Category Archives: Metabolomics

May 10, 2016, 2nd edition

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Nitrate and oral microcosms, microbial tryptophan metabolism effects on astrocytes, creating germ free plants, a systematic review of the (lack of) effect of probiotics on the gut microbiome, and a phage/host prediction tool.

Event

Starts today: Food-Microbiome Interaction: Implications for Health & Disease – New York Academy of Sciences and the Quadram Institute at The Royal Society in London

Pregnancy and birth

Prenatal and post-natal exposure to antibiotics and risk of asthma in childhood – J. Metsälä – Clinical & Experimental Allergy

Review: Obesity and overweight: Impact on maternal and milk microbiome and their role for infant health and nutrition – Izaskun Garcia-Mantrana – Molecular Nutrition and Food Research

Human respiratory microbiome

Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities – Marcos Pérez-Losada – AIMS Microbiology

Human oral microbiome

Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms – Jessica E. Koopman – Microbial Ecology

Human skin microbiome

A systematic review and meta-analysis on Staphylococcus aureus carriage in psoriasis, acne and rosacea – J. E. E. Totté – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups – Deepak Yadav – Gut Pathogens

Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials – Nadja B. Kristensen – Genome Medicine

Tissue Microbiome Profiling Identifies An Enrichment of Specific Enteric Bacteria In Opisthorchis viverrini Associated Cholangiocarcinoma – Kern Rei Chng – EBioMedicine

Editorial: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Could physical exercise help modulate the gut microbiota in chronic kidney disease? – Marta Esgalhado – Future Microbiology

Review: The Gut Microbiota and Immune System Relationship in Human Graft-versus-Host Disease – Lucrezia Laterza – Mediterranean Journal of Hematology and Infectious Diseases

Review: Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions? – David Endesfelder – Current Diabetes Reports

Animal experiments

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions – Alejandro Salgado-Flores – PLOS ONE

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants – Sheerli Kruger Ben Shabat – The ISME Journal

Book Chapter: Germ-Free Mice Model for Studying Host–Microbial Interactions – Yogesh Bhattarai – Mouse Models for Drug Discovery – Springer

Animal microbiome

Review: Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds – Anak Agung Gede Indraningrat – Marine Drugs

Plant, root, and soil microbiome

Wheat seed embryo excision enables the creation of axenic seedlings and Koch’s postulates testing of putative bacterial endophytes – Rebekah J. Robinson – Scientific Reports

Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils – Jean-Baptiste Ramond – Journal of Basic Microbiology

Plants of the Fynbos biome harbour host species-specific bacterial communities – Tsakani Miyambo – FEMS Microbiology Letters

Extremophile microbiome

In situ hydrogen dynamics in a hot spring microbial mat during a diel cycle – Niels Peter Revsbech – Applied and Environmental Microbiology

Metabolomics

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor – Veit Rothhammer – Nature Medicine

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands – Bruno Lamas – Nature Medicine

Review: Urolithins, the rescue of ‘old’ metabolites to understand a ‘new’ concept: metabotypes as a nexus between phenolic metabolism, microbiota dysbiosis and host health status – Francisco A. Tomás-Barberán – Molecular Nutrition & Food Research

Metagenomics and bioinformatics –

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data – J. A. Frank – Scientific Reports

OrfM: A fast open reading frame predictor for metagenomic data – Ben J. Woodcroft – Bioinformatics

Phages and viruses

HostPhinder: A Phage Host Prediction Tool – Julia Villarroel – MDPI Viruses

More microbiology

Nonclinical Safety Assessment of SYN-004: An Oral β-lactamase for the Protection of the Gut Microbiome From Disruption by Biliary-Excreted, Intravenously Administered Antibiotics – John F. Kokai-Kun – International Journal of Toxicology

Rapid identification of health care–associated infections with an integrated fluorescence anisotropy system – Ki Soo Park – Science Advances

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans – Narasimha Anaganti – Journal of Biosciences

Microbes in the news

Stool Bank OpenBiome Is Expanding to Somerville. The bank wants more Boston-area residents to donate – Jamie Ducharme

Do probiotics have an effect on healthy adults? It’s too early to tell – EurekAlert

The Microbiome in Pediatric Rheumatic Diseases – Matthew Stoll – The Rheumatologist

May 10, 2016

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A very selective antibiotic that does not disturb the microbiota, metabolic pathways of the Deepwater Horizon spill, and GI microbiome role in acute myeloid leukemia.

Jobs and events

Postdoc funding opportunity “Microbiology of the built environment”, Alfred P. Sloan Foundation

The 4th Microbiome R&D and Business Collaboration Forum: USA – 3-4 October 2016, La Jolla, San Diego, USA

Human gut microbiome

The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Animal experiments

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model – Philipp Dirksen – BMC Biology

Editorial: Caenorhabditis microbiota: worm guts get populated – Laura C. Clark – BMC Biology

A Pathogen-Selective Antibiotic Minimizes Disturbance to the Microbiome – Jiangwei Yao – Antimicrobial Agents and Chemotherapy

Waste, pollution, and water treatment microbiology

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states – I.B. Gomes – Science of the Total Environment

Microbes in the news

Gut Microbiome Startup CeMeT Aims to Build Reference Database from 10K Volunteers in Germany – Julia Karow – Genome Web

Microbiome linked to infectious complications in AML – Medical Xpress

Narrow-Spectrum Antibiotic Could Spare the Microbiome. A drug that singles out Staphylococcus aureus leaves gut-dwelling microbiota largely intact, a mouse study shows – Amanda B. Keener – The Scientist

Genetic potential of oil-eating bacteria from the BP oil spill decoded – University of Texas at Austin

Fooling the test: Antibiotic-resistant bacteria that look susceptible – Phys.org

A new industry that uses bacteria to remediate old mines? – Jonathan Migneault – Sudbury

The Mighty Microbes of Yellowstone – Scalding water is home to what microbiologists call extremophiles, heat-loving creatures that have figured in many scientific breakthroughs – David Quammen – National Geographic

Science, publishing, and career

John Oliver exposes how the media turns scientific studies into “morning show gossip”
– German Lopez – Vox

Tracking Career Outcomes for Postdoctoral Scholars: A Call to Action – Elizabeth A. Silva – PLOS Biology

With quotes from me: Image manipulation in biomedical papers is commonplace – Maria Burke – Chemistry World

Open-access index delists thousands of journals. Many publications did not reapply after leading directory tightened its quality criteria – Monya Baker

April 29, 2016

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After Science’s Microbiome Issue yesterday, today’s digest features Genome Biology’s special Translational Microbiome issue. Papers on detecting colon cancer, Clostridium difficile infection, high-fat diets in mice. Also check out papers on H2 metabolism in the colon, no effects of temperature rise on soil microbiome of wet tropical forests, and ultra-basic springs.

Jobs and events

Nice speaker line-up: May 16-18, Michigan Meeting on Microbial Communities: a deep dive into the world of microbes – University of Michigan

Job opening in our lab: Life Science Research Professional  – Stanford

Pregnancy and birth

Gestational age, mode of birth and breastmilk feeding all influence acute early childhood gastroenteritis: a record-linkage cohort study – Jason P. Bentley – BMC Pediatrics

Human gut microbiome

Special issue Genome Medicine: Translating the microbiome: health and disease, Guest Editor: Curtis Huttenhower

Editorial: A roadmap to translating the microbiome – Rabia Begum – Genome Medicine

Detecting colon cancer using microbiota:  Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions – Nielson T. Baxter – Genome Medicine

Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection – Anna Maria Seekatz – Genome Medicine

Use of Shotgun Metagenome Sequencing to Detect Fecal Colonization with Multi-Drug Resistant Bacteria in Children – Heidi Andersen – Journal of Clinical Microbiology

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection – Emmanuel Montassier – Genome Medicine

Impact of Helminth Infection on the Clinical and Microbiological Presentation of Chagas Diseases in Chronically Infected Patients – Fernando Salvador – PLOS Neglected Tropical Diseases

Malaria, helminths and malnutrition: a cross-sectional survey of school children in the South-Tongu district of Ghana – Patrick Ferdinand Ayeh-Kumi – BMC Research Notes

Review: The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases – Alan C. Logan – Clinical Psychopharmacology and Neuroscience

Review: Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology – Mukesh Verma – Technology in Cancer Research & Treatment

Animal models
Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows – Jitka Kasparovska – PLOS ONE

Deep-fried oil consumption in rats impairs glycerolipid metabolism, gut histology and microbiota structure – Zhongkai Zhou – Lipids in Health and Disease

Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations – Gabriella Cobellis – Journal of Animal Science and Biotechnology

Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems – Raul Franzolin – BMC Research Notes

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet – Douglas Mahana – Genome Medicine

A fish, not the bird: Combined effects of dietary mannan- and fructo-oligosaccharide on growth indices, body composition, intestinal bacterial flora and digestive enzymes activity of regal peacock (Aulonocara stuartgranti) – S. S. Mirzapour-Rezaee – Aquaculture Nutrition

Plant, root, and soil microbiome

The composition, localization and function of low-temperature adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils – Yumei Dai – Journal of Applied Microbiology

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce – Jian-Gang Li – Scientific Reports

Pichia kudriavzevii as a representative yeast of North Patagonian winemaking terroir – Silvana M. del Mónaco – International Journal of Food Microbiology

Increases in mean annual temperature do not alter soil bacterial community structure in tropical montane wet forests – Paul C. Selmants – Ecosphere

Water and extremophile microbiome

A role for fungi as parasites in the black box of marine trophic interactions – Thomas A. Richards – Environmental Microbiology Reports

Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis – Lukas Kohl – Journal of Geophysical Research

Viruses and phages

Minireview: Virus-host interplay in high salt environments – Nina S. Atanasova – Environmental Microbiology Reports

Metagenomics and bioinformatics

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques – Disha Tandon – PLOS ONE

Metabolomics

H2 metabolism is widespread and diverse among human colonic microbes – Patricia G. Wolf – Gut Microbes

Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI) – Katherine Louie – bioRxiv

Viruses and phages

The virome: a missing component of biological interaction networks in health and disease – Scott A. Handley – Genome Medicine

Microbial ecology

Commentary: Bacteriophages or bacteriovores – that is the question: variations on the theme of eating Stenotrophomonas maltophilia – Harald Brüssow – Environmental Microbiology Reports

Microbes in the news

Lots of press coverage for the Science and Genome Medicine special issues today!

Scientists think they’ve found the secret to better poop transplants – Rachel Feltman – The Washington Post

Why Are Your Gut Microbes Different From Mine? To find out, scientists collected poop from thousands of people—but they ended up with more questions than answers – Ed Yong – The Atlantic

Food you eat and medicines you take can alter your gut bacteria in both good and bad ways – Emma Tiller – NH Voice

Special microbiome issue – Science Codex

Gut Microbiome Makeup Influenced by Medication Use, Other Factors – Genome Web

In Dutch: Zijn koffie, rode wijn en chocola nou wel of niet goed voor je? – Sander Voormolen – NRC

Title fail: World’s first microbiome study reveals links between lifestyle and gut flora – EurekAlert

Lifestyle has a strong impact on intestinal bacteria – Medical Xpress

The “Friendly” Bacteria In Your Gut Isn’t As Set At Birth As We Thought – Tom Chivers – BuzzFeed

Gut bacteria may predict risk of life-threatening infections following chemotherapy – Science Daily

What Can Happen When You’re Way Too Clean – Alice Park – Time

10 Bizarre (and Wonderful) Facts About Microbes:truly amazing facts about the human microbiome – Dawn Field – TopTenz

Vancouver couple develops slime-free water dishes for dogs – Eric MacKenzie – Vancouver 24h

Podcast: Microbe Talk, April 2016, Can parasitic worms treat inflammatory diseases?

Some superbugs literally explode when they die, making them even more deadly
Ticking time bomb – Jacinta Bowler – Science Alert

Science, publishing, and career

Unconditional data sharing, plus peer review transparency, is key to research reproducibility – Leonid Schneider – The Winnower

Featuring our paper: Seeing double: Duplicated images plague research papers – Ivan Oransky and Adam Marcus – STAT News

Paper linking fecal transplants to obesity in rats retracted for faked data – Dalmeet Singh Chawla – Retraction Watch

April 23, 2016

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Pint of Science, oral microbiome dynamics, rheumatoid arthritis, mineral turnover in the rhizosphere, and the subzero microbiome.

Events

Pint of Science San Francisco Bay Area (also in other cities all over the world): 23-25 May 2016, combining beer and science

Pregnancy and birth

Microbiome and Fetus: A Relationship for Life – Janet Teodori – Journal of Prenatal & Perinatal Psychology & Health

The Tree(s) of Life: The Human Placenta and My Journey to Learn More about It – Carolyn B. Coyne – PLOS Pathogens

Human oral microbiome

Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome – Niklas Grassl – Genome Biology

Human vaginal microbiome

Effects of low dose estrogen therapy on the vaginal microbiomes of women with atrophic vaginitis – Jian Shen – Scientific Reports

Human gut microbiome

Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients – Tossawan Jitwasinkul – Journal of Global Antimicrobial Resistance

Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet’s Disease – Jun Shimizu – PLOS ONE

An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis – Jun Chen – Genome Medicine

Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. Nov. – Khelaifia Saber – OMICS

Review: Bugging inflammation: role of the gut microbiota – Sj Shen – Clinical & Translational Immunology

Review: Modulating Composition and Metabolic Activity of the Gut Microbiota in IBD Patients – Mario Matijašić – MDPI Int J Mol Sci

Animal models

Effect of Dietary Carboxymethyllysine on glucose and insulin sensitivity, cecal fatty acids and the plasma metabolome in mice fed the Total Western Diet – Robert Edwin Ward – The FASEB Journal

Animal microbiome

The Microbiome of Animals: Implications for Conservation Biology – Simon Bahrndorff – International Journal of Genomics

Review: Herbivore dung as food for dung beetles: elementary coprology for entomologists – Peter Holter – Ecological Entomology

Plant, root, and soil microbiome

Plant–Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere – R. Alegria Terrazas – Advances in Applied Microbiology

Dynamics of endophytic bacteria in plant in vitro culture: quantification of three bacterial strains in Prunus avium in different plant organs and in vitro culture phases – Mona Quambusch – Plant Cell, Tissue and Organ Culture (PCTOC)

Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils – Mengmeng Wang – Plant and Soil

Nitrogen fertilization affects bacteria utilizing plant-derived carbon in the rhizosphere of beech seedlings – Silvia Gschwendtner – Plant and Soil

Temporal dynamic of parasite-mediated linkages between the forest canopy and soil processes and the microbial community – Ana Mellado – New Phytologist

Rhizosphere priming effect on soil organic carbon decomposition under plant species differing in soil acidification and root exudation – Xiaojuan Wang – New Phytologist

Water and extremophile microbiome

Viral metabolic reprogramming in marine ecosystems – Bonnie L Hurwitz – Current Opinion in Microbiology

Review: The subzero microbiome: Microbial activity in frozen and thawing soils – Mrinalini P. Nikrad – FEMS Microbiology Ecology

Gene expression profiling of microbial activities and interactions in sediments under haloclines of E. Mediterranean deep hypersaline anoxic basins – Virginia P Edgcomb – The ISME Journal

Waste and pollution microbiology

Effect of thermal pretreatment on the biogas production and microbial communities balance during anaerobic digestion of urban and industrial waste activated sludge – Hajer Ennouri – Bioresource Technology

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters – Stefano Fazi – Microbial Ecology

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms – Yunhua Xiao – Applied Microbiology and Biotechnology

Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments – S. Jane Fowler – Frontiers in Microbiology

Food microbiology

The Potential of the Incorporation of Essential Oils and Their Individual Constituents to Improve Microbial Safety in Juices: A Review – Evandro Leite de Souza – Comprehensive Reviews in Food Science and Food Safety

Bioinformatics and metagenomics

The Metagenomic Pizza: a simple recipe to introduce bioinformatics to the layman – Marie-Claude Blatter – EMBnet

MOCAT2: a metagenomic assembly, annotation and profiling framework – Jens Roat Kultima – Bioinformatics

Temporal microbiome road-maps guided by perturbations – Beatriz García-Jiménez – bioRxiv

Fundamental Limits of Pooled-DNA Sequencing – A. Najafi – ArXiv

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity – Nam-Phuong Nguyen – NPJ Biofilms

Microbial Ecology

Influence of dormancy on microbial competition under intermittent substrate supply: insights from model simulations – Konstantin Stolpovsky – FEMS Microbiology Ecology

Viruses and phages

Giant viruses at the core of microscopic wars with global impacts – Adrien Villai – Current Opinion in Virology

Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction – V Furtak – Eurosurveillance

Metabolomics

Review: Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions – Linda S. Zhang – Genome Medicine

Microbes in the news

Your office is a veritable petri dish of bacteria – Sarah Kaplan – The Washington Post

We’re home to trillions of cells that aren’t ours and they’re keeping us alive – Katherine Ellen Foley – Quartz

These oral bacteria are linked to an increased chance of getting pancreatic cancer – Laurie McGinley – The Washington Post

April 13, 2016

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Thematic issue on effect of antibiotics on microbiomes, limited effect of probiotics on stool proteomics, culex mosquito development, ocean acidification, and new technique to determine microbial growth.

General microbiome

Thematic Issue: the effects of anthropogenic use of antibiotics on the microbiomes in various ecosystems and the implications for human health. Guest edited by Prof. Kornelia Smalla, the articles included in this issue are freely available to read til 11th May 2016. Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology
Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Editorial: Microbiome: Eating for trillions – Derrick M. Chu – Nature

Pregnancy and birth

Preview: Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites – Seth Rakoff-Nahoum – Cell Host & Microbe

Review: The interplay of host immunity and environment on risk for bacterial vaginosis and associated reproductive health outcomes – Kerry Murphy – The Journal of Infectious Diseases

Human respiratory microbiome

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype – Leopoldo N. Segal – Nature Microbiology

Human gut microbiome

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults – Carolin A. Kolmeder – PLOS ONE

Review: The gut microbiota and metabolic disease: current understanding and future perspectives – T. Arora – Journal of Internal Medicine

Animal models

A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing – Anisa S. Ismail – Cell Host & Microbe

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella – Fabian Rivera-Chávez – Cell Host & Microbe

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations – Alexander R. Moschen – Cell Host & Microbe

Animal microbiome

Culex pipiens Development Is Greatly Influenced by Native Bacteria and Exogenous Yeast – Leonardo M. Díaz-Nieto – PLOS ONE

Plant, root, and soil microbiome

Convergence of soil microbial properties after plant colonization of an experimental plant diversity gradient – Katja Steinauer – BMC Ecology

Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus – Marta Alves – Scientific Reports

Relationship between presence of the desert shrub Haloxylon ammodendron and microbial communities in two soils with contrasting textures – Yanfeng Cao – Applied Soil Ecology

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil – Samiran Banerjee – Soil Biology and Biochemistry

Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism – Nick Bouskill – Frontiers in Microbiology

Water and extremophile microbiome

Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary – Nachshon Siboni – Frontiers in Microbiology

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields – Thomas Rime – Soil Biology and Biochemistry

Implications of Ocean Acidification for Marine Microorganisms from the Free-Living to the Host-Associated – Paul A. O’Brien – Frontiers in Marine Science

Waste and pollution microbiology

Shifts in microbial community structure and diversity in a MBR combined with worm reactors treating synthetic wastewater – Jia Liu – Journal of Environmental Sciences

Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area – James F. Douglass – Journal of Soils and Sediments

The effect of seasonality upon the development of lotic biofilms and microbial biostabilisation – Holger Schmidt – Freshwater Biology

Review: The importance of sewer biofilms – Henriette Jensen – Water

Food microbiology and functional foods

Lactobacillus plantarum TWK10 Supplementation Improves Exercise Performance and Increases Muscle Mass in Mice – Yi-Ming Chen – MDPI Nutrients

Investigation of the activity of the microorganisms in a Reblochon-style cheese by metatranscriptomic analysis – Christophe Monnet – Frontiers in Microbiology

Review: Prebiotics as a modulator of gut microbiota in paediatric obesity – A. C. Nicolucci – Pediatric Obesity

Techniques

Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples – Egbert Schwartz – Current Opinion in Biotechnology

Review: A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis – Aditi Sengupta – Agricultural & Environmental Letters

Microbial ecology

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning – Manuel Delgado-Baquerizo

Influence of dormancy on microbial competition under intermittent substrate supply: Insights from model simulations – Konstantin Stolpovsky – FEMS Microbiology Ecology

More microbiology

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis – Matt S. Conover – mBio

Biostatistics

Reinventing Biostatistics Education for Basic Scientists – Tracey L. Weissgerber – PLOS Biology

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

SCSU prof Elizabeth Lewis Roberts discovers fungus, bacteria help grass (really) – Anna Bisaro – New Haven Register

Probiotics for Livestock – Reducing Antibiotic Reliance – Alex Alexiev – MicroBEnet

Taking Cues From Human Nutrition To Reduce Antibiotic Use In Livestock – Amy Mayer – NPR

Why bacteria can’t get any bigger—or smaller – Elizabeth Pennisi – Science

Digestion of lignin in the gut – Science Daily

“Truly exciting”: Probiotic may increase muscle mass, energy & performance – Stephen Daniells – Nutraingredients

Breakthrough at Binghamton furthers development of bacteria-powered energy – The Engineer

Vibrio: Aggressive infectious bacteria species found in Sydney Harbour – Daisy Dumas – Sydney Morning Herald

Science, publishing, and career

Do interventions to reduce misconduct actually work? Maybe not, says new report – Alison McCook – Retraction Watch

$250 million, 300 scientists and 40 labs: Sean Parker’s revolutionary project to ‘solve’ cancer – Ariana Eunjung Cha – Washington Post

Science fairs are as flawed as my solar-powered hot dog cooker – Carl Zimmer – STATnews

The dark side of Guardian comments: part of a series on the rising global phenomenon of online harassment – the Guardian

How one lab challenged a grant rejection and won €5 million – Ewen Callaway – Nature

April 5, 2016

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Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

Commentary: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria –  Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester

March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 17, 2016

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Metagenomics of Necrotizing Enterocolitis, sinus irrigation, variation in mice in German facilities, and bacteria vs phage.

Pregnancy and birth

The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants – Doyle V. Ward – Cell Reports

Human respiratory microbiome

Evaluation of bacterial transmission to the paranasal sinuses through sinus irrigation – Leah J. Hauser – International Forum of Allergy & Rhinology

Human gut microbiome

Fecal Microbiota Transplantation in Children: A Brief Review – Suchitra K Hourigan – Pediatric Research

Forum: Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota – Tom Konikoff – Trends in Microbiology

Commentary: Recognizing that the microbiome is part of the human immune system will advance treatment of both cancer and infections – Richard L. Gallo – Journal of the American Academy of Dermatology

Review: Low calorie sweeteners and gut microbiota – Kristian Daly – Physiology & Behavior

Animal models

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities – Philipp Rausch – International Journal of Medical Microbiology

Plant, soil, and root microbiome

Plant versus microbial controls on soil aggregate stability in a seasonally dry ecosystem – Joseph C. Blankinship – Geoderma

Soil microbial communities following bush removal in a Namibian savanna – Jeffrey S. Buyer – Soil

Monitoring benthic microflora in river bed sediments: a case study in the Anllóns River (Spain) – Diego Martiñá Prieto – Journal of Soils and Sediments

Biodiversity gradients in obligate symbiotic organisms: exploring the diversity and traits of lichen propagules across the United States – Erin A. Tripp – Journal of Biogeography

Viruses and phages

Classic Spotlight: Bacteria versus Phage—the Battle Rages! – Tina M. Henkin – Journal of Bacteriology

Techniques

Review: Confocal Microscopy Imaging of the Biofilm Matrix – Sebastian Schlafer – Journal of Microbiological Methods

Metabolomics

Optimization of Metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Review: Challenges of metabolomics in human gut microbiota research – Kirill S. Smirnov – International Journal of Medical Microbiology

Microbes in the News

Subset of E. coli bacteria linked to deadly disease in pre-term infants – Medical Xpress

Our gut microbiome is always changing; it’s also remarkably stable – Science Codex

Meeting report: Microbes in the City: Mapping the Urban Genome – New York Academy of Sciences

Viral Infections May Affect Cystic Fibrosis Patients’ Respiratory Microbiome, Study Says – Daniela Semedo – Lung Disease News

Diverse diets enrich gut microbes – Catharine Paddock – Medical News Today

Mother’s Microbiome Shapes Offspring’s Immunity – The maternal gut microbiome guides neo- and postnatal immune system development, a mouse study shows – Anna Azvolinsky – The Scientist

How bacteria get their magnetic compass – Robert Sanders – Berkeley News

Science, publishing, and career

Blogging for beginners – Andrew David Thaler – Science

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March 12, 2016

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Microbiomes of farmland frogs and grape vine, and functional structures in acid mine drainage microbes.

Human oral microbiome

Ecological changes in oral microcosm biofilm during maturation – Young-Seok Kim – Journal of Biomedical Optics

Human gut microbiome

Review: Consequences of bile salt biotransformations by intestinal bacteria – Jason M. Ridlon – Gut Micobes

Review: The microbiota–gut–brain axis and its potential therapeutic role in autism spectrum disorder – Q. Li,- Neuroscience

Animal models

Safety Evaluation of Neo Transgenic Pigs by Studying Changes in Gut Microbiota Using High-Throughput Sequencing Technology – Qingqing Wang – PLOS ONE

Animal microbiome

Changes of diet and dominant intestinal microbes in farmland frogs – Chun-Wen Chang – BMC Microbiology

Plant, soil, and microbiome

Vitis vinifera microbiome: from basic research to technological development – Cátia Pinto – BioControl

Water and extremophile microbiology

Predicting taxonomic and functional structure of microbial communities in acid mine drainage – Jialiang Kuang – The ISME Journal

Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences – Martin W Hahn – The ISME Journal

Waste and pollution microbiology

Changes of microbial composition during wastewater reclamation and distribution systems revealed by high-throughput sequencing analyses – Yiwen Lin – Frontiers of Environmental Science & Engineering

Metabolomics

Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease – Qiang Feng – Scientific Reports

Bioinformatics and metagenomics

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences – Alexey M Kozlov – BioRxiv

Microbial Ecology

Challenges in microbial ecology: building predictive understanding of community function and dynamics – Widder, S – White Rose Research Online

Microbes in the news

A cloud of distinction – Could the trails of microbes we leave behind be used to solve crimes? Julian Smith picks up the scent – Julian Smith  – New Scientist

Stick Out Your Tongue: Citizen science project draws up the first oral microbiome map for the youth: Over 4,000 people have taken part in this hands-on scientific project in Barcelona- EurekAlert

Biologicals in quest for 2050: BioConsortia is evaluating microbes that could help protect seedlings emerging in cold and wet conditions. – AgriView

Gut Microbiome Analysis for Detecting Colon Cancer Mutations – Univesrity of Minnesota

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February 28, 2016

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Viral sequences in cancers, COPD, and EDGE, an easy online tool for metagenomics analysis.

Jobs

Researcher for a project on the effect of gut microbiome in human behavior – Radboud UMC Nijmegen, The Netherlands

General microbiome

Opinion: Manipulating Bacterial Communities by in situ Microbiome Engineering – Ravi U. Sheth – Trends in Genetics

Pregnancy and birth

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants – Natalia Zeber-Lubecka – PLOS ONE

Human respiratory microbiome

Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations – Zhang Wang – European Respiratory Journal

Human gut microbiome

Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer – Shegan Gao – BMC Infectious Agents and Cancer

Human colorectal mucosal microbiota correlates with its host niche physiology revealed by endomicroscopy – Ai-Hua Wang – Scientific Reports

Review: Gut Microbiota of Nonalcoholic Fatty Liver Disease – Reham M. Abdou – Digestive Diseases and Sciences

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: Beyond the gut bacterial microbiota: The gut virome – Paola Columpsi – Journal of Medical Virology

Human tissues and infection

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers – Jens Friis-Nielsen – MDPI Viruses

Models of microbiome research

Maternal Weaning Modulates Emotional Behavior and Regulates the Gut-Brain – Pamela Farshim – Scientific Reports

Rats: Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State – Hong Lin – Scientific Reports

Animal microbiome

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species – Aitor Albaina – Ecology and Evolution

Plant, root and soil microbiome

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming – Kai Xue – Nature Climate Change

Online Springer Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book chapter: Soil Effects of Genetically Modified Trees (GMTs) – Fernando Gallardo – Biosafety of Forest Transgenic Trees

Borderline Products between Bio-fertilizers/ Bio-effectors and Plant Protectants: The Role of Microbial Consortia – Marco Nuti – David Publishing Company

Differences in substrate use efficiency: impacts of microbial community composition, land use management, and substrate complexity – Tobias Bölscher – Biology and Fertility of Soils

Comparing how land use change impacts soil microbial catabolic respiration in Southwestern Amazon – Andre Mancebo Mazzetto – Brazilian Journal of Microbiology

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau – Haiyan Chu – Environmental Microbiology

Soil and tree species traits both shape soil microbial communities during early growth of Chinese subtropical forests – Zhiqin Pei – Soil Biology and Biochemistry

Water and extremophile microbiome

Functional interactions of archaea, bacteria, and viruses in a hypersaline endolithic community – Alexander Crits-Christoph – Environmental Microbiology

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water – Dimitri Kalenitchenko – The ISME Journal

Chapter One – Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes – M. Itävaara – Advances in Applied Microbiology

Waste and pollution microbiology

Bacterial ecology of abattoir wastewater treated by an anaerobic digestor – Linda Jabari – Brazilian Journal of Microbiology

High-Resolution Phylogenetic Analysis of Residual Bacterial Species of Fouled Membranes after NaOCl Cleaning – Ronald R. Navarro – Water Research

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis – Firouz Abbasian – Biotechnology Progress

Bioinformatics

Now peer reviewed: cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies – John H. Chase – mSystems

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation – Cecilia Noecker – mSystems

Assessing the performance of DNA barcoding using posterior predictive simulations – Anthony J. Barley – Molecular Ecology

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform – Po-E Li – BioRxiv

GenSeed-HMM: A tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data – João Marcelo P. Alves – Frontiers in Microbiology

Metabolomics

Human microbial metabolites as a source of new drugs – Somdutta Saha – Drug Discovery Today

More microbiology

Microbiota–mitochondria inter-talk: consequence for microbiota-host interaction – Yann Saint-Georges-Chaumet – Pathogens and Disease

Exploitation by cheaters facilitates the preservation of essential public goods in microbial communities – Clara Moreno-Fenoll – bioRxiv

Accurate and semi-automated analysis of bacterial association with mammalian cells – C.M. Murphy – Journal of Microbiological Methods

Microbes in the news

Fungal DNA, mycotoxins, cat allergens and fatigue in classrooms – Holly Ganz – MicroBEnet

Gum Disease Bacteria Linked to Esophageal Cancer Risk – Newsmax

Video: Virginia Tech scientists turn poo into power – Virginia Tech

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