October 12, 2017

Interesting papers from every category (especially in “Animal studies, animal microbiome”), and many on molecular mechanisms. Many of the alerts are from books (specifically on yeasts and soil/plant communities) listed below, so be sure to check their table of contents out!

Events and jobs
Biomedical Scientist – microbiology – Edinburgh, Scotland – Matchtech

Technician (Microbiology) – Birmingham, Alabama – LabCorp

Instructor in Microbiology – Corvallis, OR – Oregon State University

Senior Hospital Scientist Microbiology – Tamworth, New South Wales, Australia – NSW Health Pathology

Unlocking the Microbiome – November 15, London, UK – Microbiology Society

General microbiome
The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma – Microbial Ecology

Dysbiosis and Its Discontents – Katarzyna B. Hooks – mBio

Book: Yeasts in Natural Ecosystems: Ecology – Andrey Yurkov, María I. Pozo
Contains multiple articles of interest.

Pregnancy and early life
Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment – Heidi Gumpert – Frontiers in Microbiology

Cesarean Section, Formula Feeding, and Infant Antibiotic Exposure: Separate and Combined Impacts on Gut Microbial Changes in Later Infancy – Farzana Yasmin – Frontiers in Pediatrics

Multi-site human microbiome
Oral Lactobacillus Counts Predict Weight Gain Susceptibility: A 6-Year Follow-Up Study – J.A. Rosing – Obesity Facts

Review: Nutritional habits, risk, and progression of Parkinson disease – Roberto Erro – Journal of Neurology

Review: From Osteoimmunology to Osteomicrobiology: How the Microbiota and the Immune System Regulate Bone – Emory Hsu – Calcified Tissue International

Human respiratory microbiome
Review: Role of microbiota on lung homeostasis and diseases – Jian Wang – Science China Life Sciences

Human gut microbiome
Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides – Kazune Tamura – Cell Reports

Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence – Yunus E. Tuncil – mBio

The gut microbiome in atherosclerotic cardiovascular disease – Zhuye Jie – Nature Communications

Cytotoxic and regulatory roles of mucosal-associated invariant T cells in type 1 diabetes – Ophélie Rouxel – Nature Immunology

Review: How diet can impact gut microbiota to promote or endanger health – Benoit Chassaing – Current Opinion in Gastroenterology

Review: Management of inflammatory bowel disease-related anaemia and iron deficiency with specific reference to the role of intravenous iron in current practice – Jürgen Stein – Expert Opinion on Pharmacotherapy

Review: Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis – Wei Jia – Nature Reviews Gastroenterology and Hepatology

Review: Environmental triggers in IBD: a review of progress and evidence – Ashwin N. Ananthakrishnan – Nature Reviews Gastroenterology and Hepatology

Animal experiments
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch – PNAS

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine – Leore T. Geller – Science

Increased weight gain by C-section: Functional significance of the primordial microbiome – Keith A. Martinez II – Science Advances

Epicutaneous Tolerance Induction to a Bystander Antigen Abrogates Colitis and Ileitis in Mice – David Dunkin – Inflammatory Bowel Diseases

Dietary fatty acids control the species of N-acyl-phosphatidylethanolamines synthesized by therapeutically modified bacteria in the intestinal tract – Noura S Dosoky – ACS Infectious Diseases

In Vitro Response of Rumen Microbiota to the Antimethanogenic Red Macroalga Asparagopsis taxiformis – Lorenna Machado – Microbial Ecology

Host effects on microbiota community assembly – Kathrin Näpflin – Journal of Animal Ecology
In bumblebees!

Animal microbiome
Comprehensive skin microbiome analysis reveals the uniqueness of human-associated microbial communities among the class Mammalia Ashley Anne Ross – bioRxiv

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring – Amy Apprill – mSystems
Drones were involved.

The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function – Carolina Ramirez – Frontiers in Microbiology

A Novel Lactobacilli-Based Teat Disinfectant for Improving Bacterial Communities in the Milks of Cow Teats with Subclinical Mastitis – Jie Yu – Frontiers in Microbiology

Amplicon sequencing of bacterial microbiota in abortion material from cattle – Sara Vidal – Veterinary Research

Plant, root, and soil microbiome
Book: Soil Biological Communities and Ecosystem Resilience – Editors Martin Lukac, Paola Grenni, Mauro Gamboni
Multiple articles of interest.

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities – Eric R. Hester – bioRxiv

Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities – Xiaoyan Tian – Frontiers in Plant Science

Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3 – Sumera Yasmin – Frontiers in Microbiology

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants – Dominik K Großkinsky – Experimental Botany

Gaining Insight into Plant Responses to Beneficial and Pathogenic Microorganisms Using Metabolomic and Transcriptomic Approaches – Fernando Matías Romero – Metabolic Engineering for Bioactive Compounds

Water and extremophile microbiome
Globally Important Haptophyte Algae Use Exogenous Pyrimidine Compounds More Efficiently than Thiamin – Magdalena A. Gutowskaa – mBio

Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom – Jing-YunSun – Marine Environmental Research

Built environment
Biodegradation of tetracycline antibiotics in A/O moving-bed biofilm reactor systems – Han-Yu Chen – Bioprocess and Biosystems Engineering

Food microbiology
Interindividual Variability in Metabolism of [6]-Shogaol by Gut Microbiota – Pei Wang – Journal of Agricultural and Food Chemistry

Microbial technology
Programmed Assembly of Pressure Sensors Using Pattern-Forming Bacteria – Yangxiaolu Cao – Nature Biotechnology
Press: Three words: Synthetic gene circuit. Self-assembling bacteria build pressure sensor – Andrew Silver – The Register

Probiotics / prebiotics / antibiotics
Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota – Richard Y. Wu – Microbiome

Review: Antibiotics and specialized metabolites from the human microbiota – Walaa K. Mousa – Natural Product Reports

Phages and viruses
Moderate-Throughput Identification and Comparison of Campylobacter-Infecting Bacteriophages – Tylor J. Johnson – bioRxiv

Review: Innate Viral Receptor Signaling Determines Type 1 Diabetes Onset – Zachary J. Morse – Frontiers in Endocrinology

Bioinformatics
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data – Masanori Kakuta – International Journal of Molecular Sciences

Microbes in the news
Hibernating ribosomes help bacteria survive – Saint Louis University – Science Daily
Paper: The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus – Donna Matzov – Nature Communications

A century-old vaccine vial sheds light on one of medicine’s enduring mysteries – Helen Branswell – STAT News

Predatory bacteria-the quest for a new class of antibiotics – Phys.org

Mind the Gut: Copenhagen Exhibition Explores Bacteria and Feelings – Clara Rodríguez Fernández – Labiotech.eu

Gut Love: Bacteria, Love and Immunology Intersect at Esther Klein Gallery Exhibit – PRWeb

How mouldy mushrooms and frog spawn have been turned into art on Spring Bank – Amgus Young – Hull Daily Mail

Microbes on the market
Kaleido Biosciences and CoreBiome Partner to Accelerate Microbiome Therapeutic Development – Business Wire

Tiffany’s non-microbiology picks
The rise and fall and rise again of 23andMe – Erika Check Hayden – Nature

The future of DNA sequencing – Eric D. Green – Nature

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August 3, 2017

The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature

June 25, 2017

Lots of interesting pre-prints in this post that might be worth following! Also a blog post on some cool science art with kombucha, as well as a lot of articles on rhizosphere-microbe interactions.

Events and jobs

Research Opportunities in Molecular Microbiology – Washington University in St. Louis

PhD scholarship in Metagenomics analysis and systems biology – Danmarks Tekniske Universitet

General microbiome

Microbiome yarns: microbial forensics for auditing provenance in global food chains – Timmis et al. – Microbial Biotechnology

Adjuncts and alternatives in the time of antibiotic resistance and in-feed antibiotic bans – Brüssow – Microbial Biotechnology

Human gut microbiome

Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination – Erickson et al. – bioRXiv

Chemical transformation of xenobiotics by the human gut microbiota – Koppel et al. – Science

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer – Purcell et al. – bioRXiv

Animal microbiome

Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife – Thomas et al. – bioRXiv

 

Plant, root, and soil microbiome

Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore – Pangesti et al. – FEMS Microbiology Ecology

Bioelectrochemical approach for control of methane emission from wetlands – Liu et al. – Bioresource Technology

The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks – Duke et al. – BMC Genomics

Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer – Carro et al. – International Journal of Systematic and Evolutionary Microbiology

Synthesis and Secretion of Isoflavones by Field-Grown Soybean – Sugiyama et al. – Plant Cell Physiology

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage – Qiao et al. – Scientific Reports

Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth -Promoting Rhizobacterium with Antifungal Activity – Wang et al. – Genome Anouncements

Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species – Haruna et al. – Microbial Ecology

Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome – García-Gonzalez et al. – Ecotoxicology and Environmental Safety

Water and extremophile microbiome

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs – Campbell et al. – Environmental Microbiology

Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters – Lesaulnier et al. – bioRXiv

Techniques

Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model – Anscombe et al. – bioRXiv

Microbes in the news

Do Probiotics Really Work? – Ferris Jabr – Scientific American

Fungi and bacteria team up in dental plaque – Evans – LabRoots

Scientists spy on the secret inner life of bacteria – Saey – Science News

Biofilms: The eradication has begun – McGill University Health Centre – Science Daily

Bacteria and Mental Health: Gut Bacteria Linked to Bipolar Disorder – Villamil – Medical News Bulletin

The Kombucha Craze Steps into Art and the Science of the Microbiome – Fernández – Labiotech

Microbes on the market

Global Microbiome Drugs Industry Market Research Report 2017 – Medgadget

June 22, 2017

Effects of weight loss treatment on gut microbiota and serum metabolites, mouse gut microbiota can alter visceral sensitivity, a review discussing the microbiota’s ability to shape the maternal immune system.

Pregnancy and early life

Review: The unique immunological and microbial aspects of pregnancy – Gil Mor – Nature Reviews Immunology

Human oral microbiome

Review: Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review – Gloria Inés Lafaurie – Journal of Periodontology

Human gut microbiome

Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome – S Mizuno – Digestion

Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests – Francesca Borgo – PLOS ONE

Animal experiments

Fructo-oligosaccharides and intestinal barrier function in a methionine–choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS ONE

Microbiota regulates visceral pain in the mouse – Pauline Luczynski – eLife

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle – Milton Thomas – bioRxiv

Animal microbiome

Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut – Angela Kruse – PLOS ONE

Plant, root, and soil microbiome

Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere – Qing-Lin Chen – Environmental Science & Technology

Water and extremophile microbiome

Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-l-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2 – Di Huang – Applied Microbiology and Biotechnology

Longitudinal variation of microbial communitiesin benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams – Ze Ren – Freshwater Science

Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite – Biwin A An – Frontiers in Microbiology

Phages and viruses

Viral and Bacterial Communities of Colorectal Cancer – Geoffrey D Hannigan – bioRxiv

Plasmids, Viruses, And Other Circular Elements In Rat Gut – Tue Sparholt Jørgensen – bioRxiv

Bioinformatics

The metagenomic data life-cycle: standards and best practices – Petra ten Hoopen – GigaScience

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies – Ludovic Mallet – Bioinformatics

Metabolomics

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention – Ruixin Liu – Nature Medicine

Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease – Robert A Quinn – American Journal of Respiratory and Critical Care Medicine

Coupling targeted and untargeted mass spectrometry for metabolome-microbiome-wide association studies of human fecal samples – Alexey V Melnik – Analytical Chemistry

Techniques

Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering – Maria Sardi – FEMS Yeast Research

Different amplicon targets for sequencing-based studies of fungal diversity – Francesca De Filippis – Applied and Environmental Microbiology

Microbes in the news

Modified viruses deliver death to antibiotic-resistant bacteria – Sara Reardon – Nature

Microbes on the market

EnteroBiotix raises £500k in first round of equity funding – Philip Gates – Insider.co.uk

Microbiotica To Present At Microbiome Drug Development Summit – BioSpace

Bacteria art

MIT Researchers Use Light-Illuminated Bacteria to Make ‘Living’ Pictures – Kristin Fawcett – Mental Floss

The world’s art is under attack—by microbes – Kate Baggaley – Popular Science

Science, publishing, and career

Editorial: Don’t let Europe’s open-science dream drift – Nature

June 1st, 2017

Another day of a short digest.   Enjoy the beautiful pictures demonstrating the use of bacteria in art!

Events and jobs

ASM Microbe 2017, June 1-5th in New Orleans

Gut microbiome

Recovery of ethanol-induced Akkermansia muciniphila depletion ameliorates alcoholic liver disease – Christoph Grander – BMJ

Bioinformatics

BioSharing: Harnessing Metadata Standards For The Data Commons – Susanna-Assunta Sansone – BioRXiv

Microbial communities

Recipient-Biased Competition For A Cross-Fed Nutrient Is Required For Coexistence Of Microbial Mutualists – Alexandra L. McCully – BioRXiv

Microbes in Art

Researchers Create Color Images With Bacteria
Scientists teach E.coli bacteria to ‘draw’. Bacteria draws Mario

May 11, 2017

Gram-negative gut bacteria and Toll-like receptor 4 linked to stimulation of cerebral cavernous malformations, suppression of a single gene by the microbiota promotes T cell survival in mice, quorum sensing negatively regulates toxin production in insect-associated bacteria and may facilitate stable colonization.

General microbiome

Lactobacillus plantarum producing a Chlamydia trachomatis antigen induces a specific IgA response after mucosal booster immunization – Katarzyna Kuczkowska – PLoS ONE

Human oral microbiome

The dental calculus metabolome in modern and historic samples – Irina M Velsko – bioRxiv

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico – Tasha M Santiago-Rodriguez – PeerJ

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation – M Angelo – Journal of Dental Research

Human gut microbiome

Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis – Sudarshan Paramsothy – Journal of Crohn’s and Colitis

Significantly higher faecal counts of the yeasts candida and saccharomyces identified in people with coeliac disease – Joanna Harnett – Gut Pathogens

Research Highlight: Tooling up for microbiota research – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Review: The gut microbiota: a key factor in the therapeutic effects of (poly)phenols – Juan Carlos Espín – Biochemical Pharmacology

Animal experiments

* Endothelial TLR4 and the microbiome drive cerebral cavernous malformations – Alan T Tang – Nature

* Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor – Raymond Soto – PNAS

Bifidobacterium adolescentis IM38 ameliorates high-fat diet-induced colitis in mice by inhibiting NF-κB activation and lipopolysaccharide production by gut microbiota – Su-Min Lim – Nutrition Research

Tyrosine kinase inhibitors of Ripk2 attenuate bacterial cell wall-mediated lipolysis, inflammation and dysglycemia – Brittany M Duggan – Scientific Reports

Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota – Da Zhou – Scientific Reports

Animal microbiome

* Quorum Sensing Attenuates Virulence in Sodalis praecaptivus – Shinichiro Enomoto – Cell Host & Microbe

The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota – Heiko Vogel – Nature Communications

Plant, root, and soil microbiome

Antibacterial producing actinomycetes from Extra Andean Patagonia – M S Vela Gurovic – Journal of Arid Environments

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis – Z Song – Weed Research

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil – Ahmed Elhady – PLoS ONE

Review: Plant-insect-pathogen interactions: a naturally complex ménage à trois – Flávia P Franco – Current Opinion in Microbiology

Review: CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production: A Review – Anne Anderson – Journal of Agricultural and Food Chemistry

The phosphotransferase system gene ptsi in Bacillus cereus regulates expression of soda2 and contributes to colonization of wheat roots – Tantan Gao – Research in Microbiology

Water and extremophile microbiome

Review: Microbial processes driving coral reef organic carbon flow – Cynthia B Silveira – FEMS Microbiology Reviews

Diversity of biocrust-forming cyanobacteria in a semiarid gypsiferous site from Central Spain – Concha Cano-Díaz – bioRxiv

Probiotics/prebiotics

Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: a Pilot Study in Patients With Irritable Bowel Syndrome – Maria Ines Pinto-Sanchez – Gastroenterology

Bioinformatics

dbOTU3: A new implementation of distribution-based OTU calling – Scott W Olesen – PLoS ONE

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads – Thomas Nordahl Petersen – PLoS ONE

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes – Sheng-Yong Niu – Briefings on Bioinformatics

Techniques

Review: Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions – Ying-Ning Ho – WIREs Systems Biology and Medicine

Live-Cell Nanoscopy in Antiadhesion Therapy – Joan A Geoghegan – Trends in Microbiology

Low concentration DNA extraction and recovery using a silica solid phase – Constantinos Katevatis – PLoS ONE

More microbes

When more is less: Emergent suppressive interactions in three-drug combinations – Casey Beppler – BMC Microbiology

Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli – Benedikt von Bronk – PLoS Biology

Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast – Ali R Awan – Nature Communications

Microbes in the news

Cosmetics: The next microbiome frontier – Marc S Reisch – Chemical and Engineering News

A defence mechanism that can trap and kill TB bacteria – Science Daily

Is IBS All In Your Mind? New Study Hints at Close Ties Between the Brain and the Gut – Jessica Wapner – Newsweek

Bacteria art

Scientists ‘paint’ with bacteria, create microbial masterpieces – Tom Ensey – wistv.com

April 27, 2017

An exploration of fish as an alternative to mice for models of host-microbe interactions, a review on what we can learn from Bacteroides about the gut micriobiome, a news story on successful phage therapy for a multi drug resistant infection.

Human oral microbiome

The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals – Liam Shaw – bioRxiv

Human gut microbiome

* Review: An insider’s perspective: Bacteroides as a window into the microbiome – Aaron G Wexler – Nature Microbiology

Gut Microbiota: Small Molecules Modulate Host Cellular Functions – Jacob M. Luber – Current Biology

Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis – Tzipi Braun – Scientific Reports

Animal experiments

Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice – Hiroko Kaikiri – International Journal of Food Sciences and Nutrition

Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation – Chris Flemming – Microbiome

Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction – Shiran Gerassy-Vainberg – Gut

Animal microbiome

Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases – José de la Fuente – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Review: Managing the plant microbiome for biocontrol fungi: examples from Hypocreales – Ryan M Kepler – Current Opinion in Microbiology

Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China – Yulu Tang – Environmental Science: Processes & Impact

Water and extremophile microbiome

The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions – Michael D Lee – The ISME Journal

Bringing methanotrophy in rivers out of the shadows – Felicity Shelley – Limnology and Oceanography

Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community – Andrea Di Cesare – Environmental Pollution

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production – R Kanniah Goud – Bioresource Technology

Probiotics/prebiotics

Perspective: Next-generation probiotics: the spectrum from probiotics to live biotherapeutics – Paul W O’Toole – Nature Microbiology

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Bioinformatics

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments – Arghya Mukherjee – Scientific Reports

Techniques

Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry: non-invasive diagnostics in paediatric inflammatory bowel disease – Nora van Gaal – Journal of Breath Research

Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A Lescak – Journal of Bacteriology

Synthetic and analytical strategies for the quantification of phenyl-γ-valerolactone conjugated metabolites in human urine – Nicoletta Brindani – Molecular Nutrition & Food Research

More microbes

Species ecological similarity modulates the importance of colonization history for adaptive radiation – Jiaqi Tan – International Journal of Organic Evolution

Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells – Yosuke Tashiro – Frontiers in Microbiology

Microbes in the news

Phage Therapy Saves Patient from Drug-Resistant Microbes – Genetic Engineering & Biotechnology News

Chronic fatigue syndrome linked to imbalanced microbiome – EurekAlert

Komodo Dragon Blood Could Become Tool in Fight Against Bacteria – Elizabeth Pratt – Healthline

Researchers move closer to preventing frost damage in vineyards by managing bacteria on the vines – Greg Northcutt – Western FarmPress

Underwater volcano eruptions allow new bacteria to take over seafloor – Lisa-Ann Lee – New Atlas

Microbes on the market

Taconic Biosciences Expands Microbiome Product and Service Platform – GlobeNewswire

Bacteria and art

This Art Exhibition Is Made From Bacteria, Live Insects And Human Sweat – Ryan F Mandelbaum – Gizmodo Australia

Art Made with CRISPR Aims to Raise Awareness of Antibiotic Resistance – Clara Rodríguez Fernández – Labiotech.eu

Amy’s non-microbiology picks

Microscopy: A larger palette for biological imaging – Charles H Camp Jr – Nature