July 20, 2017

A study of chemical interactions between fungi and ants by imaging mass spectrometry, characterization of forty-six Arthrobacter phages, influence of fruit fungal infestation on vertebrate fruit preferences.

Human gut microbiome

The essential genomic landscape of the commensal Bifidobacterium breve UCC2003 – Lorena Ruiz – Scientific Reports

Animal experiments

Fat binding capacity and modulation of the gut microbiota both determine the effect of wheat bran fractions on adiposity – Francesco Suriano – Scientific Reports

Effects of dietary supplementation with two alternatives to antibiotics on intestinal microbiota of preweaned calves challenged with Escherichia coli K99 – Yanliang Bi – Scientific Reports

Animal microbiome

Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants – Cristopher A Boya P – Scientific Reports

Plant, root, and soil microbiome

Population structure of an orchid mycorrhizal fungus with genus-wide specificity – M P Ruibal – Scientific Reports

Water and extremophile microbiome

Review: Cultivation of microbes from the deep-sea environments – Zenghu Zhang – Deep Sea Research Part II: Topical Studies in Oceanography

Food microbiology

Fungal infestation boosts fruit aroma and fruit removal by mammals and birds – Josep E Peris – Scientific Reports

Pre-print: Resilience mechanisms of small intestinal lactobacilli to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – bioRxiv

Probiotics/prebiotics

Dietary lipid content reorganizes gut microbiota and probiotic L. rhamnosus attenuates obesity and enhances catabolic hormonal milieu in zebrafish – Silvia Falcinelli – Scientific Reports

Phages and viruses

Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages – Karen K Klyczek – PLOS ONE

Pre-print: Isolation and characterization of BpL1, a broad acting lytic bacteriophage against Brucella – Vimlesh Gupta – bioRxiv

Microbes in the news

Bac-for good: Bacteria passed between generations benefits you more than others – Phys.org

Microbes on the market

Verily Releases Bacteria-Infected Mosquitoes To Fight Zika And Dengue: Is Wolbachia Technique Safe For Humans? – Allan Adamson – Tech Times

Science, career, and publishing

Climate scientists flock to France’s call – Declan Butler – Nature

July 6, 2017

The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

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 9, 2017

Effects of prebiotics on body fat and gut microbiota of children, a review on the phage community of the human gut, a metabolomics study of the rodent brain to analyze the influence of gut bacteria.

Pregnancy and early life

Clostridium difficile colonization and/or infection during infancy and the risk of childhood allergic diseases – Sun Hwa Lee – Korean Journal of Pediatrics

Human vaginal microbiome

Association of vaginal dysbiosis and biofilm with contraceptive vaginal ring biomass in African women – Liselotte Hardy – PLOS ONE

Human gut microbiome

Age-Related Changes in the Composition of Gut Bifidobacterium Species – Kumiko Kato – Current Microbiology

Review: The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS – Heidi M Staudacher – Gut

Animal experiments

Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut – H J Wisselink – Poultry Science

Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls – Jean A Hall – PLOS ONE

The artificial sweetener acesulfame potassium affects the gut microbiome and body weight gain in CD-1 mice – Xiaoming Bian – PLOS ONE

Effects of different n-6 to n-3 polyunsaturated fatty acids ratio on reproductive performance, fecal microbiota and nutrient digestibility of gestation-lactating sows and suckling piglets – Jia Yin – Animal Science Journal

Nucleotide-binding oligomerization domain-containing protein 2 (Nod2) modulates T1DM susceptibility by gut microbiota – Yang-yang Li – Journal of Autoimmunity

Plant, root, and soil microbiome

Kinetic analysis of aerobic biotransformation pathways of a perfluorooctane sulfonate (PFOS) precursor in distinctly different soils – Lilan Zhang – Environmental Pollution

Plant breeding goes microbial – Zhong Wei – Trends in Plant Science

Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover – Sebastian Elgueta – Journal of Environmental Science and Health, Part B

Probiotics/prebiotics

Prebiotic Reduces Body Fat and Alters Intestinal Microbiota in Children With Overweight or Obesity – Alissa C Nicolucci – Gastroenterology

Phages and viruses

Review: The Human Gut Phage Community and Its Implications for Health and Disease – Pilar Manrique – Viruses

Metabolomics

Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism – J R Swann – Journal of Pharmaceutical and Biomedical Analysis

More microbes

Multi-locus and ultra-long amplicon sequencing approach to study microbial diversity at species level using the MinION(TM) portable nanopore sequencer – Alfonso Benítez-Páez – bioRxiv

ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species – Thomas M Nero – bioRxiv

Microbes in the news

Microbiology: Many forks make light work – ScienceDaily

Fungi awake bacteria from their slumber – ScienceDaily

Microbes on the market

Seres Completes Enrollment for SER-287 Phase 1b Clinical Trial in Patients with UC – Daniela Semedo – IBD News Today

June 8, 2017

Modeling colon physiology to predict microbiota growth, a review of plant-bacteria genome-wide association studies, sporeforming bacteria isolated from beer.

General microbiome

Review: Systematic Review: The Impact of Cancer Treatment on the Gut and Vaginal Microbiome in Women With a Gynecological Malignancy – Ann Muls – International Journal of Gynecological Cancer

Pregnancy and early life

Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women – Luisa F Gomez-Arango – Scientific Reports

Human gut microbiome

Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses – Tal Korem – Cell Metabolism

* Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis – Jaeyun Sung – Nature Communications

The gut metagenome changes in parallel to waist circumference, brain iron deposition and cognitive function – Gerard Blasco – Journal of Clinical Endocrinology and Metabolism

Gut microbiota composition in relation to the metabolic response to 12-week combined polyphenol supplementation in overweight men and women – J Most – European Journal of Clinical Nutrition

Complete genome sequence of Clostridium perfringens CBA7123 isolated from a faecal sample from Korea – Yeon Bee Kim – Gut Pathogens

Review: The Research Progress on Intestinal Stem Cells and Its Relationship with Intestinal Microbiota – Qihang Hou – Frontiers in Immunology

Review: Gut microbiota: Intestinal fungi fuel the inflammatory fire in alcoholic liver disease – Hugh Thomas – Nature Reviews Gastroenterology and Hepatology

* Effect of water flow and chemical environment on microbiota growth and composition in the human colon – Jonas Cremer – PNAS

Animal experiments

Gut-Associated Lymphoid Tissue: A Key Tissue Inside the Mucosal Immune System of Hens Immunized with Escherichia coli F4 – Maria F Peralta – Frontiers in Immunology

Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles – Angela B Javurek – Scientific Reports

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

In Vitro Study of the Metabolic Characteristics of Eight Isoquinoline Alkaloids from Natural Plants in Rat Gut Microbiota – Chi-Yu He – Molecules

Animal microbiome

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

Plant, root, and soil microbiome

Applying community ecological theory to maximize productivity of cultivated biocrusts – Matthew A Bowker – Ecological Applications

Is soil microbial diversity affected by soil and groundwater salinity? Evidences from a coastal system in central Italy – Loredana Canfora – Environmental Monitoring and Assessment

* Review: Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach – Claudia Bartoli – Frontiers in Plant Science

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits – Juan E Pérez-Jaramillo – The ISME Journal

Water and extremophile microbiome

Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms – Hera Karayanni – Microorganisms

Identifying the core seed bank of a complex boreal bacterial metacommunity – Clara Ruiz-González – The ISME Journal

Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20oC to 79oC – Stephen M J Pollo – bioRxiv

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations – Zainab Abdulrahman Beiruti – bioRxiv

Food microbiology

Evolution of class 1 integrons: Mobilization and dispersal via food-borne bacteria – Timothy M Ghaly – PLOS ONE

* Sporeforming bacteria in beer: Occurrence, diversity, presence of hop resistance genes and fate in alcohol-free and lager beers – Allan R G Munford – Food Control

Probiotics/prebiotics

Probiotic Bifidobacterium bifidum G9-1 attenuates 5-fluorouracil-induced intestinal mucositis in mice via suppression of dysbiosis-related secondary inflammatory responses – Shinichi Kato – Clinical and Experimental Pharmacology and Physiology

Review: The Role of the Microbiome and the use Of Probiotics in Gastrointestinal Disorders in Adults in the Asia-Pacific Region – Uday C Goshal – Journal of Gastroenterology and Hematology

Phages and viruses

Evolution of selective-sequencing approaches for virus discovery and virome analysis – Arvind Kumar – Virus Research

Techniques

Review: Novel approaches in function-driven single-cell genomics – Devin F R Doud – FEMS Microbiology Reviews

Fast Method for the determination of Short-chain-length Polyhydroxyalkanoates (scl-PHAs) in Bacterial Samples by In Vial-Thermolysis (IVT) – Federica Abbondanzi – New Biotechnology

Microbes in the news

Are Pets the New Probiotic? – Richard Schiffman – The New York Times

Gut bacteria could protect cancer patients and pregnant women from Listeria, study suggests – EurekAlert

Impact of protective bacteria linked to infection route, study finds – EurekAlert

May 25, 2017

A review on the “vine and wine” microbiomes, a fungus that can infect and kill mosquitos through interaction with the gut microbiota, an introduction to the viruses of coral reefs.

General microbiome

The Role of Microbiota and Immunobiotics in Granulopoiesis of Immunocompromised Hosts – Susana Salva – Frontiers in Immunology

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

Human gut microbiome

TGF-β in inflammatory bowel disease: a key regulator of immune cells, epithelium, and the intestinal microbiota – Sozaburo Ihara – Journal of Gastroenterology

Review: Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions – Mark N Read – Frontiers in Immunology

Review: Genes, emotions and gut microbiota: The next frontier for the gastroenterologist – Arturo Panduro – World Journal of Gastroenterology

Animal experiments

Modulation of the gut microbiota impacts non-alcoholic fatty liver disease: a potential role for bile acids – Aafke WF Janssen – Journal of Lipid Research

Antimicrobial peptides extend lifespan in Drosophila – Gerrit Loch – PLOS ONE

Animal microbiome

Bacterial diversity of cosmopolitan Culex pipiens and invasive Aedes japonicus from Germany – Sina Zotzmann – Parasitology Research

Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria – Jan Hubert – Microbial Ecology

* Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality – Ge Wei – PNAS

Plant, root, and soil microbiome

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships – Isabelle Laforest-Lapointe – Nature

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

Review: From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept – Ignacio Belda – Frontiers in Microbiology

Phages and viruses

Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations – Maria A Bautista – Viruses

Review: Virus–host interactions and their roles in coral reef health and disease – Rebecca Vega Thurber – Nature Reviews Microbiology

Metabolomics

Inter-individual Recovery of the Microbiota and Metabolome Over Time Following Fecal Microbiota Transplantation in Patients with Recurrent Clostridium difficile Infection – Anna M Seekatz – bioRxiv

Metabolic profiling by gas chromatography-mass spectrometry of energy metabolism in high-fat diet-fed obese mice – Daxesh P Patel – PLOS ONE

Review: Livestock metabolomics and the livestock metabolome: A systematic review – Seyed Ali Goldansaz – PLOS ONE

Techniques

Review: A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia – Antonella Succurro – Journal of Bacteriology

More microbes

Decoding and reprogramming fungal iterative nonribosomal peptide synthetases – Dayu Yu – Nature Communications

Microbes in the news

Companies Pursue Diagnostics that Mine the Microbiome – Andrea Anderson – The Scientist

The fungal microbiome contributes to alcohol-induced liver damage in mice – EurekAlert

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