Category Archives: Metagenomics & Bioinformatics

January 10, 2017

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A culture-based study of 2000 nasal microbiomes, eye metabolites, cardiorespiratory fitness in breast cancer survivors, Akkermansia from a python, chickpea rhizosphere, tobacco wilt suppression, plant rhizosphere mass spectrometry, phyloSkeleton.

Human nasal microbiome

Epidemiological and ecological modelling reveal diversity in microbial population structures from a cross-sectional community swabbing study – Abigail L Coughtrie – bioRxiv

Human eye microbiome

LC-MS-Based Metabolic Fingerprinting of Aqueous Humor – Karolina Pietrowska – Journal of Analytical Methods in Chemistry

Human vaginal microbiome

MS thesis: Metagenomic characterization of the vaginal microbiome – Keshini Devakandan – University of British Columbia

Human gut microbiome

Gut microbiota composition associated with alterations in cardiorespiratory fitness and psychosocial outcomes among breast cancer survivors – Jesseca A. Paulsen – Supportive Care in Cancer

SYN-004 (ribaxamase), an oral β-lactamase designed to protect the gut microbiome from the deleterious effects of certain intravenously administered β-lactam antibiotics, degrades ceftriaxone excreted into the intestine in Phase 2a clinical studies – John F. Kokai-Kun – Antimicrobial Agents Chemotherapy

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and in eggs throughout development – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology

Combined pre-seed treatment with microbial inoculants and Mo nanoparticles changes composition of root exudates and rhizosphere microbiome structure of chickpea (Cicer arietinum L.) plants – E. N. Shcherbakova – Symbiosis

Interactions of soil particulate organic matter chemistry and microbial community composition mediating carbon mineralization in karst soils – Wei Xiao – Soil Biology and Biochemistry

Metabolic profiling of root exudates from two ecotypes of Sedum alfredii treated with Pb based on GC-MS – Qing Luo – Scientific Reports

Effects of Wetland Vegetation on Soil Microbial Composition: A Case Study in Tumen River Basin, Northeast China– Qin Lei – Chin. Geogra. Sci

Microbial communities in pyrene amended soil–compost mixture and fertilized soil – Iris K. U. Adam – AMB Express

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi – Maja Hilber-Bodmer – BMC Microbiology

Tobacco bacterial wilt suppression with biochar soil addition associates to improved soil physiochemical properties and increased rhizosphere bacteria abundance – Chengsheng Zhang – Applied Soil Ecology

Editorial: Microbial community ecology: Function over phylogeny – Sean M. Gibbons – Nature Ecology & Evolution

Review: Elucidating rhizosphere processes by mass spectrometry – A review – Ariana Rugova – Analytica Chimica Acta

Water and extremophile microbiome

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments – Marc Mußmann – The ISME Journal

Food microbiology

Review: An Integrated View of the Effects of Wine Polyphenols and Their Relevant Metabolites on Gut and Host Health – Carolina Cueva – Molecules

Microbiological quality of Brazilian UHT milk: Identification and spoilage potential of spore-forming bacteria – Claudia L O Pinto – International Journal of Dairy Technology

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Source tracking of prokaryotic communities in fermented grain of Chinese strong-flavor liquor – Xueshan Wang – International Journal of Food Microbiology

Bioinformatics

phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics – Lionel Guy – Bioinformatics

Microbes in the news

Hyperthermophiles and Cryophiles: The World’s Most Extreme Organisms – Priya Amin – Harvard Science Review

Bik’s non-microbiology picks

Responses of Human Neonates to Highly Diluted Odorants from Sweat – Helene M. Loos – Journal of Chemical Ecology

January 7, 2017

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3D modeling of endometrial interaction with vaginal bacteria, insect symbiont determined by host plants, 2011 tsunami effects on  phytoplankton, virus taxonomy, Microbiome Helper and microRNA sensitivity in intestinal stem cells.

Human vaginal microbiome

* Human three-dimensional endometrial epithelial cell model to study host interactions with vaginal bacteria and Neisseria gonorrhoeae – Paweł Łaniewski – Infection and Immunity

Human gut microbiome

Workshop Proceedings: Nutrition Across the Lifespan for Healthy Aging – Proceedings of a Workshop—in Brief – NAS

Review: Gut–brain axis in 2016: Brain–gut–microbiota axis — mood, metabolism and behaviour – Timothy G. Dinan & John F. Cryan – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Comparative Analysis of Drosophila melanogaster Gut Microbiota with Respect to Host Strain, Sex, and Age – Gangsik Han – Microbial Ecology

Impact of birth weight and postnatal diet on the gut microbiota of young adult guinea pigs – Kait Al – PeerJ

* Host plant species determines symbiotic bacterial community mediating suppression of plant defenses – Seung Ho Chung – Scientific Reports

Animal microbiome

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges – Gerald Lackner – PNAS

Plant, root, and soil microbiome

Regulation of root development in Arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria – Jana Klikno – Protoplasma

Diversity and composition of rhizospheric soil and root endogenous bacteria in Panax notoginseng during continuous cropping practices – Yong Tan – Journal of Basic Microbiology

Subsurface Microbial Ecosystems: A Photon Flux and a Metabolic Cascade – Alexander P. Petroff – Journal of Statistical Physics

Water microbiome

* Retrospective analysis of phytoplankton assemblages on the Iwate coast before and after the 2011 tsunami using cryopreserved DNA samples – Yutaka Okumura

Effects of iron deficiency on the growth and photosynthesis of three bloom-forming cyanobacterial species isolated from Lake Taihu – Kui Xu – Phycological Research

Patterns of bacterial diversity in the marine planktonic particulate matter continuum –
Mireia Mestre – The ISME Journal

Bioreactor, waste, and pollution microbiology

Biofilm composition and threshold concentration for growth of Legionella pneumophila on surfaces exposed to flowing warm tap water without disinfectant – Applied and Environmental Microbiology

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia – Zhiman Yang – Bioresource Technology

Accelerated acidification by inoculation with a microbial consortia in a complex open environment – Jiadong Yu – Bioresource Technology

Effects of a bacterial consortium from acid mine drainage on cadmium phytoextraction and indigenous soil microbial community – Jin-tian Li – Plant and Soil

Can DNA sequencing show differences between microbial communities in Polish and Danish wastewater treatment plants? – A. Miłobędzka – Water Science & Technology

Frequency dependent microbial growth during cycles of feast and famine – Jason Merritt – arXiv

Viruses and phages

* Consensus statement: Virus taxonomy in the age of metagenomics – Peter Simmonds – Nature Reviews Microbiology

Genomic evolution of bacterial populations under coselection by antibiotics and phage
– Johannes Cairns – Molecular Ecology

Bioinformatics and metagenomics

* Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research – André M. Comeau – mSystems

Transcriptomics

* Functional transcriptomics in diverse intestinal epithelial cell types reveals robust microRNA sensitivity in intestinal stem cells to microbial status – Bailey C.E. Peck – Journal of Biological Chemistry

Biofilms

Tackling Fungal Resistance by Biofilm Inhibitors – Shanchao Wu – Journal of Medical Chemistry

Microbes in the news

Featuring our research: The Secret Lives of Marine Mammal Microbes – Probing the mystery of what goes on inside the guts of dolphins and whales – Emma Hiolski – Scientific American

That cold you have might actually be the worst Bay Area flu outbreak in a decade – Kristin Hanes – SF Gate

Microbiomes in far-flung places: characterizing the arctic Inuit gut microbiome – Stephen Ornes – ASM

Microbes on the market

MoBio’s Microbiome News is back!

OptiBiotix Release: Microbiome Technology Powers The Healthy Weight Loss Company Expansion – BioSpace

Bik’s Non-Microbiology Picks

The crack in this Antarctic ice shelf just grew by 11 miles. A dramatic break could be imminent – Chris Mooney – Washington Post

Citizen Science: It’s that time of year: the annual bird count – Shawn Price – Los Angeles Times

January 5, 2017

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Microbiome of Inuit, centenarians, microbes showing differential expression when they are grown with sound, taxonomy of prokaryotic viruses.

Human gut microbiome

* Gut Microbiome of the Canadian Arctic Inuit – Catherine Girard – mSphere

* The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile – Biagi Elena – Mechanisms of Ageing and Development

Review: Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota – Jun Xu – Medicinal Research Reviews

Editorial: The microbiome as a source of new enterprises and job creation: Considering clinical faecal and synthetic microbiome transplants and therapeutic regulation – Daniel van der Lelie – Microbial Biotechnology

Animal experiments

Effect of dietary kefir on the growth performance, feed utilization and fatty acid profile of juvenile rainbow trout, Oncorhynchus mykiss – E. Gümüş – Aquaculture Nutrition

Plant, root, and soil microbiome

The Pseudomonas putida T6SS is a plant warden against phytopathogens – Patricia Bernal – The ISME Journal

Mycorrhizal Colonization Status and Rhizosphere Soil Properties of BCSIR Reserve Forest Rajshahi, Bangladesh – M. Halder – Current World Environment

Waste and pollution microbiology

Batch and continuous removal of heavy metals from industrial effluents using microbial consortia – F. Migahed – International Journal of Environmental Science and Technology

Musical microbes

* Frequency-dependent response of Chromobacterium violaceum to sonic stimulation, and altered gene expression associated with enhanced violacein production at 300 Hz – Chinmayi Joshi – bioRxiv

Bioinformatics

Book: Molecular Data Analysis Using R – Csaba Ortutay

Viruses and phages

* Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee – Evelien M. Adriaenssens – Archives of Virology

Metabolomics

Optimal allocation of metabolic functions among organisms in a microbial ecosystem – Qi Zhao – Decision and Control (CDC), 2016 IEEE 55th Conference on

Microbes in the news

CDC keeps secret its mishaps with deadly germs: CDC blacked-out information from lab incident reports – Alison Young – USA Today

Single fecal transplant no more effective than standard of care in treating C. diff – MedicalXpress

Alaska gulls are picking up antibiotic-resistant bacteria that could infect humans – Yereth Rosen – ADN

Man-made lake near Linganore drained to kill toxic pink bacteria: pink-colored cyanobacterium releases a toxin – Samantha Hogan – The Frederick News Post

Bacteria Hysteria

Dirty Money. The public health case for a cashless society – Dina Fine Maron – Scientific American
The Money in Your Wallet Might Be Covered With Poop, Mold, and Cocaine – Brad
– Money
The 5 Dirtiest Things You Touch Every Day – Markham Heid – Time

Microbes in the market

Israeli Gut Microbiome Startup Lands Mayo Clinic Venture Backing – TwinCities Business

Ritter Pharmaceuticals Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published in Proceedings of the National Academy of Sciences – Yahoo

Cambridge BioMarketing Announces Five Predictions for 2017 – Yahoo

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business – PR Newswire

Science integrity

Bavarian court sentences me to prison if I dare repeat unwelcome facts of Walles’ trachea transplants – Leonid Schneider – For Better Science

 

December 29, 2016

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A foundational coral, bacteria in tree hollows, mining and visualizing microbiome data with Calypso, viral metagenomics in aquaculture.

General microbiome

Editorial: You are not alone – M. Ludwig – Acta Physiologica

Human ear microbiome

The Relationship of the Middle Ear Effusion Microbiome to Secretory Mucin Production in Pediatric Patients with Chronic Otitis Media – Krueger, Anna – The Pediatric Infectious Disease Journal

Animal experiments

Improvement of Intestinal Immune Cell Function by Lactic Acid Bacteria for Dairy Products – Tomonori Kamiya – Microorganisms

In poultry: Zeolite food supplementation reduces abundance of enterobacteria – Tanka P. Prasai – Microbiological Research

Animal microbiome

* Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral – Elizabeth C. Shaver – Ecology

By their own devices: invasive Argentine ants have shifted diet without clear aid from symbiotic microbes – Yi Hu – Molecular Ecology

Gut content microbiota of introduced bigheaded carps (Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe – Andrea K. Borsodi – Microbiological Research

Plant, root, and soil microbiome

Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus – Sari Timonen – Microbial Ecology

Benzo(a)pyrene degradation and microbial community responses in composted soil – Fengxiao Zhu – Environmental Science and Pollution Research

* Bacteria and Hoverflies (Diptera: Syrphidae) in Tree Hollows From the Iberian Mediterranean Forest – I. R. Sánchez-Galván – Environmental Entomology

Cd immobilization and reduced tissue Cd accumulation of rice (Oryza sativa wuyun-23) in the presence of heavy metal-resistant bacteria – Ya Li – Ecotoxicology and Environmental Safety

Water microbiome

* Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control – Hetron M. Munang’andu – Frontiers in Microbiology

Food microbiology

Microbial Ecology Dynamics in Portuguese Broa Sourdough – João M. Rocha – Journal of Food Quality

Bioinformatics and metagenomics

* Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions – Martha Zakrzewski – Bioinformatics

DACE: A Scalable DP-means Algorithm for Clustering Extremely Large Sequence Data – Linhao Jiang – Bioinformatics

A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases – Xing Chen – Bioinformatics

Measuring the diversity of the human microbiota with targeted next-generation sequencing – Francesca Finotello – Briefings in Bioinformatics

More microbiology

Collective Resistance in Microbial Communities by Intracellular Antibiotic Deactivation – Robin A. Sorg – PLOS Biology
Microbes in the news

Circadian rhythms and the microbiome – Cosmos Magazine

You Don’t Even Want To Know About Bacteria On The Space Station – Trace Dominguez – Seeker

Rabbits, Bacteria and Calcium – Carl Palazzolo – Long Beach Post

Bacteria evolving more sophisticated antibiotic resistance – Brooks Hays – UPI

December 27, 2016

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Cockatiel microbiome, a hibernating frog, Baltic Sea, a book about starter cultures, microbial divisions of labor.

Human oral/respiratory microbiome

Mycobiome in the Lower Respiratory Tract – a Clinical Perspective – Robert Krause – Frontiers in Microbiology

Review: A Review of Analytical Techniques and Their Application in Disease Diagnosis in Breathomics and Salivaomics Research – David J. Beale – Int J Mol Sci

Human gut microbiome

Impact of Amoxicillin/Clavulanate and Autologous Fecal Microbiota Transplantation (FMT) on the Fecal Microbiome and Resistome – Christopher Bulow – Open Forum Infectious Diseases

Review: The Development of Our Organ of Other Kinds—The Gut Microbiota – Shirong Liu – Frontiers in Microbiology

Review: Food Additives and Contaminants: Effects on Human Gut Microbiota—A Review – Paula Roca-Saavedra – Preprints

Animal experiments

Generation of Germ-Free Ciona intestinalis for Studies of Gut-Microbe Interactions – Brittany A. Leigh – Frontiers in Microbiology

Review: Emerging Sponge Models of Animal-Microbe Symbioses – Lucia Pita – Frontiers in Microbiology

Animal microbiome

Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural – Thijs De Mulder – FEMS Microbiology Ecology

Diversity of the Bacterial Microbiota of Anopheles Mosquitoes from Binh Phuoc Province, Vietnam – Chung T. Ngo – Frontiers in Microbiology

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples – Maozhang He – Frontiers in Microbiology

* Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet – Luis David Alcaraz – PeerJ

* Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation – Francis Cheng-Hsuan Weng – BMC Genomics

Plant, root, and soil microbiome

Long-term effects of aided phytostabilization on microbial communities of metal-contaminated mine soil– Olatz Garaiyurrebaso – FEMS Microbiology Ecology

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection – Caroline De Tender – Frontiers in Microbiology

Expanding the Repertoire of Carbapenem-Hydrolyzing Metallo-ß-Lactamases by Functional Metagenomic Analysis of Soil Microbiota – Dereje D. Gudeta – Frontiers in Microbiology

High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia – Anastasia A. Ivanova – Frontiers in Microbiology

Editorial: Microbiota of Grapes: Positive and Negative Role on Wine Quality – Giuseppe Spano – Frontiers in Microbiology

Aspect has a greater impact on alpine soil bacterial community structure than elevation – Jieyun Wu – FEMS Microbiology Ecology

Water and extremophile microbiome

* Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea – Markus V. Lindh – Frontiers in Microbiology

A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition – Wei Li – Frontiers in Microbiology

Viral induced microbial mortality in Arctic hypersaline spring sediments – Jesse Colangelo-Lillis – Frontiers in Microbiology

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study – Yulia A. Frank – Frontiers in Microbiology

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments – Leah D. Brandt – Archaea

Waste and pollution microbiology

Temporal dynamics of microbial communities in microcosms in response to pollutants – Shuo Jiao – Molecular Ecology

Cultural heritage microbiology

Sloth: Survey of the state of conservation of the Mylodon listai (Xenarthra-Mylodontidae) skin fragment from the Pleistocene of Argentina kept at the Museum of La Plata (Argentina) – Daniela Silvana Nitiu – Ge-conservación

Food microbiology

* Book: Starter Cultures in Food Production – Barbara Speranza

Biofilm microbiome

Molecular methods resolve the bacterial composition of natural marine biofilms on galvanically coupled stainless steel cathodes – Athenia L. Oldham – Journal of Industrial Microbiology & Biotechnology

Metagenomics and bioinformatics

Characterization of Uncultured Genome Fragment from Soil Metagenomic Library Exposed Rare Mismatch of Internal Tetranucleotide Frequency – Yunpeng Liu – Frontiers in Microbiology

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys – Chao Xie – BMC Bioinformatics

More microbiology

Review: Chronic infections with viruses or parasites: breaking bad to make good – Andrew Godkin – Immunology

Biocontrol of Burkholderia cepacia complex bacteria and bacterial phytopathogens by Bdellovibrio bacteriovorus – Damian McNeely – Canadian Journal of Microbiology

Fitness Impact of Obligate Intranuclear Bacterial Symbionts Depends on Host Growth Phase – Chiara Bella – Frontiers in Microbiology

* Review: Understanding Microbial Divisions of Labor – Zheren Zhang – Frontiers in Microbiology

Microbes in the news

How Does a Fatty Acid Protect Pathogenic Bacteria Against Antibiotics? – Nicola M. Parry – Contagion Live

How Microcosms help us understand ecology – James MacDonald – JSTOR Daily

Takuji Yamada – Early cancer intervention with gut bacteria – Tokyo Tech Researchers

How Probiotics Could Help Prevent Atopic Dermatitis – Kenneth Bender – Specialty Pharmacy Times

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 22, 2016

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Hand washing and drying hygiene, wild and managed geese,  juvenile alpine plants.

uBiome blog

We’re Dreaming of a Brown Christmas + Winter Sale: Celebrate the holiday season with a flurry of festive feces factoids – Julie Taylor – uBiome blog

Human skin microbiome

Cleanliness in context: reconciling hygiene with a modern microbial perspective – Roo Vandegrift – bioRxiv

Human mouth microbiome

Oral Biofluid Biomarker Research: Current Status and Emerging Frontiers – Austin Wang – Diagnostics

Human gut microbiome

Hypothesis: The gut–brain connection: triggering of brain autoimmune disease by commensal gut bacteria – Hartmut Wekerle – Rheumatology

Animal microbiology

* Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus) – Wen Wang – Microbiology Open

Application of genomic technologies to measure and monitor antibiotic resistance in animals – Jian-Qiang Su – Annals of the New York Academy of Sciences

Plant, root, and soil microbiome

Microbial activity promoted with organic carbon accumulation in macroaggregates of paddy soils under long-term rice cultivation – Yalong Liu – Biogeosciences

Ozone and Nitrogen Effects on Juvenile Subalpine Plants: Complex Interactions with Species and Colonization by Arbuscular Mycorrhizal Fungi (AMF) – Seraina Bassin – Water, Air, & Soil Pollution

Food microbiology

Developing a microbial time–temperature indicator to monitor total volatile basic nitrogen change in chilled vacuum-packed grouper fillets – Hsin-I Hsiao- Journal of Food Processing and Preservation

Waste and pollution microbiology

Biological Treatment of Landfill Leachate at Elevated Temperature in the Presence of Polyurethane Foam of Various Porosity – Justyna Koc-Jurczyk – Clean Soil Air Water

Built environment microbiology

Investigation of the microbial communities colonizing prepainted steel used for roofing and walling – Tran T. Huynh – Microbiology Open

Bioinformatics, modeling, ecology and statistics

Using rarefaction to isolate the effects of patch size and sampling effort on beta diversity – Adrian C. Stier – Ecosphere

Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons – Hong-Tai Cao – BioAssays

A review of simulation and modeling approaches in microbiology – A.I. Klimenko – Russian Journal of Genetics: Applied Research

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere – Ryan J. Newton – Aquatic Microbial Ecology

Microbes in the news

* Book: Understanding the Gut Microbiota – Gerald W. Tannock

Scientists build bacteria-powered battery on single sheet of paper – Science Daily

Study: Manuka honey kills more bacteria than all available antibiotics – Amy Goodrich – Natural News

UT Southwestern researchers find new way to combat multidrug-resistant bacteria in burn injuries – News-Medical

Xylariaphilia. A blog about fungi, science, and art – Roo Vandegrift

Microbiomes Gain Momentum in Indiana’s Life Sciences – Kylie Veleta – Inside Indiana Business

December 18, 2016

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Virome of the human respiratory tract, vendor effects on mouse gut, soils under beech and spruce, variations in Scottish soils, portable pathogen detection.

Events

Poster submission started: 3rd Annual Translational Microbiome Conference – April 11-13, 2017, Boston, USA

Pregnancy and early life

Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi – Lorenzo Drago – The ISME Journal

Review: Pathogenesis of NEC: Impact of an altered intestinal microbiome – Josef Neu – Seminars in Perinatology

Human oral microbiome

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste – British Dental Journal

Human respiratory microbiome

* Review: The Virome of the Human Respiratory Tract – Kristine M. Wylie – Clinics in Chest Medicine

Human vaginal microbiome

Comparison of Culture-dependent and Culture-Independent Molecular Methods for Characterisation of Vaginal Microflora – Shirali Pandya – Journal of Medical Microbiology

Human gut microbiome

Distinct microbiome-neuroimmune signatures correlate with functional abdominal pain in children with autism spectrum disorder – Ruth Ann Luna – CMGH Cellular and Molecular Gastroenterology and Hepatology

Alterations of the gut microbiome in Chinese patients with systemic lupus erythematosus
Zhixing He – Gut Pathogens

Altered Gut Microbiota in Patients With Chronic Pancreatitis is Associated With Gut Barrier Dysfunction and Metabolic Abnormalities – Rupjyoti Talukdar

Dietary Changes Impact the Gut Microbe Composition in Overweight and Obese Men with Prostate Cancer Undergoing Radical Prostatectomy – Andrew D. Frugé – Journal of the Academy of Nutrition and Dietetics

The human intestinal microbiota of constipated-predominant irritable bowel syndrome patients exhibits anti-inflammatory properties – Alain P. Gobert – Scientific Reports

The Interactions Between Gut Microbiota and Lynch Syndrome – Xiao-juan Lu – Clinical Gastroenterology and Hepatology

Review: Enterosalivary nitrate metabolism and the microbiome: intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health – Carl D Koch – Free Radical Biology and Medicine

Review: Community metabolic modeling approaches to understanding the gut microbiome: bridging biochemistry and ecology – Helena Mendes-Soares – Free Radical Biology and Medicine

Review: Microbiota Small RNAs in Inflammatory Bowel Disease – Anca T. Filip – Journal of Gastrointestinal and Liver Diseases

Review: Intestinal Microbiome, Akkermansia muciniphila, and Medicinal Nutrition Therapy – Jeffrey Bland – integrative Medicine

Review: Using the Human Gastrointestinal Microbiome to Personalize Nutrition Advice: Are Registered Dietitian Nutritionists Ready for the Opportunities and Challenges? – Ruth Harvie – Journal of the Academy of Nutrition and Dietetics

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

Animal experiments

* Vendor Effects on Murine Gut Microbiota Influence Experimental Abdominal Sepsis – Tobias Hilbert – Journal of Surgical Research

The critical role of microbiota within cecal crypts on the regenerative capacity of the intestinal epithelium following surgical stress – Alexander Zaborin – American Journal of Physiology Gastrointestinal and Liver Physiology

Source of supplemental dietary copper, zinc, and manganese affects fecal microbial relative abundance in lactating dairy cows – M.J. Faulkner – Journal of Dairy Science

Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics – Natália C. Gaeta – Journal of Dairy Science

Animal microbiology

Riptortus pedestris and Burkholderia symbiont: an ideal model system for insect–microbe symbiotic associations – Kazutaka Takeshita – Research in Microbiology

Bird: Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota – Lindsay K Newbold – The ISME Journal

Plant, root, and soil microbiome

* Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce – Heiko Nacke – Frontiers in Microbiology

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia – Bruno L. Mello – Scientific Reports

The biogeography of soil archaeal communities on the eastern Tibetan Plateau – Yu Shi – Scientific Reports

Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic – Enzong Xiao – Environmental Pollution

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic) – Aleš Eichmeier – PLOS ONE

* Scottish soil: It is elemental: Soil nutrient stoichiometry drives bacterial diversity – Manuel Delgado-Baquerizo – Environmental Microbiology

Microbial soil community analyses for forensic science: Application to a blind test – Sandrine Demanèche – Forensic Science International

Review: Mycorrhiza: The Oldest Association Between Plant and Fungi – Jagnaseni Barman – Resonance

Book Chapter: Bioprospecting Soil Metagenomes for Antibiotics – Chiara Borsetto – Bioprospecting

Water and extremophile microbiome

The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China – Yantian Ma – Archaea

Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria – Wajdi Ben Hania – Environmental Microbiology

Book chapter: Bioprospecting Archaea: Focus on Extreme Halophiles – André Antunes – Bioprospecting

Food microbiology

Analysis of the bacterial biodiversity of peaches under refrigerated storage after treatment by high hydrostatic pressure – Maria José Grande Burgos – Food and Bioproducts Processing

Bioreactor, biotechnology, and pollution microbiology

Correlating methane production to microbiota in anaerobic digesters fed synthetic wastewater – K. Venkiteshwaran – Water Research

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes – Georgina Robinson – Scientific Reports

Trace Elements Induce Predominance among Methanogenic Activity in Anaerobic Digestion – Babett Wintsche – Frontiers in Microbiology

Bioinformatics and metagenomics

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes – Mohammadkarim Saeedghalati – arXiv

A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples – Daniel H. Huson – Journal of Biotechnology

Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota – Sébastien Raguideau – PLOS Computational Biology

Now published: IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses – Shaman Narayanasamy – Genome Biology

Metabolomics

Evaluating metabolic response to light exposure in Lactobacillus species via targeted metabolic profiling – Mengyang Xu – Journal of Microbiological Methods

Review: Phytanic acid consumption and human health, risks, benefits and future trends: A review – P. Roca-Saavedra – Food Chemistry

Viruses and phages

Perspective: Viruses and the origin of microbiome selection and immunity – Steven D Quistad – The ISME Journal

Techniques

* Detection of ESKAPE bacterial pathogens at the point-of-care using isothermal DNA-based assays in a portable, de-gas microfluidic diagnostic assay platform
Lars D. Renner – Applied and Environmental Microbiology

Press: Portable detection system can rapidly identify virulent, multi-drug resistant pathogens in remote areas – News-Medical

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing – Dieter M. Tourlousse – Nucleic Acids Research

Microbes in the news

Gardening Etcetera: Life down under in northern Arizona – Cindy Murray – AZ Daily Sun

CSI: Chem trail: a new way for investigators to narrow down suspect pools using chemical traces found on cellphones – Kelly Kasulis – Boston Globe

China expresses alarm as chilli ‘conspiracy’ heats up Indonesians – South China Morning Post

Adapting and adopting microbiome data into clinical practice – Silvio Pitlik & Omry Koren- BioMed Central

Bacteria that boost insulin-producing cells could yield new diabetes approaches – Arlene Weintraub – Fierce Biotech

Microbes in the market

Research focused on the human microbiome market worth 658 million USD by 2023 – Whatech

AOBiome Launches Phase 2 Clinical Trial Using Novel Bacterial Platform for Treatment of Hypertension – PR Newswire

Live Stock Coverage: What’s Ahead for Seres Therapeutics Inc After Today’s Huge Increase? – Linda Rogers- Frisco Fastball

 

December 14, 2016

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Gaia and her microbiome, a walk in the park, ancient teeth, fillies, bats, ticks, frogs, moss, and high-altitude potatoes.

General microbiome

Gaia and Her Microbiome – John F. Stolz – FEMS Microbiology Ecology

Human oral microbiome

Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth – Nicolás Rascovan – NPJ Biofilms and Microbiome

Influences of pH and iron on the salivary microbiome in individuals with and without caries – Jianye Zhou – Applied and Environmental Microbiology

Human gut microbiome

Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus – Xiaokai Wang – Antonie van Leeuwenhoek

Animal experiments

Intense Exercise and Aerobic Conditioning Associated with Chromium or L-Carnitine Supplementation Modified the Fecal Microbiota of Fillies – Maria Luiza Mendes de Almeida – PLOS ONE

 

Animal microbiome

Mosquitoes: Diversity of Cultivable Midgut Microbiota at Different Stages of the Asian Tiger Mosquito, Aedes albopictus from Tezpur, India – Kamlesh K. Yadav – PLOS ONE

Bats: Microbiome of the sexual scent organ of Leptonycteris yerbabuenae – Osiris Gaona – PeerJ

Ticks: Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California – Nikos Gurfield – PeerJ

Frogs: Environmental fluctuations and host skin bacteria shift survival advantage between frogs and their fungal pathogen – Ana V Longo – ISME Journal

Plant, root, and soil microbiology

Discovery of polyesterases from moss-associated microorganisms – Christina Andrea Müller – Applied and Environmental Microbiology

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil – Honggui Wang – Soil Biology and Biochemistry

Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development – Stefan Pfeiffer – FEMS Microbiology Ecology

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures – Senta Heiss-Blanquet – PLOS ONE

Effects of root exudates of woody species on the soil antierodibility in the rhizosphere in a karst region, China – Zhen hong Wang – PeerJ Preprint

Water and extremophile microbiome

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf – Jean-David Grattepanche – PLOS ONE

Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir, Beijing, China – Yongjuan Chen – Applied Microbiology and Biotechnology

Pristine but metal-rich Río Sucio (Dirty River) is dominated by Gallionella and other iron-sulfur oxidizing microbes – Alejandro Arce-Rodríguez – Extremophiles

Quantification of basal ice microbial cell delivery to the glacier margin – Mario Toubes-Rodrigo – Biogeosciences Discuss

Microbial Diversity of Source and Point-of-Use Water in Rural Haiti – A Pyrosequencing-Based Metagenomic Survey – Nabanita Mukherjee – PLOS ONE

Virus-host infection dynamics of marine single-celled eukaryotes resolved from metatranscriptomics – bioRxiv

Pollution

The Biologists’ Forum: Environmental microbial community analysis methods as applied to bioremediation – Hadassa Shira Guttman – BIOS

Food microbiology

Determination of Fungal Community Diversity in Fresh and Traditional Chinese Fermented Pepper by Pyrosequencing – Lingyan Zhao – FEMS Microbiology Letters

Metagenomics

Using Bacterial Genomes and Essential Genes for the Development of New Antibiotics – Francisco R. Fields – Biochemical Pharmacology

Antibiotic discovery is a walk in the park – Louis-Félix Nothias – PNAS

Metabolomics

Book: Microbial Metabolomics: Applications in Clinical, Environmental, and Industrial Microbiology – Editors: David J. Beale, Konstantinos A. Kouremenos, Enzo A. Palombo – Springer

Microbes in the news

Scientists trap bacteria with optical tractor beam.”The principle underlying this laser beam is similar to the concept to be found in the television series ‘Star Trek,'” said researcher Thomas Huser –  Brooks Hays – UPI

Researchers find bacterial protein that boosts insulin-producing cells in zebrafish – Science Daily

A $5 fix for a nasty parasite: Attachment of Cryptosporidium parvum oocysts to environmental biofilms – EurekAlert

Increasing Product Recalls and Growing Consumer Concerns are Driving the Global Industrial Microbiology Market – Medgadget

 

 

December 12, 2016

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Review on human milk microbiome, oral microbiome changes in seasonal athletes, gut microbiome and bipolar disorder.

Jobs

Assistant Professor In Quantitative Ecology or Evolution of Microbes – UCLA – MicroBEnet

Pregnancy and early life

Effect of probiotics in prevention of atopic dermatitis is dependent on the intrinsic microbiota at early infancy – Ekaterina Avershina – Journal of Allergy and Clinical Immunology

* Review: Got bacteria? The astounding, yet not-so-surprising, microbiome of human milk – Michelle K McGuire – Current Opinion in Biotechnology

Human respiratory microbiome

Review: Viral–bacterial co-infections in the respiratory tract – Lauren O Bakaletz – Current Opinion in Microbiology

Human oral microbiome

* I was wondering if testing same group of athletes participating in 2 different sports could not be confounded with seasonal effects of maybe different study loads during the different year. But no access to the paper, so can not see details. Elevated salivary IgA, decreased anxiety, and an altered oral microbiota are associated with active participation on an undergraduate athletic team – Ashley L. Lamb – Physiology & Behavior

Human gut microbiome

* The gut microbiome composition associates with bipolar disorder and illness severity – Simon J. Evans – Journal of Psychiatric Research

Letter of the Editor: A Microbiome Assessment of Medical Marijuana – George Thompson III – Clinical Microbiology and Infection

Review: Archaea: essential inhabitants of the human digestive microbiota – Vanessa Demonfort Nkamga – Human Microbiome Journal

Animal experiments

Application of a dynamic gastrointestinal in vitro model combined with a rat model to predict the digestive fate of barley dietary fibre and evaluate potential impact on hindgut fermentation – Cristina Teixeira – Bioactive Carbohydrates and Dietary Fibre

Animal microbiome

Characterization and identification of microbial communities in bovine necrotic vulvovaginitis – N.Y. Shpigel – The Veterinary Journal

Crab: Gut Microbiota and Metabolic Phenotype of Portunus Trituberculatus – Ting-Lan Zeng – Chinese Journal of Analytical Chemistry

Plant, root, and soil microbiome

Arsenic-enrichment enhanced root exudates and altered rhizosphere microbial communities and activities in hyperaccumulator Pteris vittata – Suvendu Das – Journal of Hazardous Materials

Food microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Bioinformatics and metagenomics

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics – Karel Sedlar – Computational and Structural Biotechnology Journal

Microbes in the news

Predatory bacteria used to release bioplastics – Tim Sandle – Digital Journal

The Secret Soviet Virus That Helps Kill Bacteria. Antibiotic resistance is threatening to render antibiotics useless, but scientists may have found their answer in bacteria-eating viruses. – Trace Dominguez – Seeker

Bacteria found in close to two-thirds of NZ supermarket chicken – TV New Zealand

Science, publishing, and career

This would not be my headline choice: Trump says ‘nobody really knows’ if climate change is real – Juliet Eilperin – Washington Post