An unusually quiet Monday to start your week of microbiome literature. In the methods section, some new protocols from Springer’s “Diagnostic Bacteriology” volume. Enjoy!

General microbiome

Review: Influences of environmental bacteria and their metabolites on allergies, asthma and host microbiota
G Jatzlauk et al. – Allergy

Human gut microbiome

Microbiome and NAFLD: Potential Influence of Aerobic Fitness and Lifestyle Modification
Matthew R. Panasevich – Physiological Genomics

Mucosa-associated microbiota signature in colorectal cancer
R. Gao et al. – European Journal of Clinical Microbiology & Infectious Diseases

Microbial diseases

Pre-print: Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA
Maho Yokoyama et al. – bioRxiv

Animal experiments

Alteration of gut microbiota in association with cholesterol gallstone formation in mice
Qihan Wang et al – BMC Gastroenterology

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts
Meriem Belheouane et al. – Microbiome

Animal microbiome

Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids
Jennifer L. Morrow et al – Microbiome

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome
Sara M. Wolff et al – Microbiome

Plant, root, and soil microbiome

Novel microbial assemblages dominate weathered sulfide-bearing rock from copper-nickel deposits in the Duluth Complex, Minnesota, USA
DS Jones et al. – Applied and Environmental Microbiology

Water, estuarine and sediment microbiome

Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor
N Stern et al. – Applied and Environmental Microbiology

Microbial biotechnology

Efficacy of Bacillus amyloliquefaciens as biocontrol agent to fight fungal diseases of maize under tropical climates: from lab to field assays in south Kivu
Parent Zihalirwa Kulimushi et al. – Environmental Science and Pollution Research

Food microbiology

RNA-based amplicon sequencing highlights the impact of the processing technology on microbiota composition of artisanal and industrial PDO Lard d’Arnad
I Ferrocino et al. – Applied and Environmental Microbiology

General microbiology and evolution

Nitrogen-source stabilization of quorum sensing in the Pseudomonas aeruginosa bioaugmentation strain SD-1
M Wang et al – Applied and Environmental Microbiology

Phages and viruses

Pre-print: Gene networks provide a high-resolution view of bacteriophage ecology
Jason Shapiro & Catherine Putonti – bioRxiv

Bioinformatics and statistics

MetabolitePredict: a de-novo human metabolomics prediction system and its applications in rheumatoid arthritis
Quan Qiu Wang & Rong Xu – Journal of Biomedical Informatics

Techniques and methods

Protocol: Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization
Silvia Fontenete et al. – Diagnostic Bacteriology

Protocol: Detection of Helicobacter pylori DNA in Formalin-Fixed Paraffin-Embedded Gastric Biopsies Using Laser Microdissection and qPCR
María Fernanda Loayza Villa et al. – Diagnostic Bacteriology

Protocol: Characterization of Sinus Microbiota by 16S Sequencing from Swabs
Thad W. Vickery et al. – Diagnostic Bacteriology

Protocol: Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples
Amanda Claire Brown & Mette T. Christiansen

Microbes in the news

Bacteria Behind Legionnaires’ Disease Found at New York Police Station
Ashley Southall – The New York Times

Science, publishing, and career

Microbiology Graduate Program – University of California

Events and jobs

Doctoral researcher in Microbiology/Virology – Helmholtz Centre for Environmental Research – UFZ – Germany

General microbiome

Review: Role of Gut Microbiota in Rheumatoid Arthritis – Y. Maeda – Journal of Clinical Medicine
Review: The Mycobiome: Impact on Health and Disease States –  N. El-Jurdi – Microbiology Spectrum

Pregnancy and early life

Review: Early-Life Host–Microbiome Interphase: The Key Frontier for Immune Development – N. Amenyogbe – Frontiers in Pediatrics

Human skin microbiome

Temporal Dynamics Of Relative Abundances And Bacterial Succession In Chronic Wound Communities – C.D. Tipton – Wound Repair and Regeneration

Human vaginal microbiome

Therapeutic Opportunities in the Vaginal Microbiome – G. Reid – Microbiology Spectrum

Human gut microbiome

Review: Microbial Impact on Host Metabolism: Opportunities for Novel Treatments of Nutritional Disorders? – H. Plovier – Microbiology Spectrum
Nickel-resistant bacteria isolated in human microbiome – E.A. Lusi – New Microbes and New Infections

Animal experiments

Keratin 8 reduces colonic permeability and maintains gut microbiota homeostasis, protecting against colitis and colitisassociated tumorigenesis – C. Liu – Oncotarget
Evolution of commensal bacteria in the intestinal tract of mice – A. Sousa – Current Opinion in Microbiology

Animal microbiome

Gut Microbiota Dysbiosis in Postweaning Piglets: Understanding the Keys to Health – R. Gresse – Trends in Microbiology
Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome – S.M. Wolff – Microbiome

Plant, root, and soil microbiome

Community analysis of Persian oak fungal microbiome under dust storm conditions – N.H. Doust – Fungal Ecology
Maternal effects on phenotype, resistance and the structuring of fungal communities in Eucalyptus grandis – M. Vivas – Environmental and Experimental Botany
Review: Iron and Immunity – E.H. Verbon – Annual Review of Phytopathology
Dispersal enhances beta diversity in nectar microbes – R.L. Vannette – Ecology Letters

Water and extremophile microbiome

Application of long amplicon propidium monoazide-PCR to assess the effects of temperature and background microbiota on pathogens in river water – A. Banihashemi – Journal of Water and Health

Microbes in the news

Gut bacteria can stop cancer drugs from working – S. Reardon – Nature News
Fungi revive starving bacteria – K. Evans – Labroots
Did the microbiome help drive human evolution? – S.E. Erdman – STAT news

Microbiology today

We have a group of nice articles on careers in microbiology and chance to view  “Women in Microbiology – Esther Lederberg” a live session from Microbe 2017. Science articles today include Predictors of phenotypic switching in bacteria, Determinants of bone mass regulation by the gut microbiota (in mice), and Phylogenetic and functional diversity of bacteria in soils.

Events and jobs

Microbiology Associate – CryoLife Inc – Kennesaw, GA

General microbiome

Preprint: Dynamical predictors of an imminent phenotypic switch in bacteria – H. Wang – BioRxiv

Preprint: Metabolic changes of the host-pathogen environment in a Cryptosporidium infection – C. Miller – BioRxiv

Human respiratory microbiome

The microbial changes in subgingival plaques of orthodontic patients: a systematic review and meta-analysis of clinical trials – R. Guo – BMC Oral Health

The lung microbiota (in French) – M. Ploton – Archives de Pédiatrie

Human gut microbiome

Review: Gut microbiota and acute graft-versus-host disease – K. Yoshioka – Pharmacological Research

Animal experiments

Preprint: Chondroitin Sulfate Flourishes Gut Sulfatase-Secreting Bacteria To Damage Mucus Layers, Leak Bacterial Debris, And Trigger Inflammatory Lesions In Mice – T. Liao – BioRxiv

Regulation of bone mass by the gut microbiota is dependent on NOD1 and NOD2 signaling – C. Ohlsson – Cellular Immunology

Plant, root, and soil microbiome

Phylogenetic and functional diversity of total (DNA) and expressed (RNA) bacterial communities in urban green infrastructure bioswale soils – A. Gill – Applied and Environmental Microbiology

Microbes in the news

Enhanced test for urinary tract infections detects more bacteria than standard test – MedicalXpress

Vaginal Bacteria Alter Sexual Transmission Of Zika And Herpes Simplex Virus-2 – ASM Press Release

Science, publishing, and career

Women In Microbiology – Esther Lederberg – Chris Condayan – ASM

Careers In Microbiology – An Insiders’ Guide To Finding A Job – Chris Condayan – ASM

Microbiology Careers: Which One Is Right For You? – Chris Condayan – ASM

There were over 100 alerts today! Here are plenty of papers after the few light digests.

Events and jobs
Bioinformatics Scientist, Microbiome – Human Longevity, Inc, Greater San Diego Area

MSc position in Microbiology – Teagasc, London/Europe

General microbiome
Review: The multi-omics promise in context: from sequence to microbial isolate – Johanna Gutleben – Critical Reviews in Microbiology

Review: Symbiosis-inspired approaches to antibiotic discovery – Navid Adnani – Natural Product Reports

Pregnancy and early life
The Microbiome of Infants Recruited to a Randomised Placebo-controlled Probiotic Trial (PiPS Trial) – Michael Millar – EBioMedicine

Safety and tolerability of Bifidobacterium longum subspecies infantis EVC001 supplementation in healthy term breastfed infants: a phase I clinical trial – Jennifer T. Smilowitz – BMC Pediatrics

Human vaginal microbiome
Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women – Nichole R. Klatt – Science

Changes in vaginal community state types reflect major shifts in the microbiome – J. Paul Brooks – Microbial Ecology in Health and Disease

Human gut microbiome
Chemoproteomic Profiling of Bile Acid Interacting Proteins – Shentian Zhuang – ACS Central Science

Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota – Tingting Chen – Scientific Reports

Vancomycin Taper and Risk of Failure of Fecal Microbiota Transplant in Patients With Recurrent Clostridium difficile Infection – Roberto L. Patron – Clinical Infectious Diseases

Surgically induced changes in gut microbiome and hedonic eating as related to weight loss: Preliminary findings in obese women undergoing bariatric surgery – Claudia P. Sanmiguel – Psychosomatic Medicine

Intestinal microbiota in patients with chronic hepatitis C with and without liver cirrhosis compared to healthy controls – Benjamin Heidrich – Liver International

Dimethyl fumarate reduces the risk of mycotoxins via improving intestinal barrier and microbiota – Ning Ma – Oncotarget

Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity – Eliot T. McKinley – JCI Insight

Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombus formation via Toll-like receptor-2 – Sven Jäckel – Blood

Review: Trust your gut – metformin and diabetes – Conor A. Bradley – Nature Reviews Endocrinology

Review: Gut microbiota: Inulin regulates endothelial function: a prebiotic smoking gun? – Francesca Fava – Nature Reviews Gastroenterology and Hepatology

Review: Gut Microbiota, Endocrine-Disrupting Chemicals, and the Diabetes Epidemic – Ganesan Velmurugan – Trends in Endocrinology and Metabolism

Review: Gut Microbiota and the Gut-Brain Axis: New Insights in the Pathophysiology of Metabolic Syndrome – de Clercq – Psychosomatic Medicine

Animal experiments
Genetic mouse models with intestinal-specific tight junction deletion resemble an ulcerative colitis phenotype – Wolfgang Stremmel – Journal of Crohn’s and Colitis

Deciphering the landscape of host barriers to Listeria monocytogenes infection – Ting Zhang – PNAS

Rifaximin exerts beneficial effects in PI-IBS mouse model beyond gut microbiota – Yu Jin – Journal of Gastroenterology and Hepatology

Farnesoid X Receptor Agonist Treatment Alters Bile Acid Metabolism but Exacerbates Liver Damage in a Piglet Model of Short-Bowel Syndrome – Prue M. Pereira-Fantini – Cellular and Molecular Gastroenterology and Hepatology

Faecal transplantation for the treatment of Clostridium difficile infection in a marmoset – Yumiko Yamazaki – BMC Veterinary Research

Effect of soybean husk supplementation on the fecal fermentation metabolites and microbiota of dogs – Htun Myint – Animal Science Journal

A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs – Kristin M. V. Herstad – BMC Veterinary Research

Animal microbiome
Host-specific assembly of sponge-associated prokaryotes at high taxonomic ranks – Georg Steinert – Scientific Reports

The feline skin microbiota: The bacteria inhabiting the skin of healthy and allergic cats – Caitlin E. Older – PLoS One

Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life – A. Schoster – BMC Veterinary Research

Cost-effective screening and isolation of xylano-cellulolytic positive microbes from termite gut and termitarium – Libin Mathew Varghese – 3 Biotech

Plant, root, and soil microbiome
Impact of metal stress on the production of secondary metabolites in Pteris vittata L. and associated rhizosphere bacterial communities – Hoang Nam Pham – Environmental Science and Pollution Research

High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism – Yun-Juan Bao – Journal of Environmental Sciences

Impact of microbial communities from tropical soils on the mobilization of trace metals during dissolution of cinnabar ore – Clarisse Balland-Bolou-Bi – Journal of Environmental Sciences

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition – Xingyu Ma – Molecular Ecology

Anthropogenic protection alters the microbiome in intertidal mangrove wetlands in Hainan Island – Juanli Yun – Applied Microbiology and Biotechnology

Water and extremophile microbiome
Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships – Justin R. Seymour – Nature Microbiology

Genetic characterization of periphyton communities associated with selenium bioconcentration and trophic transfer in a simple food chain – Vanessa Friesen – Environmental Science and Technology

Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora – Rachel M. Wright – Scientific Reports

Metabolic network analysis reveals microbial community interactions in anammox granules – Christopher E. Lawson – Nature Communications

Hot springs of Indian Himalayas: potential sources of microbial diversity and thermostable hydrolytic enzymes – Harmesh Sahay – 3 Biotech

High throughput sequencing of microbial eukaryotes in Lake Baikal reveals ecologically differentiated communities and novel evolutionary radiations – Zhenzhen Yi – FEMS Microbiology Ecology

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure – Xiao Ma – Environmental Science and Technology

Built environment
Evolution of microbial communities growing with carbon monoxide, hydrogen and carbon dioxide – Sofia Esquivel-Elizondo – FEMS Microbiology Ecology

Adaptation of microbial community of the anode biofilm in microbial fuel cells to temperature – Xiaoxue Mei – Bioelectrochemistry

Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer – Jesus D. Fernandez-Bayo – Journal of Environmental Sciences

Bacterial community structure transformed after thermophilically composting human waste in Haiti – Yvette M. Piceno – PLoS One

Food microbiology
Characterization of the peptide fraction from digested Parmigiano Reggiano cheese and its effect on growth of lactobacilli and bifidobacteria – Benedetta Bottari – International Journal of Food Microbiology

Impact of food grade and nano-TiO2 particles on a human intestinal community – William Dudefoi – Food and Chemical Toxicology

Probiotics / prebiotics
Probiotic yogurt and acidified milk similarly reduce postprandial inflammation and both alter the gut microbiota of healthy, young men – Kathryn J. Burton – British Journal of Nutrition

Phages and viruses
Phylogenetic Diversity of T4-Type Phages in Sediments from the Subtropical Pearl River Estuary – Maoqiu He – Frontiers in Microbiology

Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space – Junyu Zhang – Microbiome

Bioinformatics
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities – Jonathan L. Golob – BMC Bioinformatics

Techniques
Review: Capturing the genetic makeup of the active microbiome in situ – Esther Singer – ISME

Novel Co-Culture Plate Enables Growth Dynamic-Based Assessment Of Contact-Independent Microbial Interactions – Thomas J. Moutinho Jr. – bioRxiv

Optimization of high-yielding protocol for DNA extraction from the forest rhizosphere microbes – Sadam D. V. Satyanarayana – 3 Biotech

DNA metabarcoding to assess indoor fungal communities: Electrostatic dust collectors and Illumina sequencing – Steffi Rocchi – Journal of Microbiological Methods

Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets – Blair Lawley – PeerJ

Microbes in the news
Unhealthy vagina microbiome can make HIV drugs less effective – Bob Roehr – New Scientist
Article featured above!

Gut microbiota and melanoma treatment responses – Caroline Robert and Franck Carbonnel – OUPblog

Biologists examine biofilm as part of port field studies – Sandor Gyarmati – Delta Optimist

Bacteria used as factories to produce cancer drugs – Phys.Org

Boffins find evidence of strange uranium-producing bacteria lurking underground – Katyanna Quach – The Reigster

Man dies from flesh-eating bacteria after swimming with new tattoo – MSN

Microbes on the market
Why Should we be Excited about the Emerging Microbiome Field? – Antonio – LabBioTech

A bit of a late night Digest today! Still here though, quite a few articles about rhizosphere, a hot topic at the moment; some genome sequences from ASM Genome Announcements, and a few methods & bioinformatics papers. Enjoy!

Multi-site human microbiome

Bacterial Composition and Diversity in Breast Milk Samples from Mothers Living in Taiwan and Mainland China
Shiao-Wen Li et al. – Frontiers in Microbiology

Review: Recent advances in dental biofilm: impacts of microbial interactions on the biofilm ecology and pathogenesis
Yung-Hua Li et al. – AIMS Bioengineering

The Evolving Cystic Fibrosis Microbiome: A Comparative Cohort Study Spanning Sixteen Years
Nicole Acosta et al. – Annals of the American Thoracic Society

Human epitelial microbiome

A tale of two risks: smoking, diabetes and the subgingival microbiome
Sukirth M. Ganesan et al. – The ISME Journal

Quantitative proteomic analysis of host epithelial cells infected by Salmonella enterica serovar Typhimurium
Linlu Qi et al. – Proteomics

Human gut microbiome

Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding
Zehra Esra Ilhan et al. – The ISME Journal

Microbe Profile: Akkermansia muciniphila: a conserved intestinal symbiont that acts as the gatekeeper of our mucosa
Willem M de Vos – Microbiology

Fecal Microbiota Transplantation: From Clostridium difficile to Inflammatory Bowel Disease
Robert J. Gianotti & Alan C. Moss – Gastroenterology & Hepatology

Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome
Tao Zuo et al. – Gut

Microbial diseases

Review: ‘Omic’ Approaches to Study Uropathogenic Escherichia coli Virulence
Alvin W. Lo et al. – Trends in Microbiology

Case report: Ecthyma Gangrenosum: Escherichia coli or Pseudomonas aeruginosa?
Mohamed Abbas et al. – Frontiers in Microbiology

General environmental microbiology

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations
Felix Goldschmidt et al. – The ISME Journal

Animal microbiome

Thesis: Biotic and Abiotic Factors Influence Formation and Ontogenic Dynamics of Molecularly Defined Gastro-Intestinal Microbial Communities in Lake Sturgeon (Acipenser Fulvescens) and Channel Catfish (Ictalurus Punctatus)
Abdul Razak – Michigan State University

Plant, root, and soil microbiome

Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities
Barbara Drigo et al. – Environmental Microbiology

The biogeographic pattern of microbial functional genes along an altitudinal gradient of the Tibetan pasture
Qi Qi et al. – Frontiers in Microbiology

Communication: Microbial functionality as affected by experimental warming of a temperate mountain forest soil—A metaproteomics survey
Dong Liu et al. – Applied Soil Ecology

Letter: Leaf bacterial diversity mediates plant diversity and ecosystem function relationships
Isabelle Laforest-Lapointe et al. – Nature

Soil amendments influence Pratylenchus penetrans populations, beneficial rhizosphere microorganisms, and growth of newly planted sweet cherry
Tristan T. Watson et al. – Applied Soil Ecology

Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing
Yi Yang et al. – PLoS One

Soil Warming Increases Arsenic Availability in the Rice Rhizosphere
Rebecca B. Neumann et al. – Agricultural & Environmental Letters

Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage
Gajender Aleti et al. – Scientific Reports

Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome
Jean-Michel Hilly et al. – Plant Biotechnology Journal

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization
Wayne Dawson et al. – Frontiers in Microbiology

Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling
Linwei Wu et al. – The ISME Journal

Book chapter: Cannabis Endophytes and Their Application in Breeding and Physiological Fitness
Parijat Kusari et al. – Cannabis sativa L. – Botany and Biotechnology

Water, estuarine and sediment microbiome

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond
Zarraz M.-P. Lee et al. – Frontiers in Microbiology

Microbes influence the biogeochemical and optical properties of maritime Antarctic snow
Hodson, AJ et al. – Journal of Geophysical Research

Bacterial diversity in Shahu lake, northwest China is significantly affected by nutrient composition rather than location
Jing-Yu Li et al. – Annals of Microbiology

Built environment

Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms
Keri Ann Lydon et al. – Elementa Science

Thesis: Characterization of Microbial Contaminants Associated with Floor Material Types
Mridula Gupta – The Ohio State University

Microbial biotechnology

Magnetotactic Coccus Strain SHHC-1 Affiliated to Alphaproteobacteria Forms Octahedral Magnetite Magnetosomes
Heng Zhang et al. – Frontiers in Microbiology

Abundance and diversity of ammonia-oxidizing archaea in a biological aerated filter process
Hongyi Chen et al. – Annals of Microbiology

Biochemical Mechanisms and Catabolic Enzymes Involved in Bacterial Estrogen Degradation Pathways
Yi-Lung Chen et al. – Cell Chemical Biology

An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield
Umesh K. Bageshwar et al. – Applied and Environmental Microbiology

Biofertilizers and sustainable agriculture: exploring arbuscular mycorrhizal fungi
Nicholas O. Igiehon & Olubukola O. Babalola – Applied Microbiology and Biotechnology

Food microbiology

Removal of foodborne pathogen biofilms by acidic electrolyzed water
Qiao Han et al. – Frontiers in Microbiology

General microbiology and evolution

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes
Amoozegar MA et al. – Microbiology

Surface sensing for flagellar gene expression on solid media in Paenibacillus sp. NAIST15-1
Kazuo Kobayashi et al. – Applied and Environmental Microbiology

Complete genome sequence of a denitrifying bacterium, Pseudomonas sp. CC6-YY-74, isolated from Arctic Ocean sediment
Xuenzheng Lin et al. – Marine Genomics

Draft Genome Sequence of Acidihalobacter ferrooxidans DSM 14175 (Strain V8), a New Iron- and Sulfur-Oxidizing, Halotolerant, Acidophilic Species
Himel N. Khaleque et al. – Genome Announcements

Draft Genome Sequence of Saccharomonospora sp. Strain LRS4.154, a Moderately Halophilic Actinobacterium with the Biotechnologically Relevant Polyketide Synthase and Nonribosomal Peptide Synthetase Systems
Scarlett Alonso-Carmona et al. – Genome Announcements

Genome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida
Peili Cao et al. – Frontiers in Microbiology

Phages and viruses

Review: Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
Stephen Hayes et al. – Viruses

Bioinformatics and statistics

Predicting microbial interactions from time series data with network information
Yan Wang et al. – International Journal of Data Mining and Bioinformatics

Commentary: Bioinformatics can boost metabolomics research
René Meier et al. – Journal of Biotechnology

Techniques and methods

Thesis: Carbon dioxide titration method for soil respiration measurements
Luis Martín Rubio – Tampere University of Applied Sciences

Protocol: Harnessing the Power of PCR Molecular Fingerprinting Methods and Next Generation Sequencing for Understanding Structure and Function in Microbial Communities
Sujal Phadke et al. – PCR

An optimized extraction method to remove humic acids interferences from soil samples prior to microbial proteome measurements
Chen Qian & Robert L. Hettich – Journal of Proteome Research

Microbes in the news

Gene Drives Could Wipe Out Insect-Borne Disease — But What’s the Price?
Shelly Fan – Ontological Design

Non-microbiology picks

Application of mass spectrometry-based metabolomics approaches for food safety, quality and traceability
María Castro-Puyana et al. – Trends in Analytical Chemistry

Hunting for Nature’s Treasures or Learning from Nature?: The Narrative Ambivalence of the Ecotechnological Turn
Sanne van der Hout & Martin Drenthen – Berghahn Journals

What if you can workout while keeping cool with a pleasant smell ? In today’s post, read about researchers from MIT who have developed a ‘breathable workout suit’ using humidity-sensitive E.coli that can take care of cooling you down as you sweat.

Human vaginal microbiome

Early pregnancy vaginal microbiome trends and preterm birth – Stout MJ – Am J Obstet Gynecol.

Human gut microbiome

Chronic consequences on human health induced by microbial pathogens: Growth faltering among children in developing countries – Nataro JP – Vaccine

The gut-brain axis in Parkinson’s disease: Possibilities for food-based therapies – Perez-Pardo P – Eur J Pharmacol.

Animal experiments

Influence of Dietary Avocado on Gut Health in Rats – Paturi G – Plant Foods Hum Nutr.

Review:
Transcriptional networks in rodent models support a role for gut-brain communication in neurogenic hypertension: A review of the evidence – Zubcevic J – Physiol Genomics

Plant, root, and soil microbiome

Review: Let the Core Microbiota Be Functional – Lemanceau P – Trends Plant Sci.

An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield – Umesh K. Bageshwar – Appl Environ Microbiol.
High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils – Min X – Chemosphere

Built environment
Pathways in bacterial and archaeal communities dictated by ammonium stress in a high solid anaerobic digester with dewatered sludge – Li N – Bioresour Technol.

Microbes in the news
Experimental athletic shirt uses bacteria to keep you cool during workouts – eParisExtra
Gut Bacteria Changes After Some Weight-Loss Surgeries – tucson.com

Today’s microbiome is packed with thought-provoking insights from the status of Microbiology today and in-depth look at what is REALLY in our drinking water.

General Microbiome and Microbiology

Big Questions in Microbiology Mizrahi V. Cell

Human gut microbiome

Uncovering the trimethylamine-producing bacteria of the human gut microbiota. Rath S. Microbiome

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.Hibberd MC. Science Translational Medicine

Human microbiome and immune system

Potential Impact of Nutrition on Immune System Recovery from Heavy Exertion: A Metabolomics Perspective.Nieman DC. Nutrients

Animal and insect microbiome

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. Gontang EA. Plus One

A metagenomic approach to discover a novel β-glucosidase from bovine rumens. Suwan E. Pure and Applied Chemistry, 2017

Plant, soil, and air microbiome

Tomato root microbiota and Phytophthora parasitica-associated disease. Larousse M. Microbiome

Distance decay relationships in foliar fungal endophytes are driven by rare taxa. Oono R. Environmental Microbiology

Carbon‐driven enrichment of the crucial nitrate reducing bacteria in limed peat soil microcosms. Zhu Y. Letters in applied Microbiology

Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash. Cruz-Paredes C. Soil Biology and Biochemistry.

Inland waters and ocean microbiome

Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor.Gantt SE.FEMS Microbiology Letters.

Nutrient stoichiometry shapes microbial community structure in a shallow evaporitic pond. Lee ZMP.  Frontiers in Microbiology

Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance’s perspective. Zhang Y. Environmental Microbiology

Faecal microbiome 

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease.Khanna S. Microbiome

Probiotics

Antioxidant Properties of Probiotic Bacteria. Wang Y. Nutrients

 STUDYING HOST-MICROBIOTA MUTUALISM USING GNOTOBIOTIC DROSOPHILA. Ma D.Old Herborn University Seminar Monograph 30

Virology

Pre-Symptomatic Diagnosis of Ebola Virus Infection. Navalkar K. Emerging disease and Virology   2017

Succession in the petroleum reservoir microbiome through an oil field production lifecycle.Vigneron A. The ISME Journal

Preprint 

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. Laroche O. PeerJ

Events and jobs
Microscopist Asbestos/Microbiology – EMSL Analytical, Seattle, WA

Technician (Microbiology Team) – AsureQuality (AQ), Christchurch, Canterbury, New Zealand

Laboratory Technician I (Microbiology & Genetics) – IDEXX, Columbia, MO, US

Associate Scientist Molecular Microbiology – CheckMark Labrecruitment, South Holland

Human respiratory microbiome
Review: Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides – Wilmore C. Webley – Respiratory Research

Human gut microbiome
Review: The bidirectional gut-brain-microbiota axis as a potential nexus between traumatic brain injury, inflammation, and disease – Mark Sundman – Brain, Behavior, and Immunity

Clinical Trial Watch: ‘Targeting the gut-liver axis in liver disease’ – Reiner Wiest – Journal of Hepatology

Gluten-degrading bacteria are present in the human small intestine of healthy volunteers and celiac patients – Alexandra R. Herran – Research in Microbiology

The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans – Lloyd S. Robinson – Journal of Biological Chemistry

Plant, root, and soil microbiome
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation – José A. Siles A. Siles – Scientific Reports

Review: Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens – Ikkei Shikano – Journal of Chemical Ecology

Pseudomonas chlororaphis produces two distinct R-tailocins that contribute to bacterial competition in biofilms and on roots – Robert J. Dorosky – Applied and Environmental Microbiology

Water and extremophile microbiome
Review: A multiomics approach to study the microbiome response to phytoplankton blooms – Liyan Song – Applied Microbiology and Biotechnology

Antibiotics/probiotics/prebiotics
The Resistome Of Important Human Pathogens – Christian Munck – bioRxiv

Phages and viruses
Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer – Marie Touchon – Current Opinion in Microbiology
Part of a themed issue on MGE-HGT in prokaryotes

Bioinformatics
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees – Märt Roosaare – PeerJ

Microbes in the news
Bacteria could lead to cleaner methane power – Jon Fingas – Engadget

Luminous bacteria will help to measure radioactivity – Siberian Federal University – EurekAlert!

A ‘Superbug’ Fungus Is Spreading Across The US – Kristen V. Brown – Gizmodo

Research shows that gut bacteria tells their hosts what to eat – Cordis News

Indian researchers use a novel route to kill TB bacteria – R. Prasad – The Hindu

Bacteria Hysteria
Cash is even grosser than you knew: Dangerous bacteria survive on paper money, study finds – James Dennin – AOL