Category Archives: Human reproductive or urinary

December 26, 2016

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Prevotella and host genetics’ roles in vaginal microbiota, saliva microbiota and dental caries, microbes on tree stumps, fungi in Hammams, and a new  CRISPR–Cas system.

Human oral microbiome

* Exploration of bacterial species associated with the salivary microbiome of individuals with a low susceptibility to dental caries – Haruna Yasunaga – Clinical Oral Investigations

Human respiratory microbiome

Nasal Airway Microbiota Profile and Severe Bronchiolitis in Infants: A Case-Control Study – Hasegawa, Kohei – The Pediatric Infectious Disease Journal

Review: The Lung Microbiome and Airway Disease – Susan V. Lynch – Annals of the American Thoracic Society

Human bladder microbiome

Is there a link between urinary microbiota and bladder cancer? – Didier Raoult – European Journal of Epidemiology

Human vaginal microbiome

* Prevotella as a Hub for Vaginal Microbiota under the Influence of Host Genetics and Their Association with Obesity – Jiyeon Si – Cell Host & Microbe

Human gut microbiome

Differences in Metabolism of Ellagitannins by Human Gut Microbiota ex Vivo Cultures
– Jakub P. Piwowarski – Journal of Natural Products

Probiotic properties of Oxalobacter formigenes: an in vitro examination – Archives of Microbiology

The effects of administration of the Lactobacillus gasseri strain CP2305 on quality of life, clinical symptoms and changes in gene expression in patients with irritable bowel syndrome – K. Nobutani – Journal of Applied Microbiology

Review: The microbiome, immunity, and schizophrenia and bipolar disorder – Faith Dickerson – Brain, Behavior, and Immunity

Review: Emerging role of intestinal microbiota and microbial metabolites in metabolic control – Hilde Herrema – Diabetologia

Review: Microbial Dysbiosis in Common Variable Immune Deficiencies: Evidence, Causes, and Consequences – Roos-Marijn Berbers – Trends in Immunology

Review: Health benefits of fermented foods: microbiota and beyond – Maria L Marco – Current Opinion in Biotechnology

Animal experiments

Individual differences in stress vulnerability: the role of gut pathobionts in stress-induced colitis – Dominik Langgartner – Brain, Behavior, and Immunity

Impact of prebiotics on metabolic and behavioral alterations in a mouse model of metabolic syndrome – Lourdes Fernández de Cossío – Brain, Behavior, and Immunity

I assume this one was done in animals but not clear: Prenatal stress affects placental cytokines and neurotrophins, commensal microbes, and anxiety-like behavior in adult female offspring – Tamar L. Gur – Brain, Behavior, and Immunity

Animal microbiome

First characterization of viruses from freshwater snails of the genus Biomphalaria, the intermediate host of the parasite Schistosoma mansoni – Richard Galinier – Acta Tropica

Fish: Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr (Salvelinus alpinus) – Andreas Nyman – Aquaculture Reports

Plant, root, and soil microbiome

Interaction of chiral herbicides with soil microorganisms, algae and vascular plants – Muhammad Asad Ullah Asad – Science of the Total Environment

Mineral type and tree species determine the functional and taxonomic structure of forest soil bacterial communities – Y. Colin – Applied and Environmental Microbiology

* Colonization of Fungi and Bacteria in Stumps and Roots of Scots Pine after Thinning and Treatment with Rotstop – Katarzyna Kubiak – Journal of Phytopathology

Built environment microbiology

* Indoor fungal contamination of traditional public baths (Hammams) – Leyla Benammar – International Biodeterioration & Biodegradation

Waste and pollution microbiology

Alkaline Technosol contaminated by former mining activity and its culturable autochthonous microbiota – A. Šimonovičová – Chemosphere

Metagenomics and bioinformatics

* New CRISPR–Cas systems from uncultivated microbes – David Burstein – Nature

A small-sample multivariate kernel machine test for microbiome association studies
– Xiang Zhan – Genetic Epidemiology

Recycler: an algorithm for detecting plasmids from de novo assembly graphs –
Roye Rozov – Bioinformatics

A general framework for association analysis of microbial communities on a taxonomic tree – Zheng-Zheng Tang – Bioinformatics

Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies – Seok-Hwan Yoon – International Journal of Systematic and Evolutionary Microbiology

Microbes in the news

Genomic sequencing illuminates recent Shigella outbreaks in California. Researchers identify genes associated with toxin production and antibiotic resistance – Science Daily

Raw meat: Eating so-called ‘cannibal sandwiches’ can be deadly, health official says.Consumption of uncooked beef poses a health risk – Dave Delozier – Channel3000

Ancient Chinese malaria remedy may help fight TB – Deccan Chronicle

The natural history of cheese mites – Scott Chimileski – American Society for Microbiology

The throwaway scope: A way to ditch superbugs? – Chad Terhune – Seacoast Online

Science, publishing, and career

Life Science Controversies of 2016 – Jef Akst – The Scientist

The world’s favourite lab animal has been found wanting, but there are new twists in the mouse’s tale – The Economist

December 19, 2016

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An oral pathogen with a very long name is linked to rheumatoid arthritis, a deep-sea bone-eating snail, and the excreted microbiota of bats.

Human oral microbiome

* Aggregatibacter actinomycetemcomitans–induced hypercitrullination links periodontal infection to autoimmunity in rheumatoid arthritis – Maximilian F. Konig – Science Translational Medicine

Press: Bacteria That Causes Gum Disease Also Triggers Inflammatory Response In Rheumatoid Arthritis – Saranya Palanisamy – Tech Times

Human vaginal microbiome

The Cervicovaginal Microbiota in Women Notified for Chlamydia trachomatis Infection: A Case-Control Study at the Sexually Transmitted Infection Outpatient Clinic in Amsterdam, The Netherlands – Charlotte van der Veer – Clinical Infectious Diseases

Editorial Commentary: The Cervicovaginal Microbiota and Infection Risk After Exposure to an Exogenous Pathogen – Daniel B. DiGiulio – Clinical Infectious Diseases

Human gut microbiome

Bacterial Biofilms in Colorectal Cancer Initiation and Progression – Shan Li – Trends in Molecular Medicine

Animal experiments

Alternative protein sources in the diet modulate microbiota and functionality in the distal intestine of Atlantic salmon (Salmo salar) – Karina Gajardo – Applied and Environmental Microbiology

Animal microbiome

* The Specific and Exclusive Microbiome of the Deep-Sea Bone-Eating Snail, Rubyspira osteovora – H.S. Aronson – FEMS Microbiology Ecology

Origin of Sulfur in Diet Drives Spatial and Temporal Mercury Trends in Seabird Eggs From Pacific Canada 1968–2015 – Kyle H. Elliott – Environmental Science & Technology

Press: Bacteria control levels of dangerous pollutant in seabirds – Phys.org

The excreted microbiota of bats: evidence of niche specialization based on multiple body habitats – Muriel Dietrich – FEMS Microbiology Letters

Western Bats as a Reservoir of Novel Streptomyces Species with Antifungal Activity – Paris S. Hamm – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest – Cody R. Dangerfield – bioRxiv

Pyrosequencing of rpoB uncovers a significant biogeographical pattern of rhizobial species in soybean rhizosphere – Xing Xing Zhang – Journal of Biogeography

Ectomycorrhizal fungal response to warming is linked to poor host performance at the boreal-temperate ecotone – Christopher W. Fernandez – Global Change Biology

Review: PGPR = plant growth-promoting rhizobacteria: The Contribution of Genome Mining Strategies to the Understanding of Active Principles of PGPR Strains – Julia Paterson – FEMS Microbiology Ecology

Water microbiome

Effects of actinomycete secondary metabolites on sediment microbial communities – Nastassia V. Patin – Applied and Environmental Microbiology

Pollution and waste microbiology

Elucidating carbon sources driving microbial metabolism during oil sands reclamation – Lauren M. Bradford – Journal of Environmental Management

Techniques

Comparison of Collection Methods for Fecal Samples in Microbiome Studies – Emily Vogtmann – American Journal of Epidemiology

Microbes in the news

Refers to meeting abstract: Microbiomes interact with mental health treatment – Tim Sandle – Digital Journal

South Dakota high schools introduce students to health care: students grew bacteria in petri dishes – Jaci Conrad Pearson – Washington Times

New medicine: How the gut breaks the mind – Govind Vijaykumar – Deccan Chronicle

December 5, 2016

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Contraceptives and the vaginal microbiome, Ralstonia and CF outcome, Alzheimer’s, helminths in cats, the Mississippi River.

General microbiome and ecology

Review: Disentangling Interactions in the Microbiome: A Network Perspective – Mehdi Layeghifard – Trends in Microbiology

Book Chapter: Chapter 4 – The Human Microbiome – Jacquelyn S. Meisel – Genomic and Precision Medicine (Third Edition): Foundations, Translation, and Implementation – Chp

Pregnancy and early life

Maternal health and the placental microbiome – Elise Pelzer – Placenta

Human vaginal microbiome

* Effects of Combined Oral Contraceptives, Depot Medroxyprogesterone Acetate, and the Levonorgestrel-releasing Intrauterine System on the Vaginal Microbiome – J. Paul Brooks – Contraception

Review: Lactobacillus iners: Friend or Foe? – Mariya I. Petrova – Trends in Microbiology

Human skin microbiome

The protective effect of microbiota on S. aureus skin colonization depends on the integrity of the epithelial barrier – Marc Burian – Journal of Investigative Dermatology

Human respiratory microbiome

* Ralstonia mannitolilytica in cystic fibrosis: A new predictor of worse outcomes – I. Coman – Respiratory Medicine Case Reports

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing – Claire L. McMurray – Microbiome

Human oral microbiome (also: gut / viruses)

Transmission of viruses via our microbiomes – Melissa Ly – Microbiome

Review: Endodontic Microbiology and Pathobiology : Current State of Knowledge – Ashraf F. Fouad – Dental Clinics of North America

Human gut microbiome

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies – Euan Watt – Microbiome

Review: Crohn’s disease – Joana Torres – The Lancet

Review: The Microbiome in Neurogastroenterology – Geoffrey A. Preidis – Pediatric Neurogastroenterology

Review: The endocrine vitamin D system in the gut – Antonio Barbáchano – Molecular and Cellular Endocrinology

Microbes at nearly sterile sites

* Gram-negative bacterial molecules associate with Alzheimer disease pathology – Xinhua Zhan – Neurology

Press: Gram-negative bacteria may influence Alzheimer’s disease pathology – ScienceDaily

Animal and in vitro models

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota – A. Sloan Devlin – Cell Host & Microbe

Animal microbiome

* Helminth infections and gut microbiota – a feline perspective – Ana M. Duarte – Parasites & Vectors

Review: Defining the Core Microbiome in Corals’ Microbial Soup – Alejandra Hernandez-Agreda – Trends in Microbiology

Plant, root, and soil microbiome

Bacterial consortia inoculation mitigates the water shortage and salt stress in an avocado (Persea americana Mill.) nursery – Patricio J. Barra – Applied Soil Ecology

Heavy Metal Pollution Structures Soil Bacterial Community Dynamics in SW Spain Polluted Salt Marshes – Jennifer Mesa – Water, Air, & Soil Pollution

The Cucurbita pepo seed microbiome: genotype-specific composition and implications for breeding – Eveline Adam – Plant and Soil

Tolerance of the forest soil microbiome to increasing mercury concentrations – Aline Frossard – Soil Biology and Biochemistry

Repeated glyphosate exposure induces shifts in nitrifying communities and metabolism of phenylpropanoids – Marco Allegrini – Soil Biology and Biochemistry

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought – A. Mark Ibekwe – Science of the Total Environment

Cross-compatibility evaluation of plant growth promoting rhizobacteria of coconut and cocoa on yield and rhizosphere properties of vegetable crops – T.H Khadeejath Rajeela – Biocatalysis and Agricultural Biotechnology

Effect of rhizobacterial consortia from undisturbed arid- and agro-ecosystems on wheat growth under differing conditions – N.G. Inostroza – Letters in Applied Microbiology

Differences among Soil-Inhabiting Microbial Communities in Poa annua Turf throughout the Growing Season – Lisa A. Beirn – Corp Science

Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake – Pu Shen – PLOS ONE

Water and extremophile microbiome

* Microbial regime changes and indicators of eutrophication on the Mississippi River identified via a human-powered 2900 km transect – Michael W Henson – bioRxiv

Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River – L. Vezzulli – Microbial Ecology

Identity, ecology and ecophysiology of planktic green algae dominating in ice‑covered lakes on James Ross Island (northeastern Antarctic Peninsula) – Linda Nedbalová

Built environment microbiome

Analysis of dark crusts on the church of Nossa Senhora do Carmo in Rio de Janeiro, Brazil, using chemical, microscope and metabarcoding microbial identification techniques – Christine Gaylarde – International Biodeterioration & Biodegradation

Impact of wastewater treatment plant discharge on the contamination of river biofilms by pharmaceuticals and antibiotic resistance – Elodie Aubertheau – Science of the Total Environment

More microbiology

Human to human transmission of arthropod-borne pathogens – Byron E Martina – Current Opinion in Virology

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – Niclas Krakat – Journal of Applied Microbiology

Microbes in the news

uBiome Awards Microbiome Impact Grant to Explore Effects of Heavy Drinking and Smoking on Oral Microbiome – PR Web

Missing Link in Malaria Evolution Discovered in Historical Specimens – Ben Andrew Henry – The Scientist

Book review: The Human Microbiome Handbook, Jason Tetro, Emma Allen-Vercoe (Eds.). DEStech Publications (March 2016)– Laura M. Cox – Anaerobe

Our ideas about bacteria evolution are wrong – scientists make new discovery – Sandra Hajda – Inquisitr

Bacteria Hysteria

Soap company uses bacteria-coated billboards to prove how dirty your stuff is – Mashable

December 2, 2016

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Role of microbiome in an animal model of Parkinson’s disease, benchmarking reveals false discoveries in microbiome studies, the microbes of Patagonia, and the new uBiome blog.

The  uBiome blog

* Handshakes: Sharing the Love, Sharing the Microbes – Julie Taylor – uBiome

Jobs

Assistant Professor in Microbial Systems Biology at U. Tennessee, Knoxville – MicroBE.net

Human vaginal microbiome

Informativeness of NGS Analysis for Vaginal Fluid Identification – Saverio Giampaoli – Journal of Forensic Sciences

Animal models

* Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease – Timothy R. Sampson – Cell

News: Axial Biotherapeutics Announces the Groundbreaking Discovery of a Biological Link Between the Gut Microbiome and Parkinson’s Disease Published in Cell – Businesswire
Gut check: Newest microbiome startup concentrates on autism, Parkinson’s disease – John Carroll – Endpoints News

Multiple paternity in a wild population of Armadillidium vulgare: influence of infection with Wolbachia? – V. Valette – Journal of Evolutionary Biology

Plant, root, and soil microbiome

Field-grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential – Jennifer M. DeBruyn – GCB Bioenergy

Vertical zonation of soil fungal community structure in a Korean pine forest on Changbai Mountain, China – World Journal of Microbiology and Biotechnology

* Book: Biology and Biotechnology of Patagonian Microorganisms – Editors: Nelda Lila Olivera, Diego Libkind, Edgardo Donati – Springer

Bioinformatics

* Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies – Jonathan Thorsen – Microbiome

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography – Silvia Argimón – Microbial Genomics

More microbiology

Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases – Ryutaro Furukawa – Journal of Molecular Evolution

The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite – Tatiana Yurchenko – Open Biology

High levels of antibiotic tolerance and persistence are induced by the commercial anti-microbial triclosan – Corey S Westfall – bioRxiv

Microbes in the news

A citizen science project studying the microorganisms fauna found at the tip of our tongue – Euroscientist

Knowledge of skin microbiome provides insights into dermatological conditions – Skin microbes perform harmful and beneficial functions – Louise Gagnon – Dermatology Times

Digital Microbes Could Give More Insight into Gut Health – Nutrition Horizon

Healthy Gut, Healthy Brain? Microbes and Brain Health Under the Microscope During Mind, Mood & Microbes Conference – PR Newswire

Doctors warn about lung illness attributed to bacteria in showers and hot baths – Catherine Bosley – Cleveland19

Microbes on the market

Microbiome CNS upstart launches with $19.15M Series A – Ben Adams – Fierce Biotech

Boston startup hopes to use bacteria to treat autism – Robert Weisman

November 28, 2016

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Chronic rhinosinusitis, quantification of vaginal lactobacilli, intestinal nitrogen constraints, the eelgrass microbiome, microbes under lake ice.

Human respiratory microbiome

* Classification of Chronic Rhinosinusitis—Working Toward Personalized Diagnosis – Adam S. DeConde – Otolaryngologic Clinics of North America
Bacterial Pathogens and the Microbiome – Thad W. Vickery – Otolaryngologic Clinics of North America

 
Human skin microbiome

Comment on “Skin Microbiome Surveys Are Strongly Influenced by Experimental Design” – Patrick L.J.M. Zeeuwen – Journal of Investigative Dermatology

Establishing Tolerance to Commensal Skin Bacteria: Timing Is Everything – Tiffany C. Scharschmidt – Dermatologic Clinics

Human vaginal microbiome

* A novel real-time PCR assay for highly specific detection and quantification of vaginal lactobacilli – Vladimir V. Demkin – Molecular and Cellular Probes

Human gut microbiome

Review: Interaction of gut microbiota with bile acid metabolism and its influence on disease states – Christopher Staley – Applied Microbiology and Biotechnology

Review: Microbes Dress for Success: Tolerance or Resistance? – Janelle S. Ayres – Trends in Microbiology

* Review: Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints – Andrew J. Holmes – Cell Metabolism

Animal models

The gut microbiota in young and middle-aged rats showed different responses to chicken protein in their diet – Yingying Zhu – BMC Microbiology

The Drosophila transcriptional network is structured by microbiota – Adam J. Dobson – BMC Genomics

Review: Norovirus Regulation by Host and Microbe – Megan T. Baldridge – Trends in Molecular Medicine

Plant, root, and soil microbiome

* Global-scale structure of the eelgrass microbiome – Ashkaan K Fahimipour – bioRxiv

Rapid bacteria identification from environmental mining samples using MALDI-TOF MS analysis – Ingrid Regina Avanzi – Environmental Science and Pollution Research

Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches – Shin Ae Lee – Journal of Microbiology

Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea – Jeong Myeong Kim – Journal of Microbiology

Chemical, organic and bio-fertilizer management practices effect on soil physicochemical property and antagonistic bacteria abundance of a cotton field: Implications for soil biological quality – Rui Li – Soil and Tillage Research

Water and extremophile microbiome

* Ecology under lake ice – Stephanie E. Hampton – Ecology Letters

Food microbiology

Dynamics of bacterial communities during manufacture and ripening of traditional Caciocavallo of Castelfranco cheese in relation to cows’ feeding – Marina Giello – Food Microbiology

Metagenomics and bioinformatics

MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles – Grace Tzun-Wen Shaw – BMC Bioinformatics

Metabolomics

Metabolomic profile of children with recurrent respiratory infections – Sara Bozzetto – Pharmacological Research

Microbes in the news

Infant Microbiome: Vaginal Delivery Versus C-Section – Jef Akst – The Scientist

I did not get the first part of this title. Michael Pollan didn’t invent microbiome research, he’s a demagogue: Set of 15 bacterial species protects mice from Salmonella as effectively as natural gut microbiota – Doug Powell – Barfblog

Surprise: Probiotics Don’t Do Much At All For Our Gastrointestinal Health – Drew Smith – Forbes

#BacteriaArePlural: Ravenous Bacteria Eats Poop and Produces Power – Rhett Jones – Gizmodo

Gut bacteria study could lead to new Crohn’s treatments, researchers say – CBC News

Hospital Microbiology Testing Market Positive Long-Term Growth Outlook 2016 – 2024 – Digital Journal

Bik’s Non-Microbiology Picks

Researchers discover most winter boots are too slippery to walk safely on icy surfaces – EurekAlert

 

November 26, 2016

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Human reproductive microbiome

Una destinatio, viae diversae: Does exposure to the vaginal microbiota confer health benefits to the infant, and does lack of exposure confer disease risk? – Kjersti Aagaard – EMBO Reports

Review: Female reproductive tract microbiome in gynecological health and problems – Shyamalina Haldar – Journal of Reproductive Health and Medicine

Animal microbiome

Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria – Violetta Vacchini – Environmental Microbiol Reports

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis – Juliane Wippler – BMC Genomics

Microbial communities of lycaenid butterflies do not correlate with larval diet – Melissa Whitaker – Frontiers in Microbiology

Bees: Report on the microbiota of Melipona quadrifasciata affected by a recurrent disease – Sebastián Díaz – Journal of Invertebrate Pathology

Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants – Aline Sartori Guidolin – Microbial Ecology

Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes – Dennis Versluis – Frontiers in Microbiology

Plant, root, and soil microbiome

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks – Eduardo Pérez-Valera –  Environmental Microbiology

Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial System – Zhou Li – Environmental Microbiology

Water and extremophile microbiome

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient – C. Monard – Scientific Reports

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments – Sizhong Yang – Scientific Reports

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano – Klaudia L. Hernández – Frontiers in Microbiology

Built environment / money microbiome

Dirty Money: A Matter of Bacterial Survival, Adherence, and Toxicity – Frank Vriesekoop – Microorganisms

Metabolomics

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes – Jeremy L. Motley – Journal of Natural Products

http://pubs.acs.org/doi/full/10.1021/acs.jnatprod.6b00772

Techniques

Note: human contamination in feces samples is usually low (e.g. compared to oral or vaginal samples; not really an issue in my opinion: An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction – Jitendra Kumar – Genomics, Proteomics & Bioinformatics

More microbiology

Independent evolution of shape and motility allows evolutionary flexibility in Firmicutes bacteria – Fouad El Baidouri – Nature Ecology & Evolution

Press: Reshaping our ideas of bacterial evolution – Science Daily

Microbes in the news

This paper is not yet available online at Molecular Biology and Evolution, but already some press about it:
A comprehensive tree of prokaryotic life – Science Daily
New insights from the most comprehensive tree of prokaryotic life assembled to date – Phys.org

Bacteria taught to bond carbon and silicon for the first time – Aviva Rutkin – New Scientist

Binge-eating bacteria extract energy from sewage – Science Daily

Video: Good Germs; Bad Germs. Microbes in the kitchen, 14 households, 500 swabs – University of Oxford – YouTube

Bacteria Hysteria

Note: Sponsored by a company specialized in pest control and hygiene products. Primary school bacteria leaves teachers at risk of sickness – TES

November 25, 2016

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Human multisite microbiome (of dead bodies)

Thesis: Understanding the relationship between the human microbiome and urban decay/recovery among autopsied adults in Detroit, Michigan – Amanda T. Rzotkiewicz – Michigan State University

Human oral microbiome

The autoimmunity–oral microbiome connection – NG Nikitakis – Oral Diseases

Human reproductive and urinary tract microbiome

Potential contribution of the uterine microbiome in the development of endometrial cancer – Marina R. S. Walther-António – Genome Medicine

Proinflammatory Cytokines as Regulators of Vaginal Microbiota – E. A. Kremleva – Bulletin of Experimental Biology and Medicine

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements

Human gut microbiome

Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease – Walid Mottawea – Scientific Reports

Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods – Andrew D. Huang – Applied and Environmental Microbiology

Review: Gut Microbiota and Autism: Key Concepts and Findings – Helen T. Din – Journal of Autism and Developmental Disorders

Review: Intestinal Microbiota as an Alternative Therapeutic Target for Epilepsy – Jiaying Wu – Canadian Journal of Infectious Diseases and Medical Microbiology

Review: Irritable Bowel Syndrome: A gut microbiota-related disorder? – Yogesh Bhattarai – American Journal of Physiology – Gastrointestinal and Liver Physiology

Review: Gut Microbiota, Bacterial Translocation, and Interactions with Diet: Pathophysiological Links between Major Depressive Disorder and Non-Communicable Medical Comorbidities – Slyepchenko A. – Psychotherapy and Psychosomatics

Review: Microbiome, metabolites and host immunity – Maayan Levy – Current Opinion in Microbiology

Animal and in vitro models

* Persistent microbiome alterations modulate the rate of post-dieting weight regain – Christoph A. Thaiss – Nature

Press: Yo-yo weight gain driven by gut bacteria’s ‘memory’ of obesity, says study – Hannah Devlin – The Guardian
Breakthrough in Dieting Science: Gut Bacteria Are Behind Relapsing Obesity – Ido Efrati and Ruth Schuster – Haaretz

Effects of a gut pathobiont in a gnotobiotic mouse model of childhood undernutrition – Vitas E. Wagner – Science Translational Medicine

Antibiotics impair murine hematopoiesis by depleting intestinal microbiota – Kamilla S. Josefsdottir – Blood

Pre- and post-weaning diet alters the faecal metagenome in the cat with differences vitamin and carbohydrate metabolism gene abundances – Wayne Young – Scientific Reports

Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat – Rosemarie De Weirdt – Environmental Microbiology

Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits – Qiangchuan Hou – Scientific Reports

Evolutionary biologic changes of gut microbiota in an ‘adenoma-carcinoma sequence’ mouse colorectal cancer model induced by 1, 2-Dimethylhydrazine – Teng Sun – Oncotarget

Mini review: All Together Now: Experimental Multispecies Biofilm Model Systems – Chuan Hao Tan – Environmental Microbiology

Animal microbiome

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2 – Erinn M. Muller – Scientific Reports

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes – Hannes Horn – Frontiers in Microbiology

Plant, root, and soil microbiome

Soil Bacterial Community Response to Short-Term Manipulation of the Nitrogen Deposition Form and Dose in a Chinese Fir Plantation in Southern China – Caixia Liu – Water, Air, & Soil Pollution

Microbial community composition but not diversity changes along succession in arctic sand dunes – Anbu Poosakkannu – Environmental Microbiology

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles – Yang Li – Applied Microbiology and Biotechnology

Contrasting effects of two mammalian soil engineers on microbial communities – David J. Eldridge – Austral Ecology

* Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza – Hans Jacquemyn – Scientific Reports

 * Are there keystone mycorrhizal fungi associated to tropical epiphytic orchids? – Stefania Cevallos – Mycorrhiza

Water and extremophile microbiome

Stromatolites from the Aptian Crato Formation, a hypersaline lake system in the Araripe Basin, northeastern Brazil – Lucas Veríssimo Warren – Facies

Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River – Haohao Sun – Applied Microbiology and Biotechnology

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes – Carina Rofner – Global Change Biology

Viruses and phages

Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture – Lavinia Gambelli – Frontiers in Microbiology

Seven Bacteriophages Isolated from the Female Urinary Microbiota – Kema Malkia – Genome Announcements

Metabolomics

The role of metabolism (and the microbiome) in defining the clinical efficacy of dietary flavonoids – Aedín Cassidy – The American Journal of Clinical Nutrition

Metagenomics and bioinformatics

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains – Weinan Liao – Scientific Reports

Techniques

ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities –
Anders Bjørnsgaard Aas – Molecular Ecology Resources

Microbes in the news

Stockholmers’ poop wanted in fight against drug-resistant bacteria – RT

The modern microbiome: Are we undoing evolution? – Maria Gloria Dominguez-Bello – ASM Cultures

PhD student finds surprising secret to detecting staph infections earlier – Breanne Grady – USC News

November 22, 2016

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Vaginal Mirobiome in PPROM, Prevotella copri and rheumatoid arthritis, mice transplanted with stool from lean or obese humans, archaea in a pond.

Pregnancy and early life

High Diversity and Variability in the Vaginal Microbiome in Women following Preterm Premature Rupture of Membranes (PPROM): A Prospective Cohort Study – Teenus Paramel Jayaprakash – PLOS ONE

Human oral microbiome

Review: The oral microbiome – an update for oral healthcare professionals – M. Kilian – British Dental Journal

Human gut microbiome

Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis – C. Acharya – Alimentary Pharmacology and Therapeutics

In vitro fermentation of B-GOS: Impact on faecal bacterial populations and metabolic activity in autistic and non-autistic children – Roberta Grimaldi – FEMS Microbial Ecology

Evidence for Immune Relevance of Prevotella copri, a Gut Microbe, in Patients with Rheumatoid Arthritis – Annalisa Pianta – Arthitis & Rheumatology

Review: Human gut microbiota: the links with dementia development – Rashad Alkasir – Protein & Cell

Review: Gut hormones and gut microbiota: implications for kidney function and hypertensionGut hormones and gut microbiota: implications for kidney function and hypertension – Baris Afsar – Journal of the American Society of Hypertension

Review: Dysbiosis in the intensive care unit: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Interactions between gut microbes and host cells control gut barrier and metabolism – P D Cani – International Journal of Obesity Supplements

Review: Life history and eco-evolutionary dynamics in light of the gut microbiota – Emilie Macke – Oikos

Animal experiments

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans – Li Zhang – ISME Journal

Gut bacteria affect our metabolism – Science Daily

Animal microbiome

Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae
– Shantanu P. Shukla – Molecular Ecology

Thesis: Characterization of the juvenile green turtle (Chelonia mydas) microbiome associated with the ontogenic shift from pelagic habitats to inshore resident areas – James T. Price – Purdue University

Tick microbiome and pathogen acquisition altered by host blood meal – Andrea Swei – The ISME Journal

Plant, root, and soil microbiome

Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria – Natalia Pimentel Esposito-Polesi – Current Microbiology

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest – Witoon Purahong – Scientific Reports

High-methionine soybean has no adverse effect on functional diversity of rhizosphere microorganisms -J.G. Liang – Plant Soil Environment

Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China – Jing Yan Tang – BMC Microbiology
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0892-3
Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons – Hirokazu Toju – PLOS ONE

Isolation and Identification of Keratinolytic Bacteria that Exhibit Feather-degrading Potentials – F. O. Iruolaje – Journal of Advances in Biology & Biotechnology

Water and extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis – Margarita Kambourova – Archaea

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities – Christine N. Shulse – Microbiology Open

Conference abstract: Defining the boarders of extreme life: The study of microbial communities and their settings gives insights into Mars analogue life within the MASE project – A Perras – 16th International Symposium on Microbial Ecology

Pollution microbiology

Influence of plantation on microbial community in porous concrete treating polluted surface water – Yan Long – International Biodeterioration & Biodegradation

Food microbiology

Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR – Cristiana Garofalo – International Journal of Food Microbiology

Viruses and phages

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments – Samuel L Diaz-Munoz – bioRxiv

More microbiology

Uncovering new drugs and targets – Andrea Du Toit – Nature Reviews Microbiology

Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Microbes in the news

‘Bacteria beaters’ win Longitude Prize Discovery Award – Shan Ross – The Scotsman

Bacteria for bio-toilets by February 15 – The Times of India

Your Office Has a Microbiome, and It Might Make You Sick – Zoe Schlanger – Wired

Tomato plants are more resistant against nematodes when colonized by a fungus – Farming Futures

Scientists use bacteria to map out NZ. A team of scientists growing bacteria in the shape of New Zealand have caught the attention of their colleagues across the globe – News Australia

The cover image is a map of New Zealand drawn with pyoverdine-producing P. aeruginosa cells in an ocean of indigoidine-synthesizing E. coli. – Cell Chemical Biology

Science, publishing, and career

Citizen science: The people behind the data – Mary Goodchild – NERC Planet Earth

November 14, 2016

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Infant gut microbiota, oral microbiota of farmworkers with pesticide exposure, critically ill patients, probiotics and Alzheimer’s, Sutterella is a commensal.

Events

Cheese Cultures & Microbiology Class, December 2, 2016, Petaluma – California Artisan Cheese Guild – Eventbrite

Pregnancy and early life

A comparison of intestinal microbiota in a population of low-risk infants exposed and not exposed to intrapartum antibiotics: The Baby & Microbiota of the Intestine cohort study protocol – Julia Simioni – BMC Pediatrics

Establishment and development of the intestinal microbiota of preterm infants in a Lebanese tertiary hospital – Tarek Itania – Anaerobe

Human oral microbiome

Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure – Ian B. Stanaway – Applied and Environmental Microbiology

News: Study finds link between pesticide exposure and microbiome changes – Brooks Hays – UPI
Pesticide exposures can cause changes in oral microbiome – ASM

Molecular detection of bacteria associated to caries activity in dentinal lesions – Beatriz Gonçalves Neves – Clinical Oral Investigations

Review: Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review – Miguel Padial-Molina – J Oral Maxillofac Res

Human skin microbiome

A Precision Microbiome Approach Using Sucrose for Selective Augmentation of Staphylococcus epidermidis Fermentation against Propionibacterium acnes – Yanhan Wang – Int J Mol Sci

A novel enzyme with antioxidant capacity produced by the ubiquitous skin colonizer Propionibacterium acnes – Maria Allhorn – Scientific Reports

Skin bacteria could protect against disease – Science Daily

Human vaginal microbiome

Escherichia coli and Enterococcus faecalis are able to incorporate and enhance a pre-formed Gardnerella vaginalis biofilm – Joana Castro – Pathogens and Disease

Human gut microbiome

Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study – Jacqueline M. Lankelma – Intensive Care Medicine

Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp. – Kaisa Hiippala – Frontiers in Microbiology

Review: Impact of Microbes on the Pathogenesis of Primary Biliary Cirrhosis (PBC) and Primary Sclerosing Cholangitis (PSC) – Jochen Mattner – Int J Mol Sci

Animal microbiome

Review: Microbiota-host interplay at the gut epithelial level, health and nutrition – Jean-Paul Lallès – Journal of Animal Science and Biotechnology

Plant, root, and soil microbiome

Root bacterial endophytes alter plant phenotype, but not physiology – Jeremiah A. Henning – Peer J

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria – Pious Thomas – Microbial Ecology

Water microbiome

Unraveling the microbial community of a cold groundwater catchment system – Burga Braun – Water Research

Built environment microbiome

Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations – Min Gao – Environmental Pollution

Metabolomics

Review: Emerging roles of xenobiotic detoxification enzymes in metabolic diseases – Michael C. Petriello – Reviews on Environmental Health

Probiotics

Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind, and controlled trial – Elmira Akbari -Frontiers in Aging Neuroscience

News: Probiotics improve cognition in Alzheimer’s patients – Medical Xpress

More microbiology

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence – Yok Hian Chionh – Nature Communications

Cracking the code for dormant bacteria. Newly discovered genetic code controls bacterial survival during infections – Anne Trafton – MIT News Office

Microbes in the news

Monitoring in Real Time the Formation and Removal of Biofilms From Clinically Relevant Pathogens – PR Web

From the American College of Rheumatology Annual Scientific Meeting: Gut bacteria may be a trigger for antiphospholipid syndrome – EurekAlert

Three University of Maryland students are sending bacteria samples into space – Rachel Kuipers – the Diamondback

University of Texas at Dallas named “Milestones in Microbiology” – Joanna Urban – ASM

Bethany professor Matthew Swearingen receives research grant – Weirton Daily Times

Scientists try bacteria to halt invasive cheatgrass overwhelming the West – Keith Ridler – LA Times

November 12, 2016

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Two papers on the detection of diseases by metabolomics of breaths or fecal gases, responses of soil bacteria to solar radiation and soil warming, genotyping of probiotics.

General microbiome

Special Issue on ‘Microbe–host interactions’ – Sven Hammerschmidt – FEBS Letters

Pregnancy and early life

Serum cathelicidin, nasopharyngeal microbiota, and disease severity among infants hospitalized with bronchiolitis – Kohei Hasegawa – Journal of Allergy and Clinical Immunology

Human respiratory microbiome

Feasibility of Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics: A Pilot Study – Xiaoling Zang – Journal of Proteome Research

Features of the bronchial bacterial microbiome associated with atopy, asthma and responsiveness to inhaled corticosteroid treatment – Juliana Durack – Journal of Allergy and Clinical Immunology

Human vaginal microbiome

“Murdochiella vaginalis” sp. nov., a new bacterial species cultivated from the vaginal flora of a woman with bacterial vaginosis – Khoudia Diop – Human Microbiome Journal

Human esophagus and stomach microbiome

Editorial: The microbiome as a potential biomarker for oesophageal adenocarcinoma – Julian A Abrams – The Lancet Gastroenterology & Hepatology

A non-endoscopic device to sample the oesophageal microbiota: a case-control study – Daffolyn R Fels Elliott – The Lancet Gastroenterology & Hepatology

Human gut microbiome

Irritable bowel syndrome and active inflammatory bowel disease diagnosed by faecal gas analysis – R. B. M. Aggio – Alimentary Pharmacology and Therapeutics

Review: Formation of propionate and butyrate by the human colonic microbiota – Petra Louis

Review: The Gut Microbiota : The Gateway to Improved Metabolism – Kristina B. Martinez – Gastroenterology Clinics of North America

Review: Regulation of the gut microbiome by inflammasomes – Grace Y. Chen – Free Radical Biology and Medicine

Review: The role of the microbiome in kidney stone formation – Mansi Mehta – International Journal of Surgery

Animal models

Giardia alters commensal microbial diversity throughout the murine gut – Nanelle R Barash – bioRxiv

Animal microbiome

Virus detection using metagenomic sequencing of swine nasal and rectal swabs – Ben M. Hause – J Swine Health Prod

Plant, root, and soil microbiome

Bacterial active community cycling in response to solar radiation and their influence on nutrient changes in a high altitude wetland – Veronica Molina – Frontiers in Microbiology

Land-use change under different climatic conditions: Consequences for organic matter and microbial communities in Siberian steppe soils – Norbert Bischoff – Agriculture, Ecosystems & Environment

Identifying the microbial taxa which consistently respond to soil warming across time and space – Angela M. Oliverio – Global Change Biology

The drivers underlying biogeographical patterns of bacterial communities in soils under sugarcane cultivation – Ademir Durrer – Applied Soil Ecology

Editorial: A small soil bacterium dominates – Ursula Hofer – Nature Reviews Microbiology

Editorial/Review: The Role of Microbial Communities in Tropical Ecosystems – Silvia Pajares – Frontiers in Microbiology

Water microbiome

Cyanobacteria in lakes on Yungui Plateau, China are assembled via niche processes driven by water physicochemical property, lake morphology and watershed land-use – Jingqiu Liao – Scientific Reports

Implications of Ecological Niche Differentiation in Marine Bacteria for Microbial Management in Aquaculture to Prevent Bacterial Disease – Tom Defoirdt – PLOS Pathogens

Bacterial composition, abundance and diversity in fish polyculture and mussel–fish integrated cultured ponds in China – Xiafei Zheng – Aquaculture Research

Food microbiome

Diversity study of microbial community in bacon using metagenomic analysis – Langbo Yi – Journal of Food Safety

Probiotics

Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases – Wesley Morovic – Frontiers in Microbiology

Review: Weight gain by gut microbiota manipulation in productive animals – Emmanouil Angelakis – Microbial Pathogenesis

Viruses and phages

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs – Yi Zheng – Virology

Metabolomics

Book Chapter: A Mathematical Perspective on Microbial Processes in Earth’s Biogeochemical Cycles – Christof Meile – Mathematical Paradigms of Climate Science
Bioinformatics and metagenomics

EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms – Jason McClelland – bioRxiv

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome – José L. Martínez – Annals of the New York Academy of Sciences

More microbiology

The planktonic relationship between fluid-like electrodes and bacteria: wiring in motion
– Sara Tejedor Sanz – ChemSusChem

Experimental study and Random Forest prediction model of microbiome cell surface hydrophobicity – Yong Liu – Expert Systems with Applications

Microbes in the news

uBiome CEO Dr. Jessica Richman to Deliver Opening Keynote at American Medical Informatics Association Symposium – PR web

The impact of the rhizosphere microbiota on root system development and tolerance to environmental constraints in cereals – International Center for Biosaline Agriculture

Miami wants to introduce MORE mosquitoes to fight Zika: Officials considers bringing in bacteria-infected insects to stop spread of virus – Daily Mail

Bruker Moving Into PCR-Based Testing to Expand Clinical Microbiology, MALDI Biotyper Offerings – Genome Web