Our post today has been remodeled after some small technical problems, but here’s your fresh Friday digest of microbiome papers!

Events and jobs

Full-time visiting faculty position in biochemistry and microbiology (2017-18)
College of the Holy Cross – Worcester, Massachussets

Microbiology Laboratory Technician
Symbio Laboratories – Brisbane, Australia

Team Manager – Microbiology
AstraZeneca – Cambridge, UK

27th European Congress of Clinical Microbiology & Infectious Diseases
Vienna – Austria

General microbiome

Cryptic biogeochemical cycles: unravelling hidden redox reactions
Andreas Kappler – Environmental Microbiology

Multi-site human microbiome

Microbe-microbe and host-microbe interactions drive microbiome dysbiosis and inflammatory processes
AD Proal – Discovery Medicine

The human microbiome: an emerging tool in forensics
Jarrad T. Hampton-Marcell – Microbial Biotechnology

The salivary microbiome is altered in the presence of a high salivary glucose concentration
J. Max Goodson – Plos One

Human vaginal microbiome

Review: The role of Escherichia coli in reproductive health: state of the art.
P. Cools – Research in Microbiology

Survival of vaginal microorganisms in three commercially available transport systems.
Allison L DeMarco – Anaerobe

Human gut microbiome

Small Intestinal Bacterial Overgrowth Is Associated with Non-Alcoholic Fatty Liver Disease.
A. Fialho – Journal of Gastrointestinal and Liver Disease

Review: Roles of the intestinal microbiota in pathogen protection.
C. Ubeda – Clinical Translational Immunology

Atopic dermatitis and gut microbiota
M. Lindberg – British Journal of Dermatology

Editorial: The gut microbiota and psychiatric illness
Glenda MacQueen – Journal of Psychiatry and Neuroscience

Commentary: For Health Disparities, Don’t Ignore the Microbiome
Jennifer Abbasi – JAMA

Faecal microbiota transplantation protects against radiation-induced toxicity.
M Cui – EMBO Molecular Medicine

Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites and Metabolic Pathways
Bei Gao – Chemical Research in Toxicology

Animal experiments

Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice.
Giada de Palma – Science Translational Medicine

Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice
Aurelijus Burokas – Biological Psychiatry

Animal microbiome

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Mathieu Groussin – Nature Communications

Transition of the intestinal microbiota of dogs with age.
H. Masuoka – Biosciences Microbiota Food Health

Comparative analysis of gut microbiota of mosquito communities in central Illinois.
EJ Muturi – PLoS Neglected Tropical Diseases

Transformation, Proliferation, and Influence on Host Performance by Three Gut Bacteria in the Rice Water Weevil (Coleoptera: Curculionidae)
Yunshan Huang – Annals of the Entomological Society of America

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island
Jan M. Meyer – Environmental Microbiology

MALDI-TOF MS identification of microbiota associated with pest insect Diabrotica speciosa
Bruno Perlatti – Agricultural and Forest Entomology

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria
Alyce Taylor-Brown – Environmental Microbiology

Plant, root, and soil microbiome

Syntrophobacteraceae-affiliated species are major propionate-degrading sulfate reducers in paddy soil
Pengfei Liu – Environmental Microbiology

Next-Generation Sequencing Analyses of Bacterial Community Structures in Soybean Pastes Produced in Northeast China
Mi-Hwa Lee – Journal of Food Science

Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars
AK Mahoney – Frontiers in Plant Science

Water and extremophile microbiome

Metagenomic analysis reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea
Vadim Dubinsky – Environmental Microbiology

Bacterial activity in hydrogenetic ferromanganese crust from the Indian Ocean: a combined geochemical, experimental and pyrosequencing study
PP Sujith – Environmental Earth Sciences

Stoichiometry of Prochlorococcus, Synechococcus, and small eukaryotic populations in the western North Atlantic Ocean
Steven E. Baer – Environmental Microbiology

Built environment

Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation.
N. de Jonge – Bioresource Technology

Spread from the Sink to the Patient: in situ Study Using Green Fluorescent Protein (GFP) Expressing- Escherichia coli to Model Bacterial Dispersion from Hand Washing Sink Trap Reservoirs
Shireen Kotay – Applied and Environmental Microbiology

Phages and viruses

Pre-print: How to name and classify your phage: an informal guide
Evelien M. Adriaenssens – bioRxiv

Review: Tumor-associated macrophages: implications in cancer immunotherapy
Amy J Petty – Immunotherapy

Predation by Bdellovibrio bacteriovorus significantly reduces viability and alters the microbial community composition of activated sludge flocs and granules
Shugeng Feng – FEMS Microbiology Ecology

Techniques

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis
Sylwia Zielinska – MicrobiologyOpen

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
Jason L. Weirather – F1000 Open Research

A High-Throughput Screening Platform of Microbial Natural Products for the Discovery of Molecules with Antibiofilm Properties against Salmonella
Sonia Paytubi – Frontiers in Microbiology

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
Mohamed Mysara – GigaDB

Misc

Highlights: Evolving as a holobiont
Lauren A. Richardson – Plos Biology

Microbes in the news

Gut microbes and poor artery health – researchers probe possible link
Jim Scott – CU Boulder Today

Events and jobs
Postdoctoral Teaching and Learning Fellow in Microbiome Data Analysis – Department of Microbiology and Immunology (MICB) – University of British Columbia

Commercial Support Manager, Probiotics for Human Health & Microbiome – Hørsholm, Denmark – Chr. Hansen

Position in experimental biochemistry including microbiology – University of Warsaw

Microbiology Laboratory Technician – Milwaukee, WI – Aerotek

Human vaginal microbiome
Specific vaginal lactobacilli suppress the inflammation induced by lipopolysaccharide stimulation through downregulation of toll-like receptor 4 expression in human embryonic intestinal epithelial cells – Keisuke Tobita – Bioscience of Microbiota, Food and Health

Human gut microbiome
Editorial: The gut microbiota and psychiatric illness – Glenda MacQueen – Journal of Psychiatry and Neurosciece

Animal experiments
Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens – Eduardo Crisol-Martínez – Applied Microbiology and Biotechnology

Transition of the intestinal microbiota of dogs with age – Hiroaki Masuoka – Bioscience of Microbiota, Food and Health

Faecal microbiota transplantation protects against radiation-induced toxicity – Ming Cui – EMBO Molecular Medicine

Animal microbiome
Comparative analysis of gut microbiota of mosquito communities in central Illinois – Ephantus J. Muturi – PLoS Neglected Tropical Diseases

Plant, root, and soil microbiome
Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars – Aaron K Mahoney – Frontiers in Plant Science

Water and extremophile microbiome
Microbial community assembly and evolution in subseafloor sediment – Piotr Starnawski – PNAS

Phylogenetic Diversity and Anti-MRSA Activity of Halotolerant Actinobacteria from sediments in Great Salt Plains, Oklahoma – Ahmed H Gad – bioRxiv

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective – Danielle VanMensel – Microbial Ecology

Food microbiology
Boswellia serrata resin extract alleviates azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colon tumorigenesis – YC Chou – Molecular Nutrition Food Research

A series of review articles on the FODMAP diet has been published in the most recent issue of the Journal of Gastroenterology and Hepatology
Review: Use of the low-FODMAP diet in inflammatory bowel disease – Peter R Gibson – Journal of Gastroenterology and Hepatology
Review: How to institute the low-FODMAP diet – Jacqueline S Barrett – Journal of Gastroenterology and Hepatology
Review: When the low FODMAP diet does not work – Emma P Halmos – Journal of Gastroenterology and Hepatology
Review: Nutritional, microbiological and psychosocial implications of the low FODMAP diet – Heidi Maria Staudacher – Journal of Gastroenterology and Hepatology

The spxB gene as a target to identify Lactobacillus casei group species in cheese – Maria Luisa Savo Sardaro – Food Microbiology

Bioinformatics
GMPR: A novel normalization method for microbiome sequencing data – Jun Chen – bioRxiv

Cohesion: A method for quantifying the connectivity of microbial communities – Cristina Herren – bioRxiv

Techniques
Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation – Nadieh de Jonge – Bioresource Technology

Microbes in the news
How Bacteria Interfere with Insect Reproduction – Ruth Williams – The Scientist
This references two important papers on Wolbachia:
A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility – John F Beckmann – Nature Microbiology
Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility – Daniel P LePage – Nature

Synopsis: Racing Bacteria – Katherine Wright – APS Physics

Meet green bacteria, airport’s eco-friendly toilet cleaners – Times of India

Assessing Host-Microbiota Relationships – Richard A Stein – Genetic Engineering and Biotechnology News

Bacteria from the ancient city of Troy – Caitlin Pepperell – Microbe Post

Gut bacteria determines the beneficial impacts of soy food on heart health – David Templeton – Pittsburgh Post-Gazette

Microbes on the market
Vaginal Microbiota May Affect Tenofovir Applied Intravaginally – John Schieszer – Infectious Disease Advisor

The Human Microbiome: Advancing New Frontiers in a Rapidly Emerging Market – PR Newswire – Yahoo Finance

New research data published in Frontiers in Microbiology confirm the microbiome’s potential to impact plant health – PR Newswire – Yahoo Finance

Microbiome Therapeutics Market Growth, Forecast and Value Chain 2017-2027 – Future Market Insights – OpenPR

Random Science
Editorial: Microbiome yarns: microbiomology of curly and straight hair – Kenneth Timmis – Microbial Biotechnology

Events and jobs

Postdoctoral Fellow/Microbiology – University of Tennessee Health Science Center – Memphis, TN

QC Microbiology Analyst – Leidos – FREDERICK, MD US

General microbiome

Preprint: Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R. Theis – bioRxiv

Preprint: Genome-wide phenotypic analysis of growth, cell morphogenesis and cell cycle events in Escherichia coli – Manuel Campos – bioRxiv

Preprint: Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli – Nicole Stoesser – bioRxiv

Preprint: How to name and classify your phage: an informal guide – Evelien M Adriaenssens – bioRxiv

Pregnancy and early life

Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific reports

Multi-site human microbiome

A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology – S. E. Adams – Scientific reports

Human skin microbiome

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis – Teruaki Nakatsuji – Science translational medicine

Human vaginal microbiome

Bacterial species colonizing the vagina of healthy women are not associated with race – May A. Beamer – Anaerobes in the microbiome

Human gut microbiome

Combined Signature of the Fecal Microbiome and Metabolome in Patients with Gout – Tiejuan Shao – Frontiers in microbiology

Review: Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies – Sudarshan A. Shetty – FEMS-Microbiology reviews

The microbiome and systemic lupus erythematosus – Nurit Katz-Agranov – Immunologic Research

Animal microbiome

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Plant, root, and soil microbiome

Plant Growth Promoting Bacteria Associated with Langsdorffia hypogaea-Rhizosphere-Host Biological Interface: A Neglected Model of Bacterial Prospection – Érica B. Felestrino – Frontiers in microbiology

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees – Bram Beckers – Microbiome

Plant cultivars imprint the rhizosphere bacterial community composition and association networks – Yuji Jiang – Soil Biology and Biochemistry

Retention and survival of E. coli in stormwater biofilters: Role of vegetation, rhizosphere microorganisms and antimicrobial filter media – G.I. Chandrasena – Ecological Engineering

Nitrogen addition shifts the microbial community in the rhizosphere of Pinus tabuliformis in Northwestern China – Fenglian Lv – PLoS ONE

Investigation of the fungal community structures of imported wheat using high-throughput sequencing technology – Shi Y – PLoS ONE

Players over the Surface: Unraveling the Role of Exopolysaccharides in Zinc Biosorption by Fluorescent Pseudomonas Strain Psd – Anamika Upadhyay – Frontiers in Microbiology
Potential microbial contamination during sampling of permafrost soil assessed by tracers – Toke Bang-Andreasen – Scientific reports

Water and extremophile microbiome

Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – ISME

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water – Ivone Vaz-Moreira – Science of The Total Environment

Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation – Efstratios Nikolaivits – Frontiers in microbiology

Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach – Luz A. Betancur – PLoS ONE

Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific – Shota Nitahara – PLoS ONE

A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7 – Rafael A. Baraúna – Proteomes

Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience – Raquel Peixoto – Frontiers in microbiology

Science, publishing, and career

Preprint: Preprinting Microbiology – Patrick D. Schloss – bioRxiv

Events and jobs
Microbiology Analyst Level II – DTS Food Laboratories – Brisbane, AU

Microbial Menagerie is profiling #ActualLivingScientists, especially microbiologists! Visit here for more information, or sign up here!

4th International Symposium on the Environmental Dimension of Antibiotic Resistance – Aug 13-17, 2017 in Lansing, MI

5th Molecular Microbiology Meeting & 4th Midlands Molecular Microbiology Meeting (M4) – Sept 13-14, 2017 in Birmingham, UK

General microbiome
Metagenomic DNA sequencing for the diagnosis of intraocular infections – Thuy Doan – bioRxiv

Human skin microbiome
Bacterial biofilm in chronic lesions of hidradenitis suppurativa – H.C. Ring – British Journal of Dermatology

Human gut microbiome
Review: Bile acid control of metabolism and inflammation in obesity, type 2 diabetes, dyslipidemia and NAFLD – Oscar Chavez-Talavera – Gastroenterology

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Isolation and high-dimensional phenotyping of gastrointestinal immune cells – Bruna A. David – Imumunology
Not focused on microbes – but may be of use to those working with these cells!

Water and extremophile microbiome
Oxygenic and anoxygenic photosynthesis in a microbial mat from an anoxic and sulfidic spring – Dirk de Beer – Environmental Microbiology

A six thousand-year record of climate and land-use change from Mediterranean seagrass mats – Lourdes Lopez-Merino – Journal of Ecology
There is a hidden section on fungi.

High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Lineage – Joshua J Hamilton – bioRxiv

Are oceanic fronts ecotones? Seasonal changes along the Subtropical Front show fronts as bacterioplankton transition zones but not diversity hotspots – Sergio E Morales – bioRxiv

Built environment
Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – MicrobiologyOpen

Comparative analysis of metagenomes of Italian top soil improvers – F. Gigiliucci – Environmental Research
This does not seem available yet, so PubMed is linked rather than the paper.

Food microbiology
Diversity analysis and quantification of lactic acid bacteria in traditionally fermented yaks’ milk products from Tibet – Yan Ren – Food Biotechnology

Phages and viruses
Review: Risk of waterborne virus spread – review of survival of relevant fish and crustacean viruses in the aquatic environment and implications for control measures – Birgit Oidtmann – Reviews in Aquaculture

Microbial interactions
Local interactions lead to spatially correlated gene expression levels in bacterial groups – Simon van Vliet – bioRxiv

Science, publishing, and career
Broad Institute prevails in heated dispute over CRISPR patents – Sharon Begley – STAT News, along with six takeaways.

Wageningen University, in my home country of the Netherlands, will be holding a 2.5-day symposium in October 2017 to celebrate 100 years of microbiology research at this institute, called Microbiology Centennial. At first glance, the program looked great; many talks about microbial ecology, microbial physiology and bacterial genetics.

But alas, the list of keynote speakers is very low-diversity. All 10 keynote speakers are men.

1. Jan Roelof van der Meer
2. Mark van Loosdrecht
3. Hauke Harms
4. Bernhard Schink
5. Thijs J. G. Ettema
6. Mike Jetten
7. Hauke Smidt
8. Alfons J.M. Stams
9. John van der Oost
10. Willem M. de Vos

In addition, there are opening remarks by Alex Zehnder.

That is 11 men. No women.

The program states:

“The keynote lectures include eminent scientists (see below) who have been interacting with the Laboratory of Microbiology throughout the years. The program also features the present research group leaders of the Laboratory of Microbiology as well as the present and past chair who all have contributed to the success of the last decades. “

I guess no women have contributed to the success of the Laboratory of Microbiology in the last decades. Thanks ladies for all your hard work. Now move over, please, so that the guys can present your fantastic research!

Sadly, this lack of women in academic positions or keynote lecturers is not unique for my home country. The Netherlands, a country that likes to think its very modern, is lacking in the participation of women in science. Less than 20% of professors at Dutch Universities are women. According to this article at Times Higher Education:

“Wageningen University, one of the country’s top-ranked universities in 2016-17, has significantly improved its gender diversity in recent years, although just 12 per cent of its professors were women in 2016, the report says.”

A recent report entitled “Monitor Women Professors 2016” published by the Dutch Network of Women Professors, stated that women account for 43% of PhD students and 39% of University Lecturers, but only 18% of professors. The report states:

“not only do female academics earn less, they are also systematically awarded lower job levels”….“There is a ruthlessly thick glass ceiling between job levels,” it adds, saying the barrier stopping women progressing from a grade 1 professor to a grade 2 professor is “sky-high”.

A light digest for today’s Sunday morning. A variety of human microbiome papers and a review on the evolution of antimicrobial resistance.

Human respiratory microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. Poala J Marino. Journal of Critical Care.

Human nearly-sterile sites

Short communication: Epicardial Adipose Tissue Microbial Colonization and Inflammasome Activation in Acute Coronary Syndrome. Daniela Pedicino. International Journal of Cardiology.

Human gut microbiome

Microbiota Disruption Induced by Early Use of Broad Spectrum Antibiotics is an Independent Risk Factor of Outcome after Allogeneic Stem Cell Transplantation. Daniela Weber.
Biology of Blood and Marrow Transplantation.

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept. Vera Slomka. Clinical Periodontology.

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

Animal experiments

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes. Julia H. Kreznar. Cell Reports.

Microbes in the environment

Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds. M Herrmann. Microbial Ecology.

Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats. Adriano Cabal. Microbiology Open.

Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa. Relebohile Matthew Matobole. Marine Drugs.

Food microbiology

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods. Luana Martins Perin. Food Microbiology.

Perspective: New insights on the use of wine yeasts. Francesca Comitini. Current Opinion in Food Science.

Phages and viruses

Pre-print: Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments. Samuel L. Díaz Muñoz. bioRxiv.

Biotechnology

Virulence Inhibitors from Brazilian Peppertree Block Quorum Sensing and Abate Dermonecrosis in Skin Infection Models. Amelia Muhs. Scientific Reports.

Evolution

Review: Epistasis and the Evolution of Antimicrobial Resistance. Alex Wong. Frontiers Microbiology.

Events and jobs

Assistant Professor – Pathogen and Microbiome Institute at Northern Arizona University

Assistant Professor – Biochem & Microbiology at Rutgers University

Expert Panel Discussions to be Highlight of Agenda at the 3rd Annual Translational Microbiome Conference – prweb

General microbiome

Neutral and niche dynamics in a synthetic microbial community -NJ Cira – bioRxiv

Human respiratory microbiome

Indoor fungal diversity in primary schools may differently influence allergic sensitization and asthma in children – João Cavaleiro Rufo – Pediatric Allergy Immunology

Human gut microbiome

Mining the Human Gut Microbiota for Immunomodulatory Organisms – Naama Geva-Zatorsky – Cell

Animal experiments

The enteric nervous system promotes intestinal health by constraining microbiota composition – Annah S. Rolig – PLoS Biology

Biologists control gut inflammation by altering the abundance of resident bacteria – Science Daily

Drunk bugs: Chronic vapour alcohol exposure induces marked changes in the gut microbiome in mice – Veronica L. Peterson – Behavioural Brain Research

Mouse model of alcohol abuse shows microbiome changes – Taconic

Feeding a High Concentration Diet Induces Unhealthy Alterations in the Composition and Metabolism of Ruminal Microbiota and Host Response in a Goat Model – Canfeng Hua – Frontiers in Microbiology

Animal microbiome

Impact of levels of total digestible nutrients on microbiome, enzyme profile and degradation of feeds in buffalo rumen – Anju Kala – PLoS ONE

Immune system stimulation by the gut symbiont Frischella perrara in the honey bee (Apis mellifera) – Olivier Emery – Molecular Ecology

Integrating gut microbiota immaturity and disease-discriminatory taxa to diagnose the initiation and severity of shrimp disease – Jinbo Xiong – Environmental Microbiology

Plant, root, and soil microbiome

Linking soil biology and chemistry using bacterial isolate exometabolite profiles – Tami L Swenson – bioRxiv

Ecological and conventional viticulture gives rise to distinct fungal and bacterial microbial communities in vineyard soils – M. Likar – Applied Soil Ecology

Effects of land use on soil microbial biomass, activity and community structure at different soil depths in the Danube floodplain – J.P. van Leeuwen – European Journal of Soil Biology

*Review: How do Plants-Having Different Exudation Patterns Shape a Similar Microbial Community? – Pil Y – Journal of Botanical Sciences

Water and extremophile microbiome

Epiphytic bacterial communities of the alga Fucus vesiculosus in oil-contaminated water areas of the Barents Sea – D. V. Pugovkin – Doklady Biological Sciences

Warmer night-time temperature promotes microbial heterotrophic activity and modifies stream sediment community – Anna Freixa – Global Change Biology

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities – Heikki Mykrä – Oikos

Built environment

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor – Allison R. Perrotta – PLoS ONE

Bioinformatics

*Review: A review of bioinformatics tools for bio-prospecting from metagenomic sequence data – Despoina Deppie Roumpeka – Frontiers in Genetics

Techniques

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity – Stanislav S. Terekhov – PNAS

Microbes in the news

From mice, clues to microbiome’s influence on metabolic disease – EurekaAlert

Bacteria Hysteria

Dog parks ground zero for deadly bacteria? How to keep your pet safe from leptospirosis – ABC15

Today’s digest features a review on the major mechanisms by which the intestinal microbiota confers protection against infections, studies showing that depression alters gut microbiota while sleep restriction over several consecutive days does not overtly influence the composition of the microbiome.

General microbiome

Microbial communities change in an anaerobic digestion after application of microbial electrolysis cells – Beom Leea – Bioresource Technology

Perspective: Sharpening host defenses during infection: Proteases cut to the chase – Natalie C Marshall – Molecular and cellular proteomics

Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology

Preprint: Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica – Zhemin Zhou – bioRxiv

Preprint: In vivo structures of an intact type VI secretion system revealed by electron cryotomography – Yi-Wei Chang – bioRxiv

Eco-evolutionary feedbacks can rescue cooperation in microbial populations – Clara Moreno-Fenoll – Scientific Reports

Pregnancy and early life

Getting organized early in life – Andrea Du Toit – Nature Reviews Microbiology

Infant fungal communities: current knowledge and research opportunities – Tonya L. Ward – BMC Medicine

Human respiratory microbiome

IL-36γ is a crucial proximal component of protective type-1-mediated lung mucosal immunity in Gram-positive and -negative bacterial pneumonia – M A Kovach – MucosalImmunology

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients – Michael J. Cox – PLoS ONE

Human skin microbiome

The Role of Cutaneous Microbiota Harmony in Maintaining a Functional Skin Barrier – Hilary E. Baldwin MD – Journal of Drugs in Dermatology

Preprint: Evolutionary and functional implications of hypervariable loci within the skin virome – Geoffrey D. Hannigan – PeerJ

Human vaginal microbiome

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin – Luiz Fernando Wurdig Roesch – PLoS ONE

Influence of contraceptive choice on vaginal bacterial and fungal microflora – G. Donders – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human and rat gut microbiome composition is maintained following sleep restriction – Shirley L. Zhang – PNAS

Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T. Harach – Scientific Reports

Gut to Brain Dysbiosis: Mechanisms Linking Western Diet Consumption, the Microbiome, and Cognitive Impairment – Emily E. Noble – Frontiers in Behavioural Neuroscience

Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome – Erin M. Hill-Burns – Movement Disorders

Persepctive: Diet-induced dysmotility and neuropathy in the gut precedes endotoxaemia and metabolic syndrome: the chicken and the egg revisited – Yvonne Elikplim – The Journal of Physiology

Editorial: Gut–brain axis, psychobiotics, and mental health – Arpit Parmar – Asian Journal of Psychiatry

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLoS ONE

Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction – Kristien E. Bouter – Gastroenterology

Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome – Ohad Manor – Microbiome

Review: Roles of the intestinal microbiota in pathogen protection – Carles Ubeda – Clinical & Translational Immunology

Antibiotic-Induced Depletion of Anti-Inflammatory Clostridia is Associated with the Development of GVHD in Pediatric Stem Cell Transplant Patients – Tiffany R. Simms-Waldrip – Biology of Blood and Marrow Transplantation

Molecular analysis of the human faecal archaea in a southern Indian population – Sandya B Rani – Journal of Biosciences

Elimination diets’ efficacy and mechanisms in attention deficit hyperactivity disorder and autism spectrum disorder – Verena Ly – European Child & Adolescent Psychiatry

Differences in gut metabolites and microbial composition and functions between Egyptian and U.S. children are consistent with their diets – Shankar V – mSystems
also in the news by ASM

Animal experiments

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLoS ONE

Development and validation of a new dynamic in vitro model of the piglet colon (PigutIVM): application to the study of probiotics – Mickaël Alain Fleury – Applied Microbiology and Biotechnology

Effects of dietary nutrient levels on microbial community composition and diversity in the ileal contents of pregnant Huanjiang mini-pigs – Yujiao Ji – PLoS ONE

Nopal feeding reduces adiposity, intestinal inflammation and shifts the cecal microbiota and metabolism in high-fat fed rats – Sofia Moran-Ramos – PLoS ONE
Animal microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

Meta-analysis to estimate the load of Leptospira excreted in urine: beyond rats as important sources of transmission in low-income rural communities – Veronica Barragan – BMC Research Notes

Plant, root, and soil microbiome

The microbe-secreted isopeptide poly-γ-glutamic acid induces stress tolerance in Brassica napus L. seedlings by activating crosstalk between H2O2 and Ca2+ – Peng Lei – Scientific Reports

Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community – Lu Shi – Scientific Reports

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Lladó – PLoS ONE

Pseudomonas protegens CS1 from the lemon phyllosphere as a candidate for citrus canker biocontrol agent – G. Michavila – Plant biology

Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene? – Alice Checcucci – Frontiers in Genetics

Use of endophytic and rhizosphere bacteria to improve phytoremediation of arsenic-contaminated industrial soils by autochthonous Betula celtiberica – Victoria Mesa – Applied and Environmental Microbiology

Bioaugmentation with bacteria selected from the microbiome enhances Arthrocnemum macrostachyum metal accumulation and tolerance – Salvadora Navarro-Torre – Marine Pollution Bulletin

Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition – F. Kohrs – Anaerobe

Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species – Scott J. Meiners – Oecologia

Review: Abiotic stress responses and microbe-mediated mitigation in plants: The omics strategies – Kamlesh K. Meena – Frontiers in Plant Science

Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants – Abdur Rahim Khan – PLoS ONE

Wildfire impact: Natural experiment reveals differential short-term changes in soil microbial communities – Miranda T. Prendergast-Miller – Soil Biology and Biochemistry

Diverse microbial communities in non-aerated compost teas suppress bacterial wilt – W. K. Mengesha – World Journal of Microbiology and Biotechnology

Fumigation with dazomet modifies soil microbiota in apple orchards affected by replant disease – Lidia Nicola – Applied Soil Ecology

Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development – Heng Gui – Scientific Reports

Apple replant disorder of Pingyitiancha rootstock is closely associated with rhizosphere fungal community development – Jian Sun – Jounral of Phytopathology

Changes in soil bacterial communities in an evergreen broad-leaved forest in east China following 4 years of nitrogen addition – Jun Cui – Journal of Soils and Sediments

Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in eastern China – Bin Ma – mSystems

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate – Jiaojio Niu – Journal of Basic Microbiology
Water and extremophile microbiome

Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process – Andrew R. J. Curson – Nature Microbiology

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic – Etienne Yergeau – Scientific Reports

Response of deep subsurface microbial community to different carbon sources and electron acceptors during ~two months incubation in microcosms – Lotta Purkamo – Frontiers in Microbiology

Bacterial community dynamics are linked to patterns of coral heat tolerance – Maren Ziegler – Nature Communications

Preprint: Habitat generalists or specialists, insights from comparative genomic analyses of Thermosipho lineages – Thomas H.A. Haverkamp – bioRxiv

Culture scale-up and immobilisation of a mixed methanotrophic consortium for methane remediation in pilot-scale bio-filters – Obulisamy Parthiba Karthikeyan – Environmental technology

Effect of different enrichment strategies on microbial community structure in petroleum-contaminated marine sediment in Dalian, China – Chao Chen – Marine Pollution Bulletin

Microbial catabolic diversity in and beyond the rhizosphere of plant species and plant genotypes – Karst M. Brolsmaa – Pedobiologia

Preprint: Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations – Marcus S Bray – bioRxiv

Bioinformatics

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems – Marko Budinich – PLoS ONE

Modelling functional resilience of microbial ecosystems: Analysis of governing processes – Sara König – Environmental Modelling & Software

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – W. Duncan Wadsworth – BMC Bioinformatics

Techniques

Metabolomics: A Primer – Xiaojing Liu – Trends in biochemical sciences

Fluorescence Lectin Bar-Coding of Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate Forming Microorganisms – Thomas R. Neu – Microorganisms

Microbes in the news

Experts reveal how the microbiome in your gut is linked to weight gain and health disorders – Leah Hardy – MailOnline
Will cities of the future embrace bacteria? – Starre Vartan- MNN.com

Microbes on the market

FDA Turmoil, Biology Mystery On List Of Hurdles For Microbiome Drugs – Ben Fidler – exome

Science, publishing, and career

FICUS JGI-NERSC Microbiome Data Science Call for Proposals (Open till 1st of March)

Events and jobs
Postdoctoral research fellow in Microbiome Research – Karolinska Institutet

Postdoctoral Scientist ( Microbiome, Mycobiome, Mucosal Immunology) – Jill Roberts Institute for Research in IBD at Weill Cornell Medicine, New York City

Senior Lecturer in Food Microbiology – RMIT Bundoora Campus

Junior Specialist in Environmental Microbiology – University of California, Santa Cruz

General microbiome
Uncharacterized bacterial structures revealed by electron cryotomography – Megan J Dobro – bioRxiv

Pregnancy and early life
Review: Infant fungal communities: current knowledge and research opportunities – Tonya L. Ward – BMC Medicine

Human gut microbiome
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline – B.J. Levin – Science
Also described in this short article: New tool can help researchers identify enzymes—and their abundance—in microbiomes – Phys.org

Dynamics of the human gut microbiome in inflammatory bowel disease – Jonas Halfvarson – Nature Microbiology

Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant – Maryam Tidjani Alou – Antonie van Leewenhoek

Animal microbiome
The microbiome of bulk tank milk: Characterization and associations with somatic cell count and bacterial count – M.X. Rodrigues – Journal of Dairy Science

Dynamics of the microbiota found in the vaginas of dairy cows during the transition period: Associations with uterine diseases and reproductive outcome – M.L.S. Bicalho – Journal of Dairy Science

Prophylactic use of a standardized botanical extract for the prevention of naturally occurring diarrhea in newborn Holstein calves – A.G.V. Teixeira – Journal of Dairy Science

Plant, root, and soil microbiome
Four years of experimental warming do not modify the interaction between subalpine shrub species – Alba Anadon-Rosell – Oecologia

Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria – Md Sainur Samad – bioRxiv

Water and extremophile microbiome
Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process – Andrew R.J. Curson – Nature Microbiology
This is summed up in the short article: Marine bacteria produce an environmentally important molecule with links to climate – Phys.org

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment – Chioma C. Obi – Applied Microbiology and Biotechnology

Diversity and community composition of particle-associated and free-living bacteria in mesopelagic and bathypelagic Southern Ocean water masses: Evidence of dispersal limitation in the Bransfield Strait – Mathias Milici – Limnology and Oceanography

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type – R. Heyer – Biotechnology for Biofuels

Probiotics / prebiotics
Chapter One – Antivirulence Properties of Probiotics in Combating Microbial Pathogenesis – M. Surendran Nair – Advances in Applied Microbiology

Reclamation of Chinese herb residues using probiotics and evaluation of their beneficial effect on pathogen infection – Fanjing Meng – Journal of Infection and Public Health

Probiotic dietary supplementation in Nile tilapia as prophylaxis against streptococcosis – M.M. Yamashita – Aquaculture Nutrition

Phages and viruses
Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families – Jemma L. Geoghegan – PLoS Pathogens

Plaques formed by mutagenized viral populations have elevated co-infection frequencies – Elizabeth R. Aguilera – bioRxiv

Bioinformatics
dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes – Matthew R Olm – bioRxiv

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Techniques
A real-time PCR assay for accurate quantification of the individual members of the Altered Schaedler Flora microbiota in gnotobiotic mice – Joao Carlos Gomes-Neto – Journal of Microbiological Methods

Neutral and niche dynamics in a synthetic microbial community – NJ Cira – bioRxiv

Microbes in the news
“Archaea” unites University on sesquicentennial – Tess O’Brien – The Daily Illini (student newspaper at University of Illinois)

How to quickly identify sepsis-causing bacteria – melt it down – Lisa-Ann Lee – New Atlas
The paper referenced is Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping – Stephanie I. Fraley – Scientific Reports

Chemical engineers boost bacteria’s productivity – phys.org
The paper referenced is Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit – Apoorv Gupta – Nature Biotechnology

Microbes on the market
Human Microbiome Market is Expecting Worldwide Growth by 2020 – Persistence Market Research Study

Ritter Pharmaceuticals Announces Collaboration with University of British Columbia to Explore Development of Microbiome Therapeutics in Environmental Enteropathy – Yahoo Finance

Science, publishing, and career
The Troll Taunter – Andrew McMillen – BackChannel
This is an amazing piece: “But on that Friday night, Temple-Wood had an idea. For every harassing email, death threat, or request for nude photos that she received, she resolved to create a Wikipedia biography on a notable woman scientist who was previously unknown to the free online encyclopedia.”

Do’s and don’ts for scientists who want to shape policy – Erik Stokstad – Science

Scientists should be political but not partisan – Angela de Pace – Medium