December 12, 2017

Today we have quite a long Microbiome Digest, with many papers in Human Gut , Water, Plant/Soil Microbiome and Probiotics Sections. Among many interesting papers today, check an essay by Stilianos Louca “Probing the metabolism of microorganisms” and a perspective by Cesar de la Fuente “Neuromicrobiology: how microbes influence the brain “.

Events and jobs

LabTechnician/Microbiology, Kalamazoo, MI 49001

Instructional Associate- Microbiology, Fort Worth, TX

Visiting Professor (Part Time) Microbiology Jacksonville, FL Campus

Assistant Professor in Food Microbiology/Safety, Edinburg, Texas (US)

General microbiome

Probing the metabolism of microorganisms – Stilianos Louca – Science

Pregnancy and early life

Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants – Steven A. Frese – mSphere

 

 

Human nearly-sterile sites 

Perspective: Neuromicrobiology: how microbes influence the brain – Cesar de la Fuente-Nunez – ACS Chemical Neuroscience

Assessment of the comparability of CLSI, EUCAST and Stokes antimicrobial susceptibility profiles for Escherichia coli uropathogenic isolates – C O’Halloran – British Journal of Biomedical Science

Human gut microbiome

Gut epithelial vitamin D receptor regulates microbiota-dependent mucosal inflammation by suppressing intestinal epithelial cell apoptosis – Lei He – Endocrinology

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection – J. Jalanka – Alimentary Pharmacology & Therapeutics

Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis – Yuan Tian – The Journal of Nutritional Biochemistry

Changes in the gut microbiota composition and the plasma ghrelin level in patients with Helicobacter pylori-infected patients with eradication therapy – Hidetaka Yanagi – Gut Microbiota

Perspectives: Gut microbiota–derived short-chain fatty acids and kidney diseases – Lingzhi Li –  Drug Design, Development and Therapy

Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – bioRxiv

Changes in the gut microbiota composition and the plasma ghrelin level in patients with Helicobacter pylori-infected patients with eradication therapy  – Hidetaka Yanagi – Gut Microbiota

Enteric Microbiome Markers as Early Predictors of Clinical Outcome in Allogeneic Hematopoietic Stem Cell Transplant: Results of a Prospective Study in Adult Patients – Nicasio Mancini – Open Forum Infectious Diseases

The long-term effects of faecal microbiota transplantation for gastrointestinal symptoms and general health in patients with recurrent Clostridium difficile infection – J. Jalanka – Alimentary Pharmacology & Therapeutics

Gut Microbiota and Host Juvenile Growth – Martin Schwarzer – Calcified Tissue International

Disruption of the Gut Ecosystem by Antibiotics – Mi Young Yoon – Yonsei Med Journal

Animal experiments 

Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice – Kirsty Brown – Gut Microbes

Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens – Alexander Yitbarek – FEMS Microbiology Ecology

Comparision of the intestinal musocal microbiota in dogs diagnosed with idiopathic inflamatorz bowel disease and dogs with food/responsive diarrhea before and after treatement – K. Kalenyak – FEMS Microbiology Ecology

Lysine Restriction Affects Feed Intake and Amino Acid Metabolism via Gut Microbiome in Piglets – Yin J – Logo Cellular Physiology and Biochemistry

Animal microbiome

SPM-1-producing Pseudomonas aeruginosa ST277 clone recovered from microbiota of migratory birds – Willames M.B.S.Martins – Diagnostic Microbiology and Infectious Disease

Plant, root, and soil microbiome

Ravibacter arvi gen. nov., sp. nov., isolated from farmland soil during development of new culture techniques – Dhiraj Kumar Chaudhary – International Journal of Systematic and Evolutionary Microbiology

Mangrovitalea sediminis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from mangrove sediment – Hu Liao – International Journal of Systematic and Evolutionary Microbiology

Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients – Dajana Radujković – FEMS Microbiology Ecology

Plant–soil feedbacks promote negative frequency dependence in the coexistence of two aridland grasses – Y. Anny Chung – Proceedings of the Royal Society B

Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against root rot causing phytopathogens – Inés Martínez-Raudales – Standards in Genomic Sciences

Rhizosphere Microorganisms: Application of Plant Beneficial Microbes in Biological Control of Weeds – Satyavir S. Sindhu – Microorganisms for Green Revolution

Shifts in bacterial and fungal diversity in a paddy soil faced with phosphorus surplus – Ming Liu – Biology and Fertility of Soils

Water and extremophile microbiome

Strategies and ecological roles of algicidal bacteria – Nils Meyer – FEMS Microbiology Reviews

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations – Sarahi L. Garcia – ISME Journal

The predictability of a lake phytoplankton community, from hours to years – Mridul K. Thomas – bioRxiv

Oceaniglobus indicus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from surface seawater –  Jianyang Li –  International Journal of Systematic and Evolutionary Microbiology

Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota – Wei Qin – International Journal of Systematic and Evolutionary Microbiology

A new niche for anoxygenic phototrophs as endoliths – Daniel Roush – Applied and Environmental Microbiology

Quantitative Analysis of O2 and Fe2+ Profiles in Gradient Tubes for Cultivation of Microaerophilic Iron(II)-Oxidizing Bacteria – U. Lueder – FEMS Microbiology Ecology

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota – Lin-Xing Chen –  ISME Journal

Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes – Pacifica Sommers – FEMS Microbiology Ecology

Linking bacterial community structure to advection and environmental impact along a coast-fjord gradient of the Sognefjord, western Norway – Julia E.Storesund – Progress in Oceanography

Bacterial Succession on Sinking Particles in the Ocean’s Interior -Erik A. Pelve – Frontiers in Microbiology

Growth of Nitrosococcus-Related Ammonia Oxidizing Bacteria Coincides with Extremely Low pH Values in Wastewater with High Ammonia Content – Alexandra Fumasoli – Environmental Science & Technolology

Characteristics of Bacterial Communities in Cyanobacteria-Blooming Aquaculture Wastewater Influenced by the Phytoremediation with Water Hyacinth – Qing Zhou – Water

Biodegradation of phenol by cold-adapted bacteria from Antarctic soils – Gillian Li Yin Lee – Polar Biology

Built environment 

Bacterial community evolutions driven by organic matter and powder activated carbon in simultaneous anammox and denitrification (SAD) process – Cheng-Hao Ge – Bioresource Technology

Food microbiology

The Role of Oligosaccharides in Host-Microbial Interactions for Human Health –  Sarah Ross – Journal of Clinical Gastroenterology

Probiotics / prebiotics

An in vivo assessment of the cholesterol-lowering efficacy of Lactobacillus plantarum ECGC 13110402 in normal to mildly hypercholesterolaemic adults – Adele Costabile – PLOS One

Can Probiotics Reduce Diarrhea and Infant Mortality in Africa?: The Project of a Pilot Study – Mario Del Piano – Journal of Clinical Gastroenterology

Searching for the Perfect Homeostasis: Five Strains of Bifidobacterium longum From Centenarians Have a Similar Behavior in the Production of Cytokines –  Stefania Nicola – Journal of Clinical Gastroenterology

In Vitro Inhibition of Klebsiella pneumoniae by Lactobacillus delbrueckii Subsp. delbrueckii LDD01 (DSM 22106): An Innovative Strategy to Possibly Counteract Such Infections in Humans? – Luca Mogna – Journal of Clinical Gastroenterology

Protective Role of Postbiotic Mediators Secreted by Lactobacillus rhamnosus GG Versus Lipopolysaccharide-induced Damage in Human Colonic Smooth Muscle Cells –  Alessia Cicenia – Journal of Clinical Gastroenterology

In Vitro Activity of Lactobacillus fermentum LF5 Against Different Candida Species and Gardnerella vaginalis: A New Perspective to Approach Mixed Vaginal Infections? –  Francesca Deidda- Journal of Clinical Gastroenterology

Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review – Mahboube Ganji-Arjenaki – Journal of Cellular Physiology

Optimization of the quenching and extraction procedures for a metabolomic analysis of Lactobacillus plantarum – Qin Yang – Analytical Biochemistry

Phages and viruses

Internalization of a polysialic acid-binding Escherichia  colibacteriophage into eukaryotic neuroblastoma cells – Timo A. Leht – Nature Communication

The human respiratory virome after lung transplantation for COPD: A single centre, prospective, longitudinal study – A.B. Mitchell – Respiratory Medicine

Virome Capture Sequencing in Castleman Disease Identifies Associations with Herpesviridae Family Members but No Novel Viruses – Christopher Sheild Nabel – Blood

Bioinformatics

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation – Hyun Min Kang – Nature Biotechnology

CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences – Kristi Gdanetz – BMC Bioinformatics

Biotechnology

Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm – Matthew J Lee – Nature Chemical Biology

Engineering chemical interactions in microbial communities – Douglas J. Kenny – Chemical Society Reviews

Cyclic lipopeptide signature as fingerprinting for the screening of halotolerant Bacillus strains towards microbial enhanced oil recovery – Bárbara C. S. Farias – Applied Microbiology and Biotechnology

Techniques

Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model – Cedar L. Mitchell – PLOS Neglected Tropical Diseases

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation – John Beaulaurier – Nature Biotechnology

Microbes in the news 

Bacteria discovery in Antarctica prompts rethink of humanity’s search for alien life

When Lemur Families Cuddle, They Share Important Gut Bacteria

$3.9 million supports research to turn bacteria into biofuel producers

Bacteria and Art

Meet the Penn students using medical gauze and bacteria to create art for ‘speculative worlds’

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December 7, 2017

Meta-analysis of a collection of gut microbiome studies, characterization of two dandelion viruses, evaluation of an inclusive Research Education Community for engaging undergraduates in scientific research.

General microbiome

Bacterial social interactions and the emergence of community-intrinsic properties – Jonas Stenløkke Madsen – Current Opinion in Microbiology

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human gut microbiome

Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health – Yeong Yeh Lee – Journal of Paediatrics and Child Health

Animal experiments

Moving beyond microbiome-wide associations to causal microbe identification – Neeraj K Surana – Nature

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungus causes increased condensed tannins concentrations in shoots but decreased in roots of Lotus japonicus L – Zakaria M Solaiman – Rhizosphere

Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels – Jun Chen – Applied Soil Ecology

Multifarious plant growth promotion by an entomopathogenic fungus Lecanicillium psalliotae – C M Senthil Kumar – Microbiological Research

Water and extremophile microbiome

Pre-print: Optogenetics reprogramming of planktonic cells for biofilm formation – Aiguo Xia – bioRxiv

Phages and viruses

Pre-print: Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses – Humberto J Debat – bioRxiv

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells – Timo A Lehti – Nature Communications

Bioinformatics

Pre-print: Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals – Almut Heinken – bioRxiv

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses – Claire Duvallet – Nature Communications

Techniques

In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses – Ying Chen – PLOS ONE

More microbes

Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects – Fausto Almeida – Nature Communications

Microbes in the news

Lemur study highlights role of diet in shaping gut microbiome – Erin Mckenney – Phys.Org

What Bacteria Can Tell Us About Human Evolution – Tara C Smith – Quanta Magazine

Duke launches new microbiome center, reflecting popularity of microbiome studies – Sean Cho – Duke Chronicle

Study shows first extensive and stable microbiome remodeling via B. infantis in infants – Weber Shandwick – EurekAlert

Air-eating bacteria found in Antarctica – Cosmos

The Microbes Making Themselves at Home on the Space Station – Marina Koren – The Atlantic

Microbes on the market

Breakthrough Evidence on Vomaris Bioelectric Technology’s Impact on Wound Biofilm Infection – PR Newswire

Precision Driven Health and Orion Health release Microbiome report – Voxy

Worldwide microbiome drugs market is likely to grow substantially by 2022 – Digital Journal

Science, career, and publishing

How to Keep Students in Science – Howard Hughes Medical Institute

An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning – David I Hanauer – PNAS

Pre-print: Assessing the Landscape of U.S. Postdoctoral Salaries – Rodoniki Athanasiadou – bioRxiv

Editorial: Great mentoring is key for the next generation of scientists – Nature

Amy’s non-microbiology picks

Organocalcium-mediated nucleophilic alkylation of benzene – Andrew S S Wilson – Science

November 28, 2017

Identification of nitrite-oxidizing bacteria important for dark ocean carbon fixation, effects of antibiotic exposure to the maternal gut microbiota extend to offspring in mice and enhance colitis, a review on genome mining for natural products discovery.

Events and jobs

Postdoc position on biofilm-mediated co-evolution of industrial strains – Biologisk Institut, University of Copenhagen, Denmark

Human skin microbiome

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan – PLOS ONE

Human gut microbiome

Pre-print: Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean M Kearney – bioRxiv

Opinion: Human Gut Microbiome: Function Matters – Anna Heintz-Buschart – Trends in Microbiology

Review: The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review – Jinbing Bai – Supportive Care in Cancer

Animal experiments

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice – Anjelique F Schulfer – Nature Microbiology

Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model – Eikan Mishima – American Journal of Physiology, Renal Physiology

Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens – Luca Borrelli – Scientific Reports

Animal microbiome

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Plant, root, and soil microbiome

Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – bioRxiv

Water and extremophile microbiome

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation – Maria G Pachiadaki – Science

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation – Bingjian Cui – Journal of Environmental Sciences

Phages and viruses

Review: Viruses of archaea: Structural, functional, environmental and evolutionary genomics – Mart Krupovic – Virus Research

Bioinformatics

Review: Omics-based natural product discovery and the lexicon of genome mining – Henrique Machado – Current Opinion in Microbiology

More microbes

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris – Glenna J Kramer – BMC Genomics

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism – Cristian Botta – Scientific Reports

Microbes in the news

Researchers conduct novel wheat microbiome analysis under four management strategies – Phys.Org

Fertility clinics treat abnormal vaginal bacteria aiming to improve reproductive outcome – Medical Xpress

Microbe threat to Mars – Andrew Masterson – Cosmos

Flies’ Feet Can Spread Bacteria – Kerry Grens – The Scientist

Despite Their Tiny Genome, A Beetle’s Bacteria Pack A Big Punch – Julianna LeMieux – American Council on Science and Health

CRISPR Harnessed to Turn Bacteria into Microscopic Tape Recorders – Genetic Engineering & Biotechnology News

Bacteria hysteria

Warning: Those lipstick samples could be loaded with poop, investigation finds – Mandy Matney – Sacramento Bee

Science, career, and publishing

Pre-print: A design framework and exemplar metrics for FAIRness – Mark D Wilkinson – bioRxiv

November 21, 2017

A review discussing metabolic-flux dependent regulation in microbes, diversity of coral-associated viral communities, what an Antarctic fungus can tell us about astrobiology.

General microbiome

Pre-print: Extending species-area relationships (SAR) to diversity-area relationships (DAR)© – Zhanshan Ma – aRxiv

Beneficial microbiomes: Biodiversity and potential biotechnological applications for sustainable agriculture and human health – Ajar Nath Yadav – Journal of Applied Biology and Biotechnology

Pregnancy and early life

Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants – Anuradha Ravi – FEMS Microbiology Ecology

Human respiratory microbiome

Pre-print: Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children – Shu Mei Teo – bioRxiv

Human gut microbiome

Pre-print: A perturbation model of the gut microbiome’s response to antibiotics – Liam P Shaw – bioRxiv

Animal experiments

Pre-print: Within host selection for faster replicating bacterial symbionts – Ewa Chrostek – bioRxiv

Plant, root, and soil microbiome

Molecular characterization of Associative N2 fixing bacterium isolated from the roots of Finger millet (Eleusine coracana L.) and its interaction effects with microbial consortia on growth and yield – G B Santosha Gowda – Research Journal of Biotechnology

Significance of temperature and water availability for soil phosphorus transformation and microbial community composition as affected by fertilizer sources – Dasheng Sun – Biology and Fertility of Soils

Water and extremophile microbiome

Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile – Maria Eugenia Farias – PLOS ONE

Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring – Takafumi Kataoka – Archives of Microbiology

Microbes in space

Resistance of an Antarctic cryptoendolithic black fungus to radiation gives new insights of astrobiological relevance – Laura Selbmann – Fungal Biology

Phages and viruses

Pre-print: Coral-associated viral communities show high levels of diversity and host auxiliary functions – Karen D Weynberg – PeerJ

Biological Control of Pectobacterium carotovorum Via Specific Lytic Bacteriophage – Eman Marei – Journal of Basic and Applied Scientific Research

Bioinformatics

Book chapter: Chapter 1 – Metagenomics: A Paradigm Shift in Microbiology – Andrey V Mardanov – Metagenomics

More microbes

Review: Metabolic-flux dependent regulation of microbial physiology – Athanosios Litsios – Current Opinion in Microbiology

Microbes in the news

High-salt diet throws microbiome out of whack – Katharine Sanderson – Chemical & Engineering News

Rare Bacterial Taxa May Play Outsize Role in Soil Microbiome Structure, Study Suggests – Genome Web

Forsyth Institute researcher Floyd Dewhirst named as AAAS Fellow – EurekAlert

What makes soil, soil? Researchers find hidden clues in DNA – Phys.Org

Microbes on the market

PathoQuest Announces Formation of Scientific Advisory Board – Business Wire

November 17, 2017

Jobs and events

Lab Assistant – Microbiology, Dublin Ohio

General microbiome

Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications? – Chantal Villeneuve, Microbes and Infection

Human gut microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour, Microbiome

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks – Anubhav Das, Scientific Reports

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut – Natalya Yutin, Nature Microbiology

Fecal Transplantation for Treatment of Clostridium Difficile Infection in Elderly and Debilitated Patients – Tali Friedman-Korn, Digestive Diseases and Sciences

Myocardial infarction and gut microbiota: an incidental connection – Sepideh ZununiVahed, Pharmacological Research

Anxiety, Depression, and the Microbiome: A Role for Gut Peptides – Gilliard Lach, Neurotherapeutics

The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location – John P. Haran, Journal of Medical Microbiology

Human nearly-sterile sites

Risk of Subsequent Sepsis within 90 Days of a Previous Hospital Stay by Type of Antibiotic Exposure – James Baggs, Clinical Infectious Diseases

Human vaginal microbiome

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women – Supriya D. Mehta, Scientific Reports

Animal experiments

The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure – Eun Sung Jung, PLOS ONE

Acute Administration of the Nonpathogenic, Saprophytic Bacterium, Mycobacterium vaccae, Induces Activation of Serotonergic Neurons in the Dorsal Raphe Nucleus and Antidepressant-Like Behavior in Association with Mild Hypothermia – Philip H. Siebler, Cellular and Molecular Neurobiology

Maternal High Fat Diet and its Consequence on the Gut Microbiome: A Rat Model – Phyllis E. Mann, Gut Microbes

Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice – Alessandra Bragonzi, International Journal of Molecular Sciences

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis – Marion Darnaud, Gastroenterology

Animal microbiome

Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil – Andressa Zelenski de Lara Pinto, PLOS ONE

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li, PLOS ONE

Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study – Veronika Jílková, Soil Biology and Biochemistry

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola – Aubree J. Hill, EcoHealth

Plant, root, and soil microbiome

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils – Xian Xiao, Molecular Ecology

Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils – Gabriel Sigmund, Journal of Hazardous Materials

Epiphytic Bacteria Alter Floral Scent Emissions – Carola Helletsgruber, Journal of Chemical Ecology

In vitro bacterization of banana (Musa spp.) with native endophytic and rhizospheric bacterial isolates: Novel ways to combat Fusarium wilt – M. Kavino, European Journal of Plant Pathology

Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn, PeerJ

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert – Cristina Montiel-González, PeerJ

Entomopathogenic Fungi as Dual Control Agents against Both the Pest Myzus persicae and Phytopathogen Botrytis cinerea – Hwi-Geon Yun, Mycobiology

Glycomyces rhizosphaerae sp. nov., isolated from the root and rhizosphere soil of wheat (Triticum aestivum L.) – Wenchao Li, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation – G. Llorens-Blanch, Waste Management

Iron Chloride Flocculation of Bacteriophages from Seawater – Bonnie T. Poulos, Bacteriophages

Multi-Level Contact Oxidation Process Performance When Treating Automobile Painting Wastewater: Pollutant Removal Efficiency and Microbial Community Structures – Yufang Zhu, Water

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments – Brodie Sutcliffe, Microbial Ecology

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization? – Dave R. Clark, Global Ecology and Biogeography

Diversity of microbiota found in coffee processing wastewater treatment plant – Josiane Ferreira Pires, World Journal of Microbiology and Biotechnology

Food microbiology

Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions – M. Oliveira, Letters in Applied Microbiology

Bioinformatics

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities – Weizhi Song, PeerJ

Techniques

Significance estimation for large scale metabolomics annotations by spectral matching – Kerstin Scheubert, Nature

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) – Mette Myrmel, PLOS ONE

Developing selective media for quantification of multispecies biofilms following antibiotic treatment – Eva Vandeplassche, PLOS ONE

Microbes in the news

Microbiology: Bacteria disarm host-defence proteins – John D. MacMicking, Nature News and Views

Probiotics: Health boost or waste of cash? – Anne Allred, 5-ON-YOUR-SIDE

Cygnus Open for Business; Crew Unloading New Bacteria, Plant and Tech Studies – Mark Garcia, NASA blog

Bacteria Hysteria

Your supermarket is filled with germs — here are 7 facts that will make you dread grocery shopping –  Joanna Fantozzi, Insider

November 12, 2017

General microbiome

Rapid colonization of artificial endolithic uninhabited habitats – Charles S. Cockell, International Journal of Astrobiology

A bacterial pioneer produces cellulase complexes that persist through community succession – Sebastian Kolinko, Nature Microbiology

Endoglucanase and Xylanase Production by Chryseobacterium Species Isolated from Decaying Biomass – Asisipho Nkohla, Polish Journal of Environmental Studies

Human gut microbiome

Extended screening costs associated with selecting donors for fecal microbiota transplantation for treatment of metabolic syndrome-associated diseases – Laura J Craven, Open Forum Infectious Diseases

Fecal microbiota signatures of adult patients with different types of short bowel syndrome – Yuhua Huang, Gastroenterology

Association Between Small Intestinal Bacterial Overgrowth by Glucose Breath Test and Coronary Artery Disease – Andre Fialho, Digestive Diseases and Sciences

Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions – Jiayan Li, Microbial Ecology

Animal experiments

Transcriptomics-driven lipidomics (TDL) identifies the microbiome-regulated targets of ileal lipid metabolism – Anirikh Chakrabarti, npj Systems Biology and Applications

Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis – Yuan Tian, The Journal of Nutritional Biochemistry

Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish – Victor Schmidt, mSystems

Effect of partially replacing a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows – E. Castillo-Lopez, Journal of Applied Microbiology

How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota – Alyssa Bost, Molecular Ecology

Gut microbiomes and reproductive isolation in Drosophila – Philip T. Leftwich, PNAS

Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages – Shenzheng Zeng, PeerJ

Animal microbiome

FVD: The fish-associated virus database – Yaxin Chen, Infection, Genetics and Evolution

Bats host diverse parvoviruses as possible origin of mammalian dependoparvoviruses and source for bat–swine interspecies transmission –  Susanna K. P. Lau, Journal of General Virology

Forest canopy, water level, and biopesticide interact to determine oviposition habitat selection in Aedes albopictus – Christopher A. Binckley, Journal of Vector Ecology

Ecological characterization of Aedes aegyptilarval habitats (Diptera: Culicidae) in artificial water containers in Girardot, Colombia – Diana C. Garcia-Sánchez, Journal of Vector Ecology

Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water – Renata Medina-Silva, Antonie van Leeuwenhoek

Plant, root, and soil microbiome

Changes in the soil bacterial community along a pedogenic gradient – Manuel Sánchez-Marañón, Scientific Reports

 

Rhizosphere activity and atmospheric methane concentrations drive variations of methane fluxes in a temperate forest soil – Jens-Arne Subke, Soil Biology and Biochemistry

The Impact of the Diurnal Cycle on the Microbial Transcriptome in the Rhizosphere of Barley – Divyashri Baraniya, Microbial Ecology

The temperature sensitivity of soil organic matter decomposition is constrained by microbial access to substrates – Gabriel Y.K. Moinet, Soil Biology and Biochemistry

Application of Aspergillus aculeatus to rice roots reduces Cd concentration in grain – Yan Xie, Plant and Soil

Screening Bacillus species as biological control agents of Gaeumannomyces graminis var. tritici on wheat – Lirong Yang, Biological Control

Soil geochemical factors regulate Cd accumulation by metal hyperaccumulating Noccaea caerulescens (J. Presl & C. Presl) F.K. Mey in field-contaminated soils – Carla E. Rosenfeld, Science of The Total Environment

Antibiotics in the Soil: Sources, Environmental Issues, and Bioremediation – Umesh B. Jagtap, Antibiotics and Antibiotics Resistance Genes in Soils

Water and extremophile microbiome

Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach – Paula M. Tribelli, Journal of Industrial Microbiology & Biotechnology

Potential Role of Halophile in Crude Glycerol Based Biorefinery – Noopur Singh, Biorefining of Biomass to Biofuels

Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein – Chen Wang, PLOS one

Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp. – Jake V. Bailey, mBio

Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation – Jonathan Botha, Extremophiles

Prospects of Solvent Tolerance in Butanol Fermenting Bacteria – Shuvashish Behera, Biorefining of Biomass to Biofuels

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead – Susanna M. Blunt, Science of the Total Environment

Effect of TiO2 and CeO2 nanoparticles on the metabolic activity of surficial sediment microbial communities based on oxygen microelectrodes and high-throughput sequencing – Lingzhan Miao, Water Research

Performance and microbial communities in a combined bioelectrochemical and sulfur autotrophic denitrification system at low temperature – Dan Chen, Chemosphere

Ongoing biodegradation of Deepwater Horizon oil in beach sands: Insights from tracing petroleum carbon into microbial biomass – Joel T. Bostic, Marine Pollution Bulletin

Antibiotic degradation and microbial community structures during acidification and methanogenesis of swine manure containing chlortetracycline or oxytetracycline – Fubin Yin, Bioresource Technology

Metagenomics profiling for assessing microbial diversity in both active and closed landfills – Mohamad Yusof Zainun, Science of The Total Environment

Development of a microbial community-based index of biotic integrity (MC-IBI) for the assessment of ecological status of rivers in the Taihu Basin, China – Lihua Niu, Ecological Indicators

Microbial community response to silver nanoparticles and Ag+in nitrifying activated sludge revealed by ion semiconductor sequencing – Carley A. Gwin, Science of The Total Environment

Anaerobic co-digestion of pig manure and food waste; effects on digestate biosafety, dewaterability, and microbial community dynamics – C. Dennehy, Waste Management

Evaluating the impacts of triclosan on wastewater treatment performance during startup and acclimation – R. M. Holzem, Water Science and Technology

Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage – Bhargavi Ramanathan, Frontiers in Microbiology

Live Faecalibacterium prausnitzii induces greater TLR2 and TLR2/6 activation than the dead bacterium in an apical anaerobic co-culture system – Eva Maier, Cellular Microbiology

Food microbiome

A mathematical model to predict early quality attributes in hake during storage at low temperature – C. Vilas, Journal of Food Engineering

Chemical, Physiochemical, and Microstructural Properties, and Probiotic Survivability of Fermented Goat Milk Using Polymerized Whey Protein and Starter Culture Kefir Mild 01 – Hao Wang, Food Microbiology & Safety

Re-evaluation of mono- and di-glycerides of fatty acids (E 471) as food additives – EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS), European Food Safety Authority

Opportunities and hurdles of edible insects for food and feed – D. Dobermann, Nutrition Bulletin

Re-evaluation of alginic acid and its sodium, potassium, ammonium and calcium salts (E 400–E 404) as food additives – EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS), European Food Safety Authority

The SALAMANDER project: SALivAry bioMarkers of mediterraneAN Diet associated with long-tERm protection against type 2 diabetes – G. B. Proctor, Nutrition Bulletin

Polyphenols and health: Interactions between fibre, plant polyphenols and the gut microbiota – C. A. Edwards, Nutrition Bulletin

Techniques

Optimization of Culture Conditions for the Production of Halophilic Protease by Newly Isolated Bacillus sonorensis – S. Sankaralingam, American-Eurasian Journal of Agricultural & Environmental Science

November 8, 2017

Photosynthesizing bacteria printed on paper, investigations of microbial communities in water dispensers and mines, a review on the health benefits of natural products from truffles.

Human respiratory microbiome

Review: Airway Microbiota and Allergic Diseases: Clinical Implications – Eman M Fouda – International Journal of Pulmonary and Respiratory Sciences

Human oral microbiome

Proton pump inhibitor alters oral microbiome in gastrointestinal tract of healthy volunteers – Tsuyoshi Mishiro – Journal of Gastroenterology and Hematology

Human gut microbiome

Gut Microbiota Interacts with Markers of Adipose Tissue Browning, Insulin Action and Plasma Acetate in Morbid Obesity – José María Moreno-Navarrete – Molecular Nutrition and Food Research

Is there a relationship between intestinal microbiota, dietary compounds, and obesity? – Joanna Kałużna-Czaplińska – Trends in Food Science and Technology

Animal experiments

Combination of quercetin and resveratrol reduces obesity in high-fat diet-fed rats by modulation of gut microbiota – Le Zhao – Food and Function

Post-weaning social isolation of rats leads to long-term disruption of the gut microbiota-immune-brain axis – Fionn Dunphy Doherty – Brain, Behavior, and Immunity

Host-microbiota interaction induces bi-phasic inflammation and glucose intolerance in mice – Antonio Molinaro – Molecular Metabolism

Obesogenic diet-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis – June-Chul Lee – PLOS ONE

Animal microbiome

Gut region influences the diversity and interactions of bacterial communities in pikas (Ochotona curzoniae and Ochotona daurica) – Huan Li – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Nitrate induction and physiological responses of two maize lines differing in nitrogen use efficiency: effects on N availability, microbial diversity and enzyme activity in the rhizosphere – Zeno Varanini – Plant and Soil

The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface – J R Halliwell – Scientific Reports

Co-existence of Rhizobia and Diverse Non-Rhizobial Bacteria in the Rhizosphere and Nodules of Dalbergia odorifera Seedlings Inoculated with Bradyrhizobium elkanii,Rhizobium multihospitium–like and Burkholderia pyrrocinia–like Strains – Junkun Lu – Frontiers in Microbiology

Diversity of endophytic bacteria from Piper spp. with antagonistic property against Phytophthora capsici causing foot rot disease in black pepper (Piper nigrum L.) – Nadiya Kollakkodan – Journal of Tropical Agriculture

Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests – Sten Anslan – Soil Biology and Biochemistry

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Resource availability underlies the plant-fungal diversity relationship in a grassland ecosystem – Lauren C Cline – Ecology

Water and extremophile microbiome

Microflora Thermarum Atlas project: biodiversity in thermal spring waters and natural SPA pools – F Valeriani – Water Science and Technology: Water Supply

Modes of carbon xation in an arsenic and CO2-rich shallow hydrothermal ecosystem – Nolwenn Callac – Scientific Reports

Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea – Tiantian Yu – Applied Microbiology and Biotechnology

Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula – Catherine M Luria – Frontiers in Microbiology

Built environment

Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine – Yanping Bao – Science of the Total Environment

Investigation of microbial communities in water dispensers – Sangjung Park – Applied Biological Chemistry

Food microbiology

Review: Potential health benefits of natural products derived from truffles: A review – Seema Patel – Trends in Food Science and Technology

Probiotics/prebiotics

Review: The development of seaweed-derived bioactive compounds for use as prebiotics and nutraceuticals using enzyme technologies – Suvimol Charoensiddhi – Trends in Food Science and Technology

Phages and viruses

Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes – Judith Villager – The ISME Journal

Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures – Joana Oliveira – Journal of Dairy Science

Bioinformatics

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks – Zhu Chengsheng – Nucleic Acids Research

Metabolomics

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database – Wailing Huang – Nucleic Acids Research

mVOC 2.0: a database of microbial volatiles – Marie C Lemfack – Nucleic Acids Research

Techniques

Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems – Karsten Karczewski – Limnologica Ecology and Management of Inland Waters

More microbes

Review: Our microbes not only produce antibiotics, they also overproduce amino acids – Sergio Sanchez – The Journal of Antibiotics

Disruption of N-acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria – José A Gutiérrez-Barranquero – Microbial Biotechnology

Microbes in the news

Bacteria-Activated Wallpaper that Generates Electricity – Katharine Keane – Architect Magazine

US government approves ‘killer’ mosquitoes to fight disease – Emily Waltz – Nature News

Bacteria may help babies’ digestive tracts more than suspected, scientists find – EurekAlert

Using neutrons to study how resistant bacteria evolve – Phys Org

Researchers identify mechanisms through which H. pylori bacteria cause gastric cancer – News Medical Life Sciences

New model reveals possibility of pumping antibiotics into bacteria – EurekAlert

Microbes on the market

Seres Therapeutics Awarded Grant from CARB-X to Support Development of Microbiome Therapeutic Candidate – Business Wire

Michael J. Fox Foundation, 23andMe to Jointly Advance Parkinson’s Disease Research – Carolina Henriques – Parkinson’s News Today