Category Archives: Techniques

June 24, 2016

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Placenta samples not distinguishable from controls, gut microbiome in ME/CFS and PKU patients, childhood undernutrition, corals’ microbial sentinels, and plant root traps.

Pregnancy and birth

I was hoping for this study to be done: Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota – Abigail P. Lauder – Microbiome

Systematic review: Treatment of bacterial vaginosis in pregnancy in order to reduce the risk of spontaneous preterm delivery – a clinical recommendation – Thor Haahr – Acta Obstetricia et Gynecologica Scandinavica

Human ear microbiome

The microbiome of otitis media with effusion – Chun Ling Chan – The Laryngoscope

Human gut microbiome

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome – Ludovic Giloteaux – Microbiome

Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing – Felipe Pinheiro de Oliveira – PLOS ONE

Review: Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics – Laura V. Blanton – Science

Editorial: Gut microbiota and undernutrition – Caroline Ash – Science

Infection and microbiology

Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology – Lars F. Westblade – Journal of Clinical Microbiology

Novel Taxa Associated with Human Fungal Black-Grain Mycetomas: Emarellia grisea gen. nov., sp. nov., and Emarellia paragrisea sp. nov. – Andrew M. Borman – Journal of Clinical Microbiology

Sociomicrobiology and Pathogenic Bacteria – Joao B. Xavier – Microbiology Spectrum

Paleomicrobiology Data: Authentification and Interpretation – Michel Drancourt – Microbiology Spectrum

Animal experiments

Dietary fucoidan modulates the gut microbiota in mice by increasing the abundance of Lactobacillus and Ruminococcaceae – Qingsen Shang – Food & Function

Animal microbiome

Perspective: Corals’ microbial sentinels – Tracy D. Ainsworth – Science

Plant, root, and soil microbiome

Escaping Underground Nets: Extracellular DNases Degrade Plant Extracellular Traps and Contribute to Virulence of the Plant Pathogenic Bacterium Ralstonia solanacearum – Tuan Minh Tran – PLOS Pathogens

Press: An ‘arms race’ raging beneath our plants: A crop’s DNA-laden root trap manages to hold on to only a quarter of its bacterial prisoners. – Amy Middleton – Cosmos Magazine

Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China – Chengjie Ren – Scientific Reports

Spatial Shifts in Soil Microbial Activity and Degradation of Pasture Cover Caused by Prolonged Exposure to Cement Dust – Fuensanta Caravaca – Land Degradation & Development

Water and extremophile microbiome

Biogeochemical and 16S rRNA gene sequence evidence supports a novel mode of anaerobic methanotrophy in permanently ice-covered Lake Fryxell, Antarctica – Matthew A. Saxton – Limnology and Oceanography

Food microbiology

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis – Yongjie Zhang – PLOS ONE

More microbiology

Sugar Synthesis from CO2 in Escherichia coli – Niv Antonovsky – Cell

Press: Eating air, making fuel. Scientists engineer bacteria to create sugar from the greenhouse gas carbon dioxide – Science Daily

Not a scientific paper, just a list of links: Web Alert: Synthetic microbial communities: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Techniques

High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy – Yuichiro Nishimoto – Gut

Microbes in the news

New life form discovered in saliva is linked to human disease – Andy Coghlan – New Scientist

Seagulls Are Carrying a Dangerous Superbug Through the Skies – Maryn McKenna – National Geographic
Beware of Seagulls Carrying This Dangerous Superbug – Laura Lorenzetti – Fortune

Microbes In The Body Affect Success Of Organ Transplants: Study – Katrina Pascual -Tech Times

Scientists just found a compound that kills 98% of a drug-resistant bacteria – Fiona MacDonald – Science Alert

Milken Institute School of Public Health researchers awarded $7 million to study microbiome – Sera Royal – The GW Hatchet

Mycobacterium in olive oil for cancer treatment – EurekAlert

Scientists discover unsuspected bacterial link to bile duct cancer – MedicalXpress

Bik’s completely-not-microbiology Picks

The social dilemma of autonomous vehicles – Jean-François Bonnefon – Science

June 21, 2016

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An invertebrate gets its amino acids from microbial symbionts, microbiota and allograft rejection, high-altitude Andes lakes, and determining absolute microbiota abundances by spiking-in bacteria.

Jobs and events

Postdoctoral Researcher Microbial Ecology & Bioinformatics – NIOO-KNAW, WUR, Wageningen, The Netherlands

Report from the Microbiome R&D and Business Collaboration Forum, April 11–12, 2016, London, UK – Duc H. Le – EBioMedicine

General microbiome

Review: Diversity at low abundance: The phenomenon of the rare bacterial biosphere – M. Yu. Skopina – Microbiology

Workshop report: Culture-Independent Diagnostics for Health Security – Doggett Norman A.- Health Security

Viewpoint: Addressing Infectious Disease Challenges by Investigating Microbiomes – Emily P. Balskus – ACS Infectious Diseases

Human oral microbiome

Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing – Yumi Imabayashi – Scientific Reports

Human reproductive tract microbiome

Review: Chlamydia trachomatis Genital Tract Infections: When Host Immune Response and the Microbiome Collide – Noa Ziklo – Trends in Microbiology

Human gut microbiome

Review: Microbes, Immunity and Behaviour: Psychoneuroimmunology Meets the Microbiome – Timothy G Dinan – Neuropsychopharmacology

Review: Emerging roles for antigen presentation in establishing host–microbiome symbiosis – Nicholas J. Bessman – Immunological Reviews

Book Chapter: The Effect of H. pylori Infection on the Gastric Microbiota – Hyun Jin Jo – Helicobacter Pylori (Springer book)

Animal and in vitro experiments

The composition of the microbiota modulates allograft rejection – Yuk Man Lei – The Journal of Clinical Investigation

Press: Microbiota affect the rate of transplant acceptance and rejection – MedicalXpress

Maternal Metabolic Syndrome Programs Mitochondrial Dysfunction via Germline Changes across Three Generations – Jessica L. Saben – Cell Reports

Press, extrapolated conclusion: Obese Pregnant Women With Poor Diets May Worsen The Childhood Obesity Epidemic: Study – Samantha Olson – Medical Daily

Diet-dependent, microbiota-independent regulation of IL-10-producing lamina propria macrophages in the small intestine – Takanori Ochi – Scientific Reports

Characterization of Cimex lectularius (bedbug) defensin peptide and its antimicrobial activity against human skin microflora – Akanksha Kaushal – Biochemical and Biophysical Research Communications

Variability of arsenic bioaccessibility and metabolism in soils by human gut microbiota using different in vitro methods combined with SHIME – Naiyi Yin – Science of The Total Environment

Transient activation of mucosal effector immune responses by resident intestinal bacteria in normal hosts is regulated by interleukin-10 signalling – Cong Wu – Immunology

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community – Prabhakar D. Pandit – Bioresource Technology

Review: Strategies to modulate the intestinal microbiota of Tilapia (Oreochromis sp.) in aquaculture: a review – Alyssa M. Haygood – Reviews in Aquaculture

Animal microbiome

Seasonality and Locality Affect the Diversity of Anopheles gambiae and Anopheles coluzzii Midgut Microbiota from Ghana – Jewelna Akorli – PLOS ONE

A Nightmare for Males? A Maternally Transmitted Male-Killing Bacterium and Strong Female Bias in a Green Lacewing Population – Masayuki Hayashi – PLOS ONE
http://journals.plos.org/plosone/article?

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows
– Camilo Escallón – Functional Ecology

The dominant detritus-feeding invertebrate in arctic peat soils derives its essential amino acids from gut symbionts – Thomas Larsen – Journal of Animal Ecology

Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp – Yong Wang – Environmental Microbiology

Review: Is gastrointestinal microbiota relevant for endogenous mercury methylation in terrestrial animals? – R.C. Rodríguez Martín-Doimeadios – Environmental Research

Plant, root, and soil microbiome

Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient – Anders Lanzén – Scientific Reports

Integrated analysis of root microbiomes of soybean and wheat from agricultural fields – Nicolás Rascovan – Scientific Reports

Dark stains on rock surfaces in Driny Cave (Little Carpathian Mountains, Slovakia)
Rafał Ogórek – Extremophiles

Water and extremophile microbiome

Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes – Júlia Margit Aszalós – Extremophiles

Microbial interactions lead to rapid micro-scale successions on model marine particles –
Manoshi S. Datta – Nature Communications

Bacteriophages in Arctic and Antarctic low-temperature systems – S. N. Filippova – Microbiology

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka) – A. Y. Merkel – Microbiology

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey) – Seval Çınar – Extremophiles

Techniques

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria – 
Frank Stämmler – Microbiome

Metagenomics and bioinformatics

Data Labours: How the Sequence Databases GenBank and EMBL-Bank Make Data – Tahani Nadima – Science as Culture

Principle, analysis, application and challenges of next-generation sequencing: a review – Khalid Raza – arXIv

Microbes in the news

Does a pipette work in space? with NASA Astronaut Dr Kate Rubins – Microbe Talk – Microbe Post

An Antarctic sponge offers new hope against deadly MRSA infection – Matt Windsor – UAB

Dental Microbes Not All in the Family. Kids often acquire cavity-causing bacteria from non-family members, researchers report at the American Society for Microbiology annual meeting – Tanya Lewis – The Scientist

Never-Before Human-Detected, Potentially Pathogenic Bacterium Found in Children With Acute Leukemia Human Microbiology Institute investigates potential role of previously unknown bacteria – PR Newswire

Geisinger’s Donna Wolk recognized for work in microbiology – Daily Item

Microbial mass extinctions were kicked off by human evolution – Andy Coghlan – New Scientist

Global Microbiome Initiative Explores Subways for Drug-Resistance Markers:
MetaSUB Consortium will collect DNA and RNA samples from high-traffic areas in subway systems, buses, and parks in 54 cities worldwide – GenEngNews

June 20, 2016

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The temperate tree phyllosphere, Qaanaaq Glacier, effect of human activities on Hong Kong coast microbes, and genome assembly from read clouds.

Events

Microbiome R&D and Business Collaboration Forum: USA, October 3-4, San Diego

Pregnancy and birth

Putative periodontopathic bacteria and herpesviruses in pregnant women: a case-control study – Haixia Lu – Scientific Reports

Human gut microbiome

Letter to Editor: Reduction of antibiotic resistance genes in intestinal microbiota of recurrent Clostridium difficile patients after fecal microbiota transplantation – Hanne Jouhten – Clinical Infectious Diseases Advance Access

Review: The Gut Microbiota and Inflammatory Bowel Diseases – Jun Miyoshi – Translational Research

Review: Links Between the Microbiome and Bone – C.J. Hernandez – Journal of Bone and Mineral Research

Animal models

Interactions between the colonic transcriptome, metabolome and microbiome in mouse models of obesity-induced intestinal cancer – Anna C. Pfalzer – Physiological Genomics

Plant, root, and soil microbiome

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure – Isabelle Laforest-Lapointe – Microbiome

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations – Quan Li – Scientific Reports

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan – E. V. Pershina – Eurasian Soil Science

A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands – Austin B. Harbison – FEMS Microbiology Letters

Water and extremophile microbiome

Microbial community variation in cryoconite granules on Qaanaaq Glacier, NW Greenland – Jun Uetake – FEMS Microbiology Ecology

Mechanisms driving Antarctic microbial community responses to ocean acidification: a network modelling approach – Roshni C. Subramaniam – Polar Biology

Video article: Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR – Enrico Tatti – Journal of Visualized Experiments

Waste and pollution microbiology

Microorganisms in heavy metal bioremediation: strategies for applying microbial-community engineering to remediate soils – Jennifer L. Wood – AIMS Bioengineering

Impacts of Human Activities on Distribution of Sulfate Reducing Prokaryotes and Antibiotic Resistance Genes in Marine Coastal Sediments of Hong Kong – Feng Guo – FEMS Microbiology Ecology

Shotgun metagenomic profiles have a high capacity to discriminate activated sludge according to wastewater type – Federico M. Ibarbalz – Applied and Environmental Microbiology

Characteristics of Sediment Bacterial Community in Response to Environmental Impacts in a Sewage Polluted River – Jialin Li – Journal of Coastal Research

Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil – Jakub Ridl – Frontiers in Microbiology

Food microbiology

Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane – Francois J. Duvenage – Journal of the Science of Food and Agriculture

Book: Acetic Acid Bacteria: Ecology and Physiology – Springer

Metagenomics and bioinformatics

Genome assembly from synthetic long read clouds – Volodymyr Kuleshov – Bioinformatics

Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method – Yun Liu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Bioreactor microbiology

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

From ASM Microbe 2016: Bacteria Can Persist on Gloves, Transfer to Surfaces – Neil Osterweil – Medscape

Ischemic stroke therapy – does the gut microbiota hold the key? – Sara Adães – PLOS Neuro Community

French microbiologist hopes CRISPR/Cas9 can be used medically, with Emmanuelle Charpentier – Focus Taiwan

Chipotle Bosses Accused Of Insider Trading During Bacteria Scandals – Scott Heins – Gothamist

Bik’s Not-Microbiology Picks

Why Did Scientists Release Dead Sea Turtles into Chesapeake Bay? – Erica Tennenhouse – The Science Explorer

June 17, 2016

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Gastric bypass induces persistent gut microbiome changes, omnivorous lizards going vegetarian, new Borrelia species in Australian ticks, a free-living Bradyrhizobium, plant responses to phyllosphere commensals, and chemotrophic microbial populations in Yellowstone hot springs.

Events

HT: Jonathan Eisen: June 20-21 Meeting #2 for NAS Microbiomes of the Built Environment Study. Click here to register for the webcast (free!).

Human respiratory microbiome

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children – Marcos Pérez-Losada – Microbiome

Human gut microbiome

Antibiotic-induced gut microbiota disruption during human endotoxemia: a randomised controlled study – Jacqueline M Lankelma – Gut
Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota – Albert Palleja – Genome Medicine

Review: Metabolomics of autism spectrum disorders: early insights regarding mammalian-microbial cometabolites – Michele Mussap – Expert Review of Molecular Diagnostics

Review: How the microbiota shapes rheumatic diseases – Tom Van de Wiele – Nature Reviews Rheumatology

Animal and other experiments

Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard – Kevin D. Kohl – Journal of Experimental Biology

Press: How does a lizard go vegetarian? By growing its gut – Patrick Monahan – Science Magazine

Nasal commensal Staphylococcus epidermidis counteracts influenza virus – Hui-Wen Chen – Scientific Reports

Animal microbiome

Diversity, structure and convergent evolution of the global sponge microbiome – Torsten Thomas – Nature Communications

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism? – Jia Xu – BMC Veterinary Research

Novel Borrelia species detected in echidna ticks, Bothriocroton concolor, in Australia – Siew-May Loh – Parasites & Vectors

Press: New bacteria discovered in Australian ticks – MedicalXpress

Plant, root, and soil microbiome

Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison – Frances Patricia Jones – Scientific Reports

Press: Study unlocks surprising behaviour of soil bacteria – Mark Kinver – BBC

The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health – Christine Vogel – New Phytologist

DNA from dust: comparative genomics of vaccine-break virus in the field – Utsav Pandey – bioRxiv

Water and extremophile microbiome

Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs – Daniel R. Colman – FEMS Microbiology Ecology

Large shifts among eukaryotes, bacteria, and archaea define the vertical organization of a lake sediment – Christian Wurzbacher – bioRxiv

Microbes in the news

Featuring an All Male Panel: That Gut Feeling: Part One. Dan Saladino discovers the world of the gut microbiota, the vast array of microbes within us all – BBC Radio

Bik’s Picks

Klinefelter’s syndrome (47,XXY) is in excess among men with Sjögren’s syndrome –
Valerie M. Harris – Clinical Immunology

Press: Does X mark the spot? A new clue why autoimmune diseases target women – Oklahoma Medical Research Foundation

June 9, 2016

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Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan – Environmental Microbiology

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader –
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

June 1, 2016

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Cystic fibrosis, microbial detoxification in the Sage Grouse, salinity gradient in the Baltic Sea, and testing different 16S rRNA gene primer pairs.

Human respiratory microbiome

Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients – H. Al-momani – Scientific Reports

The Dynamics of Disease Progression in Cystic Fibrosis – Frederick R. Adler – PLOS ONE

Human gut microbiome

Alterations and correlations of the gut microbiome, metabolism, and immunity in patients with primary biliary cirrhosis – Long-Xian Lv – Environmental Microbiology

Review: Analysis and Interpretation of the Human Microbiome – Ashton, James J. – Inflammatory Bowel Diseases

Review: Gut microbiota and colorectal cancer – Mayuko Yamamoto – Genes and Environment

Animal experiments

The Impact of Lactobacillus casei on the Composition of the Cecal Microbiota and Innate Immune System Is Strain Specific – Busra Aktas – PLOS ONE

Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat – D. W. Pitta – Frontiers in Microbiology

Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens – Lingling Wang – Frontiers in Microbiology

Animal microbiome

Snapshot of a Bacterial Microbiome Shift during the Early Symptoms of a Massive Sponge Die-Off in the Western Mediterranean – Andrea Blanquer – Frontiers in Microbiology

Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse – Kevin D. Kohl – FEMS Microbiology Letters

Plant, root, and soil microbiome

Understory herb layer exerts strong controls on soil microbial communities in subtropical plantations – Kai Yin – Scientific Reports

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Diversity Enhances NPP, N Retention, and Soil Microbial Diversity in Experimental Urban Grassland Assemblages – Grant L. Thompson – PLOS ONE

Water and extremophile microbiome

Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea – Tue O. O. Hu – Frontiers in Microbiology

Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities – Ali Nawaz – Frontiers in Microbiology

Culture-independent characterization of novel psychrophilic magnetotactic cocci from Antarctic marine sediments – Fernanda Abreu – Environmental Microbiology

Food microbiology

Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine – Xutao Hong – Scientific Reports

Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar – Zong-Min Wang – Scientific Reports

Bioreactor microbiology

Mycoalgae biofilm: development of a novel platform technology using algae and fungal cultures – Aravindan Rajendran – Biotechnology for Biofuels

Techniques

Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies – Bram Beckers – Frontiers in Microbiology

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases – Victor Satler Pylro – Journal of Microbiological Methods

Microbes in the news

Unlocking the secrets of bacterial biofilms – to use against them – Karin Sauer – The Conversation

CDC to set up network of labs to fight tough bacteria – Dale Shoemaker – The Morning Call

Stick insects produce bacterial enzymes themselves. In the course of evolution, genes of gut microbes ‘jumped’ to their insect host – EurekAlert

Tobacco Smoke Makes Germs More Resilient – University of Louisville – NewsWise

Malaria, Zika and Dengue Could Meet Their Match in Mosquito-Borne Bacteria. A common bacteria that infects mosquitoes seems to prevent them from carrying more deadly diseases – Brian Handwerk – Smithsonian

Wild Culture: The Wild Side of Beer Brewing – Anna Brones – Paste Magazine

Unlocking the Mysteries of the Microbiome – J Craig Venter Institute

Science, publishing, and career

Nondisclosure of Financial Interest in Clinical Practice Guideline Development: An Intractable Problem? – Hilda Bastian – PLOS Medicine

Financial Relationships between Organizations That Produce Clinical Practice Guidelines and the Biomedical Industry: A Cross-Sectional Study – Paul Campsall – PLOS Medicine

Pseudoscience

Why Is Big Naturopathy Afraid Of This Lone Whistleblower? – Kavin Senapathy – Forbes

May 26, 2016

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Bioinformatics Symposium tomorrow at Stanford with free live stream, development of upper respiratory tract microbiome in infants, coral microbiome in Hawaii, calcified red algae microbiome, and metagenomics pathogen detection tool.

Events

Tomorrow, starts at 8am Pacific Time: Bioinformatics for the Microbiome, Stanford University. Will also be live streamed (and recording will be kept here for a while too) at Stanford Webcast. Due to family circumstances I won’t be able to be there, unfortunately 😦

Targeting the Microbiome – September 19-22, Boston, MA

Report from meeting earlier this week: Frontiers in Human Microbiota Symbiotic Interactions” 3rd Annual Meeting of the Bridging Biomedical Worlds Series

Jobs

Postdoc position in Pat Schloss group – Department of Microbiology & Immunology at the University of Michigan

General microbiome

Bioengineering microbial communities: Their potential to help, hinder and disgust – Diane Sivasubramaniama – Bioengineered

Pregnancy and birth

Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery – Astrid A.T.M. Bosch – EBioMedicine

Human respiratory microbiome

Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection – Inês N. Silva – mSystems

Study shows how bacteria evolve in lungs of cystic fibrosis patients – Science Daily

Upper airway microbial colonization in patients with neuromuscular disorders – Florian Stehling – Respirology

Human gut microbiome

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study – Toshitaka Odamaki – BMC Microbiology

Metagenomic characterization of microbial communities in situ within the deeper layers of the ileum in Crohn’s Disease – Chandra Sekhar Pedamallu – CMGH Cellular and Molecular Gastroenterology and Hepatology

Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium – Elizabeth R. Volkmann – Arthritis & Rheumatology

Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice – Joseph D. Planer – Nature

Animal experiments

Impact of a High-Fat or High-Fiber Diet on Intestinal Microbiota and Metabolic Markers in a Pig Model – Sonja N. Heinritz – MDPI Nutrients

Immunological Consequences of Intestinal Fungal Dysbiosis – Matthew L. Wheeler – Cell Host & MIcrobe

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease – Hiutung Chu – Science

Editorial: Microbiome: Does the brain listen to the gut? – Thomas Kuntz – eLIFE

Animal microbiome

Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago – Jennifer L. Salerno – FEMS Microbiology Ecology

Codivergence of the primary bacterial endosymbiont of psyllids versus host switches and replacement of their secondary bacterial endosymbionts – Aidan A. G. Hall – Environmental Microbiology

An exploration of the fungal assemblage in each life history stage of the butterfly, Lycaeides melissa (Lycaenidae), as well as its host plant Astragalus canadensis (Fabaceae) – Joshua G. Harrison – Fungal Ecology

Comparison of the fecal microbiota in horses with Equine Metabolic Syndrome (EMS) and metabolically normal controls fed a similar all forage diet – S. Elzinga – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga – Juliet Brodie – FEMS Microbiology Ecology

Relative importance of soil properties and microbial community for soil functionality: insights from a microbial swap experiment – Manuel Delgado-Baquerizo – Functional Ecology

Effect of agricultural practices and coastal constraints on soil microbial functional properties in Mediterranean olive orchards – N. Boukhdoud – European Journal of Soil Science

Functional breadth and home-field advantage generate functional differences among soil microbial decomposers – Nicholas Fanin – Ecology

Book Chapter: Bacteria and Non-lichenized Fungi Within Biological Soil Crusts – Stefanie Maier – Biological Soil Crusts: An Organizing Principle in Drylands

Metagenomics, bioinformatics, and techniques

HoloVir: A workflow for investigating the diversity and function of viruses in invertebrate holobionts – Patrick W. Laffy – Frontiers in Microbiology

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling – Steven Flygare – Genome Biology

Metagenomics pathogen detection tool could change how infectious diseases are diagnosed – EurekAlert

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing – Matthew Thoendel – Journal of Microbiological Methods

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies – Victor S. Pylro – Microbial Ecology

Functional foods

Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms – Christos Stefanis – Current Research in Nutrition and Food Science

Microbes in the news

Polio-free world? Not if scientists refuse to destroy their research specimens – Helen Branswell – STAT news

The secret history of ancient toilets. By scouring the remains of early loos and sewers, archaeologists are finding clues to what life was like in the Roman world and in other civilizations – Chelsea Wald – Nature

Using Gut Bacteria To Save The Planet – John Farrell – Forbes

The Emergent Microbiome: A Revolution for the Life Sciences – Part VI, Diagnostics – Jessica L. Miles and Anthony D. Sabatelli – Lexology

May 25, 2016

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The sinonasal microbiome in chronic rhinosinusitis, walnut consumption in a mouse model, and treatment of cows with antibiotics has effects on dung beetle microbiomes.

Jobs and Grants

Assistant professor of food science, microbial ecology – Penn State

American Gastroenterological Association Invites Applications for Gut Microbiome Award – Philanthropy news digest

Three Post-Doctoral Fellowships for Tropical Microbial Ecologists in Panama – Smithsonian Tropical Research Institute

Events

1st International Conference on the Marine Microbiome – Discovery & Innovation for science and industry, 27 June 2016 — 30 June 2016, Berlin, Germany

Pregnancy and birth

Connections between the gut microbiome and metabolic hormones in early pregnancy in overweight and obese women – Luisa F Gomez-Arango – Diabetes

Human oral microbiome

Minireview: A practical guide to the oral microbiome and its relation to health and disease – K Krishnan – Oral Diseases

Human respiratory microbiome

Review: A systematic review of the sinonasal microbiome in chronic rhinosinusitis – Martin Anderson – American Journal of Rhinology & Allergy

Human gut microbiome

Letter: Faecal microbiota profiles as diagnostic biomarkers in primary sclerosing cholangitis – Malte Christoph Rühlemann – Gut

Review: Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children – Evalotte Decker – Gut Microbes

Human vaginal microbiome

Progresses in vaginal microflora physiology and implications for bacterial vaginosis and candidiasis – Gary Ventolini – Women’s Health

Animal experiments

Pulmonary Th17 Antifungal Immunity Is Regulated by the Gut Microbiome – Jeremy P. McAleer – The Journal of Immunology

Microbial modulation of behavior and stress responses in zebrafish larvae – Daniel J. Davis – Behavioural Brain Research

Effects of walnut consumption on colon carcinogenesis and microbial community structure – Masako Nakanishi – Cancer Prevention Research

Animal microbiome

Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata – Sonny T. M. Lee – Frontiers in Microbiology

Free-Living Species of Carnivorous Mammals in Poland: Red Fox, Beech Marten, and Raccoon as a Potential Reservoir of Salmonella, Yersinia, Listeria spp. and Coagulase-Positive Staphylococcus – Aneta Nowakiewicz – PLOS ONE

Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles – Tobin J. Hammer – Proceedings of the Royal Society B

Immune response and gut microbial community structure in bumblebees after microbiota transplants – Kathrin Näpflin – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing – Linkun Wu – Scientific Reports

Effects of heavy metals and chelants on phytoremediation capacity and on rhizobacterial communities of maize – Giovanni Vigliotta – Journal of Environmental Management

Comparative assessment of fungal augmentation treatments of a fine-textured and historically oil-contaminated soil – Stefano Covino – Science of the Total Environment

Water microbiome

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Variations in Bacterial Community in a Temperate Lake Associated with an Agricultural Watershed – Liyan Song – Microbial Ecology

Built environment microbiome

Review: The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review – Marcus H. Y. Leung – Microbiome

Review: Use of Homogeneously-Sized Carbon Steel Ball Bearings to Study Microbially-Influenced Corrosion in Oil Field Samples – Gerrit Voordouw – Frontiers in Microbiology

Food microbiology

Indigenous Georgian Wine-Associated Yeasts and Grape Cultivars to Edit the Wine Quality in a Precision Oenology Perspective – Ileana Vigentini – Frontiers in Microbiology

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages – Jyoti P. Tamang – Frontiers in Microbiology

Bioinformatics

mockrobiota: a public resource for microbiome bioinformatics benchmarking – Nicholas A Bokulich – PeerJ Preprints

SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals – Yevgeny Nikolaichik

Techniques

Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics – Linn Sgie – Nature Communications

Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly – Christopher Huptas – BMC Research Notes

Microbes in the news

Inner Workings: Ancient teeth reveal clues about microbiome evolution – Jyoti Madhusoodanan – PNAS

Study shows cows on antibiotics produce dung with higher levels of greenhouse gases – DW

May 12, 2016

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Dandruff, archaeological dental calculus methanogens, extreme longevity, UK twins, and dissemination of human-derived bacteria into the Antarctic microbiome.

Pregnancy and birth microbiome

Early-life gut microbiome composition and milk allergy resolution – Supinda Bunyavanich – Journal of Allergy and Clinical Immunology

Human skin microbiome

Dandruff is associated with the conjoined interactions between host and microorganisms – Zhijue Xu – Scientific Reports

Human oral microbiome

Restricted diversity of dental calculus methanogens over five centuries, France – Hong T. T. Huynh – Scientific Reports

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer – Kaitlin J. Flynn – mSphere

Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study – Vanessa Sousa – Clinical Oral Implants Research

Human respiratory microbiome

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study – Moana Mika – The Lancet Respiratory Medicine

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR – Joshua R. Stokell – Antonie van Leeuwenhoek

Human gut microbiome

Gut Microbiota and Extreme Longevity – Elena Biagi – Current Biology

Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study – C Walton – European Journal of Clinical Nutrition

Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study – Christian Milani – Scientific Reports

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing – Emily Vogtmann – PLOS ONE

Review: Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection – Caná L. Ross – Anaerobe

Preview: What’s LPS Got to Do with It? A Role for Gut LPS Variants in Driving Autoimmune and Allergic Disease – Taylor Feehley – Cell Host & Microbe

Review: Koch’s postulates, microbial dysbiosis and inflammatory bowel disease – Benjamin P. Willing – Clinical Microbiology and Infection

Review: Impact of gut microbiota on diabetes mellitus – G. Blandino – Diabetes & Metabolism

Review: Microbiota and the nitrogen cycle: Implications in the development and progression of CVD and CKD – David Briskey – Nitric Oxide

Review: Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract – Jenessa A. Winston – Anaerobe

Review: The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases – Rodney R. Dietert – Reproductive Toxicology

Animal experiments

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica) – Eduardo Crisol-Martínez – PeerJ

Structural modulation of gut microbiota by chondroitin sulfate and its oligosaccharide – Qingsen Shang – Macromolecules

Administration of probiotic kefir to mice with Clostridium difficile infection exacerbates disease – Jennifer K. Spinler – Anaerobe

Editorial: Immunology: You Remind Me of a Microbe I Know – Ray Soto and June Round – Current Biology

Forum: Human Microbiota-Associated Mice: A Model with Challenges – Marie-Claire Arrieta – Cell Host & Microbe

Plant, root, and soil microbiome

Geography and agronomical practices drive diversification of the epiphytic mycoflora associated with barley and its malt end product in western Canada – Wen Chen – Agriculture, Ecosystems & Environment
http://www.sciencedirect.com/science/article/pii/S0167880916301669

Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere –
Alec Cobban – MicrobiologyOpen
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.374/abstract

 

Water and extremophile microbiome

Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome – Michelle L. Power – Environmental Pollution

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands – Felix Oloo – Scientific Reports

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants – Ghada A. Mustafa – Environmental Pollution

Conference Highlight: Decoding Microbial “Relationship Statuses” at OSM 2016 – Kelsey Ellis – Bulletin Limnology and Oceanography

Phages and viruses

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology – Angela L. Rasmussen – Cell Host & Microbe

Techniques

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface – Pranjul Shah – Nature Communications

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants – Cian J. Hill – Microbiome

Video: Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – JOVE

Microbial Ecology

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments – Scott W. Olesen – PLOS ONE

More microbiology

Self-driven jamming in growing microbial populations – Morgan Delarue – bioRxiv

Review: Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics – Elizabeth Klemm – Cell Host & Microbe

Microbes in the news

Osel, Inc.’s Lead Product LACTIN-V Enters Phase 2b Study to Prevent Recurrence of Bacterial Vaginosis– Digital Journal

Bacteria Battle Can Lead to Dandruff – Jennifer Viegas – Discovery
Bacteria the yin and yang of dandruff, says study – MedicalXpress

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development
– PR Newswire

Experts react to ‘waste of money’ headlines against probiotics – Adi Menayang – NutraIngredients

How scientists are harnessing the ice-making powers of bacteria – Zach St. George – The Week

Researchers Engineer Bacteria to Streamline Biofuel Production Process – IndiaWest

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development – PR Newswire

Twin study finds that gut microbiomes run in families – EurekAlert

From the American Urological Association meeting: Gut Bugs Differ in Chronic Prostatitis. Difference in taxa may aid biomarker, researchers say – MedPageToday

In Infants With Necrotizing Enterocolitis, Gut Dysbiosis Precedes Disease – Julie A. Jacob – JAMA

Science, publishing, and career

Reminder to deposit DNA sequences – Mark Blaxter – Science

Unexpected revelations for study volunteer: What health information do researchers owe the volunteers in their studies – Jennifer Couzin-Frankel – Science

Bik’s Picks

WATCH: What happened to astronaut Scott Kelly’s DNA during his year in space – Carl Zimmer – STAT News

May 7, 2016

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Drosophila male-killing spiroplasma, chitin in potting soil, temperature constraints for complex life, a book on microbial diversity, and monitoring sewer health.

General microbiome

Review: Design, analysis and application of synthetic microbial consortia – Xiaoqiang Jia – Synthetic and Systems Biotechnology

Review: Metabolic network modeling of microbial interactions in natural and engineered environmental systems – Octavio Perez-Garcia – Frontiers in Microbiology

Opinion: Mirror, mirror on the wall: which microbiomes will help heal them all? – Renuka R. Nayak – BMC Medicine

Hypothesis: Do microbiotas warm their hosts? – Eugene Rosenberg – Gut Microbes

Human respiratory microbiome

Microbiome diversity in the sputum of patients with pulmonary tuberculosis – P. Krishna – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Literature review: The gut microbiota: a major player in the toxicity of environmental pollutants? – Sandrine P Claus – NPJ Biofilms and Microbiomes

Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study – Zoltan Pataky – Digestive Diseases and Sciences

n=1: Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report – Bumjo Oh – Clinical Nutrition Research

Conference abstract: Associations Between Physical Activity and the Intestinal Microbiome of College Freshmen – Corrie M Whisner – The FASEB Journal

Animal experiments

Male-Killing Spiroplasma Alters Behavior of the Dosage Compensation Complex during Drosophila melanogaster Embryogenesis – Becky Cheng – Current Biology

Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities – Kevin D. Kohl – Frontiers in Microbiology

Conference abstract: Soy positively impacts cecal microbiota of ovariectomized rats selectively bred for low aerobic capacity – Tzu-Wen Liu – the FASEB Journal

Animal microbiome

Midgut Transcriptome of the Cockroach Periplaneta americana and Its Microbiota: Digestion, Detoxification and Oxidative Stress Response – Jianhua Zhang – PLOS ONE

Plants, roots, and soil microbiome

Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology – Jane Debode – Frontiers in Microbiology

Litter microbial and soil faunal communities stimulated in the wake of a volcanic eruption in a semiarid woodland in Patagonia, Argentina – Paula Berenstecher – Functional Ecology

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China – Jianli Ding – Applied Soil Ecology

Conference abstract: Multi-omics of the Soil Microbiome – Janet K Jansson – The FASEB Journal

Review: Life cycle specialization of filamentous pathogens — colonization and reproduction in plant tissues – Janine Haueisen – Current Opinion in Microbiology

Review: Interspecific hybridization impacts host range and pathogenicity of filamentous microbes – Jasper RL Depotter – Current Opinion in Microbiology

Water and extremophile microbiome

From climate models to planetary habitability: temperature constraints for complex life – Laura Silva – arXiv preprint

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems – Roberto Danovaro – Science Advances

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer – Robert Danczak – Frontiers in Earth Science

External controls on the distribution, fabrics and mineralization of modern microbial mats in a coastal hypersaline lagoon, Cayo Coco (Cuba) – Anthony Bouton

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling – Kenneth Wasmund – mBio

Book: Their World: A Diversity of Microbial Environments – Editors: Christon J. Hurst – Springer

Review: Marine microorganisms as a promising and sustainable source of bioactive molecules – G. Romano – Marine Environmental Research

Waste and pollution microbiology

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed – Elliott P. Barnharta – International Journal of Coal Geology

Review: Does bioleaching represent a biotechnological strategy for remediation of contaminated sediments? – Viviana Fonti – Science of The Total Environment

Review: Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure – Sevcan Aydin – Applied Microbiology and Biotechnology

Viruses and phages

Editorial overview: The megaviromes – Didier Raoult – Current Opinion in Microbiology

More microbiology

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development – Ryan H. Hansen – PLOS ONE

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria – Kelly C Wrighton – The ISME Journal

Research Highlight: A time to gather chromosomes together – Naomi Attar – Nature Reviews Microbiology

Conference abstract: Metabolic Exchange In Microbial Communities – Andrei Osterman – The FASEB Journal

Microbes in the news

Pipe Dreams: Tapping into the Health Information in Our Sewers – Carrie Arnold – Environmental Health Perspectives

Deep sea microbes may be key to oceans’ climate change feedback – Howard Lee – The Guardian

Exploiting Male Killing Bacteria Could Control Insect Pest Species in the Future – SciCasts

Fifty people warned about possible exposure to drug-resistant bacteria at University of Alberta Hospital – Keith Gerein