril – Bulletin of Mathematical Biology

 

Microbes in the news

Woods: The art of aging cheese – Lake Geneva News

Methane-Munching Bacteria Could Poop Out Your Future Clothes – Geek.com

XOMA (XOMA) Announces Multiple New License Agreements for Proprietary Phage Display Libraries – Biospace

Superbug superweapon: Identifying antibiotic-resistant bacteria in 30 minutes – New Atlas

New fundamental insight into the battle against bacteria – Science Daily

Ribaxamase Protects Gut Microbiome, Cuts Opportunistic C. diff Risk – MPR

October 4, 2017

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Today’s digest features excellent reviews on recent advances in cryo-electron microscopy technology for understanding bacterial ribosome assembly,  and impact of gut microbiome on therapeutics. Happy reading!

General microbiome

Towards standards for human fecal sample processing in metagenomic studies – Paul I Costea – Nature Biotechnology

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium – Rashmi Sinha – Nature Biotechnology

Editorial : Microbiome yarns: microbiome basis of memory – Kenneth Timmis – Microbial Biotechnology

Review : Cross Talk: The Microbiota and Neurodevelopmental Disorders – John R. Kelly – Frontiers in Neuroscience

Review : Gut Microbiota, Immune System, and Bone – P. D’Amelio – Calcified Tissue International

Pregnancy and early life

Meconium microbiome as a new source of information about long-term health and disease: questions and answers – P. Wilczyńska – The Journal of Maternal-Fetal & Neonatal Medicine

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life – Lionel Brazier – Plos one

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children – Susannah J. Salter – Plos one

Human gut microbiome

Review : Microbiota in digestive cancers: our new partner? – Anthony Lopez – Carcinogenesis

*Review : Impacts of the Human Gut Microbiome on Therapeutics – Yoshiki Vázquez-Baeza – Annual Reviews

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors – C Liu – Leukemia

Natural polyreactive IgA antibodies coat the intestinal microbiota – Jeffrey J. Bunker – Science

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota – Jennifer L Kaczmarek – The American Journal of Clinical Nutrition

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – Liang Chi – Toxicological Sciences

Animal experiments

Probiotics modulate gut microbiota and improve insulin sensitivity in DIO mice – Renata A.Bagarolli – The Journal of Nutritional Biochemistry

Decaffeinated green and black tea polyphenols decrease weight gain and alter microbiome populations and function in diet-induced obese mice – Susanne M. Henning – European Journal of Nutritional

Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism – Anna V. Golubeva – EBioMedicine

Repeated Oral Exposure to Nε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice – Nesreen ALJahdali – Digestive Disease Sciences

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery – Eric R. Burrough – Frontiers in Veterinary Science

Animal microbiome

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses – Chiara Ferrario – Environmental Microbiology

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood – Tomas Erban – PeerJ

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – Qi Xu – Plos One

Plant, root, and soil microbiome

Implication of graphene oxide in Cd-contaminated soil: A case study of bacterial communities – TingXiong – Journal of Environmental Management

Elucidating the microbial community associated with the protein preference of sludge degrading worms – Steef de Valk – Environmental Technology

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition – Srisailam Marupakula – Environmental Microbiology

A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics – Xiao-ZhongZhong -Bioresource Technology

Water and extremophile microbiome

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness – Simone Fontana – The ISME Journal

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – Catarina L.Amorim – Ecotoxicology and Environmental Safety

Food Microbiology

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – Maren Vollmer – Food Research International

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Beneficial effects of a probiotic blend on gastrointestinal side effects induced by leflunomide and amlodipine in a rat model – S.C. Song – Beneficial Microbes

Phages and viruses

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin – Simone Rampelli – Environmental Microbiology

Metabolomics

Identification of phenolic metabolites in human urine after the intake of a functional food made from grape extract by a high resolution LTQ-Orbitrap-MS approach – Gemma Sasot – Food Research International
http://www.sciencedirect.com/science/article/pii/S0963996917300297?via%3Dihub

Bioinformatics

A broken promise: microbiome differential abundance methods do not control the false discovery rate – Stijn Hawinkel – Briefings in Bioinformatics
https://academic.oup.com/bib/article/doi/10.1093/bib/bbx104/4091293/A-broken-promise-microbiome-differential-abundance

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson – Briefings in Bioinformatics

Ananke: temporal clustering reveals ecological dynamics of microbial communities – Michael W. Hall – PeerJ

Detection of Increased Plasma Interleukin-6 Levels and Prevalence of Prevotella copri and Bacteroides vulgatus in the Feces of Type 2 Diabetes Patients – Aline Zazeri Leite – Frontiers in Immunology

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets – David Ainsworth – Nucleic Acids Research

Techniques

* The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly – Aida Razi – Nucleic acids Research

Anitha’s non-microbiology picks

A cold, clear view of life wins chemistry Nobel

Nobel physics prize awards discovery in gravitational waves

Medicine Nobel Prize Goes to Circadian Rhythm Researchers

New portable blood analyzer could improve anemia detection worldwide

Computational study sheds doubt on latest theory of birds’ mysterious magnetic compass

 

October 2, 2017

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This Monday we have quite short digest with interesting review from K. Rosenthal about microbial single cell analysis,  T. K. Hattenrath-Lehmann tells us about microbes associated with harmful algal blooms while G. Chen demonstrates mutualistic interaction between bacteria in anaerobic mixed culture. Enjoy your reading.

Events and jobs

Tenure Track Faculty Position in Microbial Systems/Synthetic Biology, Chestnut Hill, Massachusetts

General microbiome

Review: Beyond the bulk: disclosing the life of single microbial cells  – Katrin Rosenthal – FEMS Microbiology Reviews

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture – Gao Chen – Environmental Microbiology

Human skin microbiome

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria – S. Patrick – The Bone & Joint Journal

Human nearly-sterile sites 

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation – E Xiao – Stem Cell Research & Therapy

Human gut microbiome

Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells – Cláudia Mara Lara Melo Coutinho –  Microbial Pathogenesis

Animal experiments

Changes in the microbiota cause genetically modified Anopheles to spread in a population – Andrew Pike – Science

Plant, root, and soil microbiome

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – bioRxiv

Novel archaeal thermostable cellulases from an oil reservoir metagenome – Anna Lewin – AMB Express

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem – Kai Zhang – Scientific Reports

Water and extremophile microbiome 

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata -Theresa K.Hattenrath-Lehmann – Harmful Algae

Metagenomic insights into zooplankton-associated bacterial communities – Daniele De Corte – Environmental Microbiology

Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community – Anyi Hu – Environmental Microbiology

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – Alexandra Pontefract – Frontiers in Microbiology

Bioinformatics

SAMSA2: A standalone metatranscriptome analysis pipeline – Samuel T. Westreich – bioRxiv

Microbes in the news 

Oral sex spreading unstoppable bacteria

 

October 1, 2017

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Events and jobs

Microbiome Center Networking Event – Plant Pathology and Environmental Microbiology, Penn State Agricultural College – October 3, 2017, 4:30 PM – 6:30 PM

General microbiome

Review: Old friends, microbes, and allergic diseases – N Shimojo – Allergology International

 

Human skin microbiome

Study of skin and nail Candida species as a normal flora based on age groups in healthy persons in Tehran-Iran – Z Rafat – Journal de Mycologie Médicale

 

Human gut microbiome

Variability in Eating Frequency is Associated with the Human Gastrointestinal Microbiota –  E Banishay – Journal of the Academy of Nutrition and Dietetics

Animal experiments 

The gut-liver axis: impact of a mouse model of small-bowel bacterial overgrowth –  Q Wang – Journal of Surgical Research

Metagenomic insights into the effects of oligosaccharides on the microbial composition of cecal contents in constipated mice – L Wang – Journal of Functional Foods

Effects of gut microbiota disturbance induced in early life on the expression of extrasynaptic GABA-A receptor α5 and δ subunits in the hippocampus of adult rat  – L Liang – Brain Research Bulletin

A Subset of Polysaccharide Capsules in the Human Symbiont Bacteroides thetaiotaomicron Promote Increased Competitive Fitness in the Mouse Gut – NT Porter – Cell and Host Microbe

Animal microbiome 

Hype or Opportunity? Using Microbial Symbionts in Novel Strategies for Insect Pest Control – AK Arora – Journal of Insect Physiology

Nutritional immunology: Diversification and diet-dependent expression of antimicrobial peptides in the black soldier fly Hermetia illucens – H Vogel – Developmental & Comparative Immunology

The impact of antibiotics on the Intestinal microbiota needs to be re-defined in order to optimize the antibiotic usage – E Ruppé – Clinical Microbiology and Infection

Pathogen invasion changes the intestinal microbiota composition and induces innate immune responses in the zebrafish intestine – HT Yang – Fish & Shellfish Immunology

Plant, root and soil microbiome

Experimental warming reduces the diversity and functional potential of the Sphagnum microbiome – AA Carrell – bioRxiv

Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome – S Jacquiod – Journal of Hazardous Materials

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms – M Wang – Ecotoxicology and Environmental Safety

Built environment 

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – CL Amorim – Ecotoxicology and Environmental Safety

Food microbiology

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management – JJ Lee –  Food Research International

Review: Novel insights into the microbiology of fermented dairy foods – G Macori – Current Opinion in Biotechnology

Simulated gastrointestinal conditions increase adhesion ability of Lactobacillus paracasei strains isolated from kefir to Caco-2 cells and mucin – AA Bengoa – Food Research International

Chapter: Chapter 6 – Genetically Modified Microorganisms: Harmful or Helpful? – O Csutak – Genetically Engineered Foods

 

Techniques

Enhancement of subsoil denitrification using an electrode as an electron donor – S Qin – Soil Biology and Biochemistry

Organic amendment type and application frequency affect crop yields, soil fertility and microbiome composition – G Cesarano – Applied Soil Ecology

Next Generation Sequencing: Problems and opportunities for next generation studies of microbial communities in food and food industry – G Cardinali – Current Opinion in Food Science

An integrated electrolysis – electrospray – ionization antimicrobial platform using Engineered Water Nanostructures (EWNS) for food safety applications – N Vaze – Food Control

Inactivation of microbiota from urban wastewater by single and sequential electrocoagulation and electro-Fenton treatments – E Anfruns-Estrada – Water Research

Microbes in the news

I’ve always wondered: Why don’t hippos get cholera? – The Conversation

Women’s bacteria thwarted attempt at anti-HIV vaginal gel – Ottawa Citizen

How to Use Your Second Brain: Microbiome Expert Laure Ysebrant on Strategic Eating, Building Immunity, and Fake Fibre. – Thrive Global

A New Drug Uses CRISPR to Fight Antibiotic-Resistant Bacteria – Futurism

A TURNING OF PHAGE – Study Break

PEOPLE ARE MORE INTERESTING THAN BACTERIA: THE DR. CYRIL SHERER SAGA – The Jerusalem Post

September 30, 2017

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Events and jobs

Master of Biomedical Science – University of Melbourne – Start Date: February

Visiting Professor (Part Time) Microbiology – Chamberlain College of Nursing, Jacksonville, FL Campus

Assistant Professor of Biology, Microbiology – The Department of Biology at Barnard College, Columbia University – Starting July 2018

 

General microbiome

What will membrane vesicles (MVs) bring to bacterial communication? – M Toyofuku – Microbes and Environments

Direct and context-dependent effects of light, temperature, and phytoplankton shape bacterial community composition – SF Paver – Ecosphere

 

 

Human skin microbiome

The response of human bacteria to static magnetic field and radiofrequency electromagnetic field.  – DPE Crabtree – The Journal of Microbiology

 

 

Human gut microbiome

Gut inflammation and dysbiosis in human motor neuron disease – J Rowin – Physiological Reports

Review: Tart Cherries and health: Current knowledge and need for a better understanding of the fate of phytochemicals in the human gastrointestinal tract. – AC Mayta-Apaza – Critical Reviews in Food Science and Nutrition

Mechanisms of gut microbiota-mediated bone remodeling. – J Yan – Gut Microbes

Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron – ZA Costliow – mSystems

A gut feeling about multiple sclerosis – FJ Quintana – Proceedings of the National Academy of Sciences of the United Sates of America

 

Animal experiments 

Vancomycin and ceftriaxone can damage intestinal microbiota and affect the development of the intestinal tract and immune system to different degrees in neonatal mice. – RY Cheng – Pathogens and Diseases

Dietary soy, meat, and fish proteins modulate the effects of prebiotic raffinose on composition and fermentation of gut microbiota in rats. – G Bai – International Journal of Food Sciences and Nutrition

 

Animal microbiome 

Effects of obesity, energy restriction and neutering on the faecal microbiota of cats. – MM Fischer – The British Journal of Nutrition

The lipopolysaccharide core oligosaccharide of Burkholderia plays a critical role in maintaining a proper gut symbiosis with the bean bug Riptortus pedestris – JK Kim – Journal of Biological Chemistry

 

Plant, root and soil microbiome

Nectar-inhabiting microorganisms influence nectar volatile composition and attractiveness to a generalist pollinator. – CC Rering – The New Phytologist

Fossil Asterinaceae in the phyllosphere of the eastern Himalayan Neogene Siwalik forest and their palaeoecological significance – A Vishnu (née Mandal) – Botanical Journal of the Linnean Society

African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils – DK Puozaa – PLoS One

 

Microbiome of built environment 

Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding. – BI Cayford – Biofouling

 

Food microbiology

Yeast community in traditional Portuguese Serpa cheese by culture-dependent and -independent DNA approaches – MTP Gonçalves Dos Santos – International Journal of Food Microbiology

 

 

Techniques

Prediction of the intestinal resistome by a novel 3D-based method – E Ruppe – bioRxiv

PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media – DBH Barton – bioRxiv

Validation of standards suitable for genome size estimation of fungi – P Talhinhas – Journal of Microbiological Methods

Optimization of media components for production of antimicrobial compound by Brevibacillus brevis EGS9 isolated from mangrove ecosystem – T Arumugam – Journal of Microbiological Methods

Development of a set of multiplex PCRs for detection of genes encoding cell wall-associated proteins in Staphylococcus pseudintermedius isolates from dogs, humans and the environment – N Phumthanakorn – Journal of Microbiological Methods

Microbial Forensic Analysis of Human-Associated Bacteria Inhabiting Hand Surface – J Park – Forensic Science International: Genetics Supplement Series

Models of microbiome evolution incorporating host and microbial selection – Q Zeng – Microbiome

Control of Clostridium difficile Infection by Defined Microbial Communities. – J Collins – Microbiology Spectrum

Wholly Rickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells – TP Driscoll – mBio

NMR window of molecular complexity showing homeostasis in superorganisms – J Kikuchi – Analyst

Lipid and protein fingerprinting for Fusarium oxysporum f. sp. cubense strain-level classification – D.F.O. Rocha – Analytical and Bioanalytical Chemistry 

 

Microbes in the news

Drink Up! Volunteers Swallow Bacteria That Causes Typhoid – npr

Gordon receives 2017 Horwitz Prize – Washington University School of Medicine

HyGIeaCare® Receives First Patent from USPTO – EIN News Desk

Why Does My Vagina Smell Like Cheese? An Expert Explains – Romper

Benefits of polyphenols on gut microbiota and implications in human health – Nutra Ingredients