Category Archives: Microbes in the News

March 28, 2018

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The impact of the microbiota on bone marrow transplantation in mice, differences in phage infection efficiency in nearly identical hosts, bacterial diversity of Brazilian artisanal cheese.

Events and jobs

Research Associate in the Department of Twin Research and Genetic Epidemiology, School of Life Cours – King’s College London

Research Associate in Department of Twin Research_School of Life Course Sciences – King’s College London

General microbiome

Variations in the relative abundance of Wolbachia in the gut of Nasutitermes arborum across life stages and castes – Michel Diouf – FEMS Microbiology Letters

Pregnancy and early life

HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort – Shantelle Claassen-Weitz – Scientific Reports

Human respiratory microbiome

Exacerbation induces a microbiota shift in sputa of COPD patients – Eric Jubinville – PLOS ONE

Human oral microbiome

Review: Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Pre-print: Characterization of the salivary microbiome in people with obesity – Yujia Wu – PeerJ

Review: The oral microbiota – a mechanistic role for systemic diseases – G Jia – British Dental Journal

Human gut microbiome

Differences in epidemiological features between ulcerative colitis and Crohn’s disease: the early life-programmed versus late dysbiosis hypothesis – Laurent Beaugerie – Medical Hypotheses

Analysis of changes in intestinal flora and intravascular inflammation and coronary heart disease in obese patients – Xv Li – Experimental and Therapeutic Medicine

Animal experiments

Nutritional Support from the Intestinal Microbiota Improves Hematopoietic Reconstitution after Bone Marrow Transplantation in Mice – Anna Staffas – Cell Host & Microbe

High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats – Klaudia Bielinska – Nutrition

High salt diet exacerbates colitis in mice by decreasing Lactobacillus levels and butyrate production – Pedro M Miranda – Microbiome

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression – Smruti Pushalkar – Cancer Discovery

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice – Fengwei Pan – Microbiome

Deletion of choline acetyltransferase in enteric neurons results in postnatal intestinal dysmotility and dysbiosis – Carl D Johnson – The FASEB Journal

At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota – Stephen Baldwin – PLOS ONE

Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs – Mohamed Zeineldin – Microbial Pathogenesis

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

Pre-print: Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses – William H Palmer – bioRxiv

Proanthocyanidin‐Rich Grape Seed Extract Modulates Intestinal Microbiota in Ovariectomized Mice – Guangwen Jin – Journal of Food Science

Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis – Zhaoxia Wang – Food & Function

Animal microbiome

Pre-print: Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding – Milica Ciric – bioRxiv

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’ – Alistair R Legione – PLOS ONE

Pre-print: Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E Dahlhausen – PeerJ

Comparison of gizzard and intestinal microbiota of wild neotropical birds – M Alexandra García-Amado – PLOS ONE

Fecal microbiota in the female prairie vole (Microtus ochrogaster) – J Thomas Curtis – PLOS ONE

Disentangling factors that shape the gut microbiota in German Shepherd dogs – Åsa Vilson – PLOS ONE

Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp – Han Liu – Microbial Biotechnology

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring – Ursula M McCormack – mSystems

Plant, root, and soil microbiome

Tetracycline resistance genes are more prevalent in wet soils than in dry soils – Yijun Kang – Ecotoxicology and Environmental Safety

Functional diversity of ectomycorrhizal fungal communities is reduced by trace element contamination – Álvaro López-García – Soil Biology and Biochemistry

Long- and short-term effects of mercury pollution on the soil microbiome – Aline Frossard – Soil Biology and Biochemistry

Structure of surface polysaccharides from Aeromonas sp. AMG272, a plant-growth promoting rhizobacterium isolated from rice rhizosphere – Rocío Contreras Sánchez-Matamoros – Carbohydrate Research

Review: Sniffing bacterial volatile compounds for healthier plants – Rouhallah Sharifi – Current Opinion in Plant Biology

Arbuscular mycorrhizal fungi influence decomposition and the associated soil microbial community under different soil phosphorus availability – Jing Xu – Soil Biology and Biochemistry

Water and extremophile microbiome

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion-Clipperton zone of the Pacific Ocean – Markus V Lindh – Environmental Microbiology Reports

Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures – Deni Ribicic – Marine Pollution Bulletin

Built environment

Pre-print: Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials – Marja I Roslund – PeerJ

Food microbiology

Interspecies variation in biofilm-forming capacity of psychrotrophic bacterial isolates from Chinese raw milk – Lei Yuan – Food Control

Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons – Mayra Carla de Freitas Martins – Food Research International

Probiotics/prebiotics

Salecan stabilizes the microstructure and improves the rheological performance of yogurt – Renjie Fu – Food Hydrocolloids

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Routine Supplementation of Lactobacillus rhamnosus GG and Risk of Necrotizing Enterocolitis in Very Low Birth Weight Infants – Andrea F Kane – The Journal of Pediatrics

Phages and viruses

Continued Need for Comprehensive Genetic and Phenotypic Characterization of Viruses: Benefits of Complementing Sequence Analyses with Functional Determinations – Aaron C Brault – The American Journal of Tropical Medicine and Hygiene

Detection of Hantaviruses and Arenaviruzses in three-toed jerboas from the Inner Mongolia Autonomous Region, China – Zhiqiang Wu – Emerging Microbes & Infections

Enteric Virome Sensing—Its Role in Intestinal Homeostasis and Immunity – Rebecca N Metzger – Viruses

Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O Anonye – Frontiers in Cellular and Infection Microbiology

Multiple mechanisms drive phage infection efficiency in nearly identical hosts – Cristina Howard-Verona – The ISME Journal

Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples – Virginie Sauvage – PLOS ONE

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa – Marike Geldenhuys – PLOS ONE

Pre-print: Ecological and evolutionary consequences of viral plasticity – Melinda Choua – bioRxiv

Bioinformatics

Pre-print: Taxonomy annotation errors in 16S rRNA and fungal ITS sequence databases – Robert C Edgar – bioRxiv

Metabolomics

Analysis of paper foxing by newly available omics techniques – Justyna Szulc – International Biodeterioration & Biodegradation

Review: Targeting human urinary metabolome by LC–MS/MS: a review – Jose Rodríguez-Morató – Bioanalysis

GC-MS Based Metabolomics and NMR Spectroscopy Investigation of Food Intake Biomarkers for Milk and Cheese in Serum of Healthy Humans – Alessia Trimigno – Metabolites

Techniques

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples – Jeremiah J Minich – mSystems

eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems – Ihsanul Khaliq – FEMS Microbiology Ecology

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species – Xia Liu – Preparative Biochemistry and Biotechnology

More microbes

Review: New therapeutics from Nature: The odd case of the bacterial cytotoxic necrotizing factor 1 – Zaira Maroccia – Biomedicine & Pharmacotherapy

Pre-print: An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition – Karthik Hullahalli – bioRxiv

Microbes in the news

Here’s Why Antibiotics May Give Viruses a Leg Up – Christopher Wanjek – Live Science

‘Nanobot’ viruses tag and round up bacteria in food and water – Carolyn Wilke – ScienceNews

Your rubber ducky is probably crawling with bacteria, scientists say – STAT

Newly discovered bacteria can break down biomass – Phys.Org

Microbes on the market

Biocodex funds microbiome research on link between diet, colon cancer, IBD – Healio

Rebiotix’s Lee Jones to Receive TRUST 2018 Courageous Women in Health Care Award – PR Newswire

March 26, 2018

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Suggestions to read in today’s digest are: a review about microbiological methods applied in studies following the deepwater horizon oil spill by S.Zhang, a paper by W. Pootakham on dynamics of coral‐associated microbiomes during a thermal bleaching event and a paper by X. Jiang on a novel auxotrophic interaction among soil microbes. Enjoy!

Oral microbiome

Reduced salivary secretion contributes more to changes in the oral microbiome of patients with primary Sjögren’s syndrome than underlying disease – Taco A van der Meulen – Annals of the Rheumatic Diseases

Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Human gut microbiome

Plant sterols and human gut microbiota relationship: An in vitro colonic fermentation study – María Cuevas-Tena – Journal of Functional Foods

Fecal microbiome composition and stability in 4- to 8-year old children is associated with dietary patterns and nutrient intake  – Kirsten Berding – The Journal of Nutritional Biochemistry

Gut Microbiota Profiles in Treatment-naïve Children with Attention Deficit Hyperactivity Disorder – Hai-yin Jiang – Behavioural Brain Research

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn’s Disease patients, but not in healthy controls – Holger Schäffler – Journal of Digestive Diseases

Review: The Impact of Klebsiella pneumoniae in Lower Gastrointestinal Tract Diseases – Christina Parvinder Kaur – Journal of Digestive Diseases

Differential immune responses and microbiota profiles in children with autism spectrum disorders and co-morbid gastrointestinal symptoms – Destanie R. Rose – Brain, Behavior, and Immunity

Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies – Marina Panek – Scientific Reports

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

Animal experiments 

Chitosan oligosaccharides improve the disturbance in glucose metabolism and reverse the dysbiosis of gut microbiota in diabetic mice – Junping Zheng – Carbohydrate Polymers

Comparative study of effects of assemblages AII and BIV of Giardia duodenalis on mucosa and microbiota of the small intestine in mice – Mariana Felgueira Pavanelli – Biomedicine & Pharmacotherapy

Lifelong calorie restriction affects indicators of colonic health in aging C57Bl/6J mice – Dieuwertje E.G. Kok – The Journal of Nutritional Biochemistry

Effects of oxidative stress induced by high dosage of dietary iron ingested on intestinal damage and caecal microbiota in Chinese Yellow broilers – Z. Y. Gou – Journal of Animal Physiology and Animal Nutrition

Animal microbiome 

Effects of short term lead exposure on gut microbiota and hepatic metabolism in adult zebrafish – Jizhou Xia – Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Effects of commercial dietary prebiotic and probiotic supplements on growth, innate immune responses, and intestinal microbiota and histology of Totoaba macdonaldi – Mayra L. González-Félix – Aquaculture

Plant, root, and soil microbiome

Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil – Olatz Larrañaga – Environment International

The fruit microbiome: A new frontier for postharvest biocontrol and postharvest biology – Samir Droby – Postharvest Biology and Technology

Earthworms differentially modify the microbiome of arable soils varying in residue management – Xin Gong – Soil Biology and Biochemistry

Subterranean infestation by Holotrichia parallela larvae is associated with changes in the peanut (Arachis hypogaea L.) rhizosphere microbiome – Li-Li Geng – Microbiological Research

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

Mycobiota of maize seeds revealed by rDNA‐ITS sequence analysis of samples with varying storage times – Hui – Qin Xing – Microbiology Open

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root‐associated soil of a wild perennial herb – Pil U. Rasmussen – New Phytologist

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – The ISME Journal

Water and extremophile microbiome 

Nutrient enrichment during shrimp cultivation alters bacterioplankton assemblies and destroys community stability – Wen Yang – Ecotoxicology and Environmental Safety

Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support – Guillaume Pillot – Bioresource Technology

Changes in microbial communities during volatile fatty acid production from cyanobacterial biomass harvested from a cyanobacterial bloom in a river – Hyun Uk Cho – Chemosphere

Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities – Jèssica Subirats – Water Research

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints – Gang Liu – Water Research

Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free‐living bacteria in the water column – Limei Shi – Microbiology Open

Dynamics of coral‐associated microbiomes during a thermal bleaching event – Wirulda Pootakham – Microbiology Open

Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan) – FEMS Microbiology Ecology

Review: A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill – Shuangfei Zhang – Frontiers in Microbiology

Built environment

Sulfate-reducing mixed communities with the ability to generate bioelectricity and degrade textile diazo dye in microbial fuel cells – Waheed Miran – Journal of Hazardous Materials

Work scheme to isolate the different microorganisms found in hydrogen-producing reactors: A study of effectiveness by pyrosequencing analysis – Laura Fuentes  – Journal of Applied Microbiology

Effect of hydraulic retention time on microbial community structure in wastewater treatment electro-bioreactors – Nancy A. ElNaker – Microbiology Open

Food microbiology

Presence of Clostridium difficile in poultry and poultry meat in Egypt – Mostafa Y. Abdel-Glil – Anaerobe

Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments – Francesco Fancello – International Journal of Food Microbiology

Post-harvest processing decreases the richness of bacterial taxa in the phyllosphere of broccoli – Min-Soo Kim  – Journal of Applied Microbiology

Probiotics / prebiotics

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Complete genome sequence of Bifidobacterium choerinum FMB-1, a resistant starch-degrading bacterium – Dong-Hyun Jung – Journal of Biotechnology

Structural studies of the cell wall polysaccharide from Lactococcus lactis UC509.9 – Evgeny Vinogradov – Carbohydrate Research

Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge – Laureen Crouzet – Scientific Reports

Microbes in the news

 

 

This Hungry Bacteria Could Help Clean Up Heavy Metals And Greenhouse Gases

March 24, 2018

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Events and jobs
Senior Phage Display Scientist: Antibodies – Cambridgeshire, England – Paramount Recruitment

General microbiome
Metagenomic mining of regulatory elements enables programmable species-selective gene expression – Nathan I Johns – Nature Methods

Pregnancy and early life
Seeding of the Fetal Gut Microbiome: Insights Into Origins and Significance – LF Stinson – Journal of Paediatrics and Child Health

Evidence of dysbiosis in the intestinal microbial ecosystem of children and adolescents with primary hyperlipidemia and the potential role of regular hazelnut intake. – Giorgio Gargari – Fems Microbiology Ecology

Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century – Bethany M Henrick – Msphere

Multi-site human microbiome
Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier. – Lesley Hoyles – Microbiome

Human vaginal microbiome
Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in China – Hongwei Zhang – Scientific Reports

Human nearly-sterile sites (blood, organs, brain)

Human gut microbiome
The current state and future direction of DoD gut microbiome research: a summary of the first DoD gut microbiome informational meeting – Steven Arcidiacono – Standards in Genomic Sciences

Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders. – Joby Pulikkan – Microbial Ecology

An Aberrant Microbiota is not Strongly Associated with Incidental Colonic Diverticulosis. – Roshonda B Jones – Scientific Reports

Untargeted metabolomics identifies trimethyllysine, a TMAO-producing nutrient precursor, as a predictor of incident cardiovascular disease risk. – Xinmin S Li – Jci Insight

Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis – Xinyue Huang – IOVS

Microbial interactions
Cell death as a trigger for morphogenesis. – Boris Aguilar – Plos One

Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred – Apuã C. M. Paquola – Journal of Molecular Evolution

Animal experiments
Preprint: Social communication between microbes colonizing the social honey bee Apis mellifera – Irene Newton – bioRxiv

Dietary butyrate glycerides modulate intestinal microbiota composition and serum metabolites in broilers – Xiaojian Yang – Scientific Reports

Bacterial lactase genes diversity in intestinal mucosa of mice with dysbacterial diarrhea induced by antibiotics – Chengxing Long – 3 Biotech

Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata. – Euan R O Allan – The Journal Of Heredity

Tall oil fatty acid inclusion in the diet improves performance and increases ileal density of Lactobacilli spp. in broiler chickens. – K Vienola – British Poultry Science

Effects of dietary Bacillus amyloliquefaciens supplementation on growth performance, intestinal morphology, inflammatory response, and microbiota of intra-uterine growth retarded weanling piglets – Yue Li – Journal Of Animal Science And Biotechnology

Temperature-Dependent Effects of Cutaneous Bacteria on a Frog’s Tolerance of Fungal Infection. – Matthew J Robak – Frontiers In Microbiology

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice. – Fengwei Pan – Microbiome

Animal microbiome
Review: The mosquito holobiont: fresh insight into mosquito-microbiota interactions – Morgane Guégan – Microbiome

Plant, root, and soil microbiome
Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields – Kunkun Fan – Soil Biology and Biochemistry

Seasonal Effects on Microbial Community Structure and Nitrogen Dynamics in Temperate Forest Soil – Tomohiro Yokobe – forests

High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. – Yu-Jie Wei – Plos One

Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities. – Annelein Meisner – Frontiers In Microbiology

Vanillic acid changed cucumber (Cucumis sativus L.) seedling rhizosphere total bacterial, Pseudomonas and Bacillus spp. communities. – Xingang Zhou – Scientific Reports

Review: Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences. – Mohammadhossein Ravanbakhsh – Microbiome

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. – E Gonzalez – Microbiome

Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture – Nicholas Ozede Igiehon – Int. J. Environ. Res. Public Health

Vascular plant-mediated controls on atmospheric carbon assimilation and peat carbon decomposition under climate change – Konstantin Gavazov – Global Change Biology

Water and extremophile microbiome
Preprint: Dynamics and interactions of highly resolved marine plankton via automated high frequency sampling – David M. Needham – bioRxiv

Bioremediation of PCB-contaminated shallow river sediments: The efficacy of biodegradation using individual bacterial strains and their consortia. – Hana Horváthová – Chemosphere

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community – Xavier Mayali – FEMS Microbiology Ecology

Built environment
Community Structure Analysis and Biodegradation Potential of Aniline-Degrading Bacteria in Biofilters – Luanfeng Hou – Current Microbiology

Food microbiology
Review: The influence of diet on anti-cancer immune responsiveness – Laura Soldati – Journal of Translational Medicine

The Efficacy of a Chewing Gum Containing Phyllanthus emblica Fruit Extract in Improving Oral Health. – Ya-Ting Chuang – Current Microbiology

Review: The Microbial Diversity of Sherry Wines – Gustavo Cordero-Bueso – Fermentation

Probiotics / prebiotics / antibiotics
The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster – Khachik E. Labachyan – Gut Pathogens

Bacillus clausii inhibits bone loss by skewing Treg-Th17 cell equilibrium in postmenopausal osteoporotic mice – Hamid Y. Dar – Nutrition

Prebiotic Potential of Herbal Medicines Used in Digestive Health and Disease. – Christine Tara Peterson – Journal Of Alternative And Complementary Medicine (New York, N.Y.)

Phages and viruses
Identification of Novel Viruses in Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks – Rafal Tokarz – Msphere

Microbes in the news
Skin spray heals US woman’s flesh-eating bacteria wounds – Alice Klein – New Scientist

March 23, 2018

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Optogenetic regulation of transcription to promote biosynthesis of desired chemicals from fungi, the effect of yeast and bacteria on floral nectar, guidelines and best practices for human microbiome sampling/sequencing/processing.

Plant, root, and soil microbiome

Evaluation of conventional and response surface level optimisation of n-dodecane (n-C12) mineralisation by psychrotolerant strains isolated from pristine soil at Southern Victoria Island, Antarctica – Syahir Habib – Microbial Cell Factories

Analysis of microbiota in bellflower root, Platycodon grandiflorum, obtained from South Korea – Daeho Kim – Journal of Microbiology and Biotechnology

Contrasting effects of yeasts and bacteria on floral nectar traits – Rachel L Vannette – Annals of Botany

Water and extremophile microbiome

Mechanisms of Methyl Mercury Net Degradation in Alder Swamps: The Role of Methanogens and Abiotic Processes – Rose-Marie Kronberg – Environmental Science & Technology Letters

Microbial mat of the thermal springs Kuchiger Republic of Buryatia: species composition, biochemical properties and electrogenic activity in biofuel cell – Denis Aleksandrovich Yuriev – IOP Conference Series: Earth and Environmental Sciences

Bioinformatics

Pre-print: A comprehensive automated pipeline for human microbiome sampling, 16S rRNA gene sequencing and bioinformatics processing – Luisa W Hugerth – bioRxiv

Pre-print/Review: Real-time analysis and visualization of pathogen sequence data – Richard A Neher – bioRxiv

Techniques

Yeast Biofilm as a Bridge Between Medical and Environmental Microbiology Across Different Detection Techniques – Luca Roscini – Infectious Diseases and Therapy

More microbes

Optogenetic regulation of engineered cellular metabolism for microbial chemical production – Evan M Zhao – Nature

Pre-print: Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators – Benjamin Hommel – bioRxiv

Pre-print: High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions – Rieza Aprianto – bioRxiv

Pre-print: Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39 – Jelle Slager – bioRxiv

Microbes in the news

Oral microbiome and anthropometry changes following caries arrest using silver-nitrate/fluoride-varnish – EurekAlert

Metagenomics of early childhood oral health and early childhood caries – EurekAlert

Synergistic effects of smoking and obesity on the subgingival microbiome – EurekAlert

Gut bacteria can mean life or death for birds – EurekAlert

Its name is LUCA. Now it’s needing second thoughts – Stephen Fleischfresser – Cosmos

Plants really do feed their friends – ScienceDaily

Bacteria eats greenhouse gas with a side of protein – Phys.org

Survival of the Slimiest: The Persistent Nature of Biofilms – Sonali D Advani – Medscape

Amy’s non-microbiology picks

Editorial: Asymmetry symposium unites economists, physicists and artists – Nature

March 22, 2018

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Of special note today: A randomized double blind controlled clinical trial on the impacts of probiotics on Alzheimer’s demonstrated an improvement in cognitive function, triglycerides, insulin sensitivity and C reactive protein; and a meta-analysis of the lung microbiome in tuberculosis identified specific species that are characteristic of the disease.

Events and jobs

Research Associate – Kintai Therapeutics – Cambridge, MA

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Human respiratory microbiome

*Meta-analysis of the lung microbiota in pulmonary tuberculosis – Bo-young Hong – Tuberculosis

Human skin microbiome

Longitudinal study of the psoriasis-associated skin microbiome during therapy with ustekinumab in a randomized Phase 3b clinical trial – Michael Loesche – Journal of Investigative Dermatology

Human oral microbiome

The subgingival microbiome in patients with established rheumatoid arthritis – Ted R Mikuls – Rheumatology

Self-reported bovine milk intake is associated with oral microbiota composition – Ingegerd Johansson – PLOSone

Human uro-genital microbiome

A Distinctive Urinary Metabolomic Fingerprint Is Linked With Endoscopic Postoperative Disease Recurrence in Crohn’s Disease Patients – Ammar Hassanzadeh Keshteli – Inflammatory Bowel Diseases

Human gut microbiome

Review: Interrelation of Diet, Gut Microbiome, and Autoantibody Production – Ioanna Petta – Frontiers in Immunology

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Animal experiments

Microbiome-metabolome signatures in mice genetically prone to develop dementia, fed a normal or fatty diet – Elena Sanguinetti – Scientific Reports

Influence of dietary protein and fructooligosaccharides on fecal fermentative end-products, fecal bacterial populations and apparent total tract digestibility in dogs – Carlo Pinna – BMC Veterinary Research

Animal microbiome

Review: The tripartite interactions between the mosquito, its microbiota and Plasmodium – Ottavia Romoli – BMC Parasites & Vectors

Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development – XiaoLi Bing – mBio

Lower dietary concentrate level increases bacterial diversity in the rumen of Cervus elaphus yarkandensis – Wenxi Qian- Canadian Journal of Microbiology

Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows – Svetlana Ferreira Lima – PLOSone

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ

Effects of high ambient temperature on the community structure and composition of ileal microbiome of broilers – X J Wang – Poultry Science

Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv

Plant, root, and soil microbiome

High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits – Marta Maciejewska – Antibiotics

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly – Kateryna Zhalnina – Nature Microbiology

Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms – Ma del Carmen Orozco-Mosqueda – Microbiological Research

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth – Terry J. McGenity – The ISME Journal

Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system – Ilonka C. Engelhardt – The ISME Journal

Water and extremophile microbiome

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition – Geoff A. Christensen – PLOSone

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

Microbial parasites make cyanobacteria blooms less of a trophic dead end than commonly assumed – Matilda Haraldsson – The ISME Journal

Air Microbiome

Deposition rates of viruses and bacteria above the atmospheric boundary layer
– Isabel Reche – The ISME Journal

Microbial Ecology

Review: Understanding Microbiome Stability in a Changing World – Ashley Shade – mSystems

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Probiotics / prebiotics

*Effect of Probiotic Supplementation on Cognitive Function and Metabolic Status in Alzheimer’s Disease: A Randomized, Double-Blind and Controlled Trial – Elmira Akbari – Frontiers in Aging Neuroscience

Bioinformatics

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes – Joel A Boyd – Nucleic Acids Research

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing – Hiroshi Mori – BMC Systems Biology

Machine learning for tackling microbiota data and infection complications in immunocompromised patients with cancer – J. Luis Espinoza – Journal of Internal Medicine

A highly adaptive microbiome-based association test for survival traits – Hyunwook Koh – BMC Genomics

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Microbes in the news

Making intricate images with bacterial communities – Psy.Org

Many Non-Antibiotic Drugs Affect Gut Bacteria. A new study finds that more than 200 human-targeted, non-antibiotic drugs inhibit the growth of bacterial species that make up part of the human microbiome – Catherine Offord

‘New life form’ answers question about evolution of cells – Science Daily

Bacteria and Art

This watercolour painting was created by artistic bacteria – Sarah Roberts had a germ of an idea: let bacteria take creative control – Anna Marks – Wired

Crocheted and Embroidered Bacteria Grow in Elin Thomas’s Fiber Art Petri Dishes – Laura Staugaitis – Colossal

 

March 20, 2018

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Still short and sweet. Highlights include combining bacterial and archaeal membranes, a reference catalog for the rumen microbiome and your gut microbiome keeping you awake at night, but really?

Jobs

Research Associate, Microbiology – Kintai Therapeutics – Cambridge, MA

Partners with relevant publications are needed – Faculty of Agriculture, Ain Shams University – Egypt

Biomedical Scientist or Trainee Biomedical Scientist (Microbiology) – York Teaching Hospital, UK

General microbiology

Identification of Biofilm Inhibitors by Screening Combinatorial Libraries of Metal Oxide Thin Films – Michal M. Dykas et al. – Applied Materials and Interfaces

** Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane – Antonella Caforio et al. – PNAS, USA

Press: Scientists engineer new life form with mixed Bacteria and Archaea membrane – Tibi Puiu – ZME Science

Preprint: Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine signaling – Arnau Domenech et al. – bioRxiv

Animal microbiome

** Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection – Rekha Seshadri et al. – Nature Biotechnology

Press: A reference catalog for the rumen microbiome – Joint Genome Institute, DOE

Water and extremophile microbiome

Preprint: Growth arrest in the active rare biosphere – Bela Hausmann et al. – bioRxiv

Phages and viruses

Preprint: Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection – Maxine Zylberberg et al. -bioRxiv

Technology

Essay: Which experimental systems should we use for human microbiome science? – Angela E. Douglas – PLoS Biology

Preprint: Efficient genome editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 system for analyzing magnetotactic behavior – Haitao Chen et al. – bioRxiv

Microbes in the news

Could the Microbiome Treat Side Effects of Stem Cell Transplants? – Alexander Burik – Labiotech

Rapid Starch Increases, Decreases in Horse Diets Upset Gut Microbiome – Kristen M. Janicki – the Horse

** Could it be your gut keeping you awake at night? – Kate Leaver – the Guardian

Molecular cuisine for gut bacteria – ScienceDaily

Bacteria churn out a million potential protein drugs – KATRINA KRÄMER – ChemistryWorld

Bacteria that can kill wild sheep and goats has never turned up in Alaska — until now – Zaz Hollander – Anchorage Daily News

News Bites: New molecule able to kill drug-resistant bacteria, FDA approves at-home breast cancer risk test – Chu Meiyi – MIMS Today

Non-antibiotic drugs promote antibiotic resistance – The Economist

Microbes on the market

Microbiome Therapeutics Market Overview with Qualitative analysis, Competitive landscape & Forecast 2023 – Healthcare Journal

March 19, 2018

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Enjoy today’s micro-Microbiome Digest!

More microbes

Pre-print: The Pseudomonas aeruginosa LasR quorum-sensing receptor balances ligand selectivity and sensitivity – Amelia R McCready – bioRxiv

Microbes in the news

Living sensor can potentially prevent environmental disasters from fuel spills – Phys.org

Bacteria found in water at Glasgow Royal Hospital for Children – BBC News

March 18, 2018

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An interesting book and multiple animal microbiome papers for today’s digest!

General microbiome
Book: Clinical Immunology (Fifth Edition): Principles and Practice – Robert R. Rich, Thomas A. Fleisher, William T. Shearer, Harry W. Schroeder, Anthony J. Frew, Cornelia M. Weyand
Multiple chapters may be of interest, including:

Human skin microbiome
Review: Cutaneous Barriers and Skin Immunity: Differentiating A Connected Network – Stefanie Eyerich – Trends in Immunology

Human gut microbiome
TonB-dependent transport by the gut microbiota: novel aspects of an old problem – David N Bolam – Current Opinion on Structural Biology

Review: Frailty and the gut – Antonio Di Sabatino – Digestive and Liver Disease

Animal experiments
Chronic exposure to low concentrations of lead induces metabolic disorder and dysbiosis of the gut microbiota in mice – Jizhou Xia – Science of the Total Environment

Polystyrene microplastics induce gut microbiota dysbiosis and hepatic lipid metabolism disorder in mice – Liang Lu – Science of the Total Environment

Expression of recombinant human lysozyme in bacterial artificial chromosome transgenic mice promotes the growth of Bifidobacterium and inhibits the growth of Salmonella in the intestine – Lu Dan – Journal of Biotechnology

Comparative analysis of gut microbial community in healthy and tibial dyschondroplasia affected chickens by high throughput sequencing – Xiaole Tong – Microbial Pathogenesis

Polysaccharide of Hericium erinaceus Attenuates Colitis in C57BL/6 Mice via Regulation of Oxidative Stress, Inflammation-related Signaling Pathways and Modulating the Composition of the Gut Microbiota – Yilin Ren – The Journal of Nutritional Biochemistry

Variations in methane yield and microbial community profiles in the rumen of dairy cows as they pass through stages of first lactation – Tamsin Lyons – Journal of Dairy Science

Animal microbiome
Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata – Euan R O Allan – Journal of Heredity

Microbiomes associated with bovine periodontitis and oral health – Ana C. Borsanelli – Veterinary Microbiology

Review: Current perspectives of the chicken gastrointestinal tract and its microbiome – D. Borda-Molina – Computational and Structural Biotechnology Journal

Built environment
Review: Bioremediation of a pentacyclic PAH, Dibenz(a,h)Anthracene- A long road to trip with bacteria, fungi, autotrophic eukaryotes and surprises – Vidya Vasudevan – Chemosphere

Food microbiology
Microbial community dynamics of a blue-veined raw milk cheese from the United Kingdom – Dewi Yunita – Journal of Dairy Science

Probiotics / prebiotics / antibiotics
A mathematical model of multiple delayed feedback control system of the gut microbiota—Antibiotics injection controlled by measured metagenomic data – Yueping Dong – Nonlinear Analysis: Real World Applications

Review: Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics – Zachary JS Mays – Current Opinion in Biotechnology

Review: The role of the gut microbiota in the pathology and prevention of liver disease – Alejandra Altamirano-Barrera – The Journal of Nutritional Biochemistry

Phages and viruses
Preprint: Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem – Divya Venkatesh – bioRxiv

New Genomes
Sanguibacter massiliensis sp. nov., Actinomyces minihominissp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov., and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples. – Melhem Bilen – New Microbes and New Infections

Microbes in the news
Weighty challenge: Untangling obesity’s hidden picture – Jamie Morton – NZ Herald

Microbes on the market
Seres Therapeutics (NASDAQ:MCRB) Upgraded at Zacks Investment Research – Amber Thompson – Register Journal

March 14, 2018

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Today’s Digest adds to the growing literature of microbiome research. Highlights include the synergistic relationship between fungi and an invasive plant, enteral nutrition may help maintain the gastrointestinal function of critically ill patients, and the NCI calls for advancing epidemiologic research on the human microbiome.

Jobs

Student Trainee Microbiology Student Trainee Usda Pathways Internship Program Job in SAINT LOUIS, MO – Opening from 3/12-3/16, 2018

General microbiology

Antibiotic-induced population fluctuations and stochastic clearance of bacteria – Jessica Coates et al. – eLife

Press: Biophysicists discover how small populations of bacteria survive treatment – Science Daily

Preprint: Division of labor during biofilm matrix production – Anna Dragos et al. – bioRxiv

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals – Chin-Yi Chen et al. – PLoS One

Human nasal microbiome

Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities – Yaqi You et al. – PLoS One

Human oral microbiome

In vitro: pH changes of mixed biofilms of Streptococcus mutans and Candida albicans after exposure to sucrose solutions in vitro – Thamires Priscila Cavazana et al. – Archives of Oral Biology

Human lung microbiome

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis – Lisa A. Carmody et al. – PLoS One

Human gut microbiome

** Review: Effects of enteral nutrition on gastrointestinal function in patients who are critically ill – Michael Schörghuber and Sonja Fruhwald – The Lancet Gastroenterology & Hepatology

An overview on the interplay between nutraceuticals and gut microbiota – Adrian Catinean et al. – PeerJ

Animal experiments

Aronia berry (Aronia mitschurinii ‘Viking’) inhibits colitis in mice and inhibits T cell tumour necrosis factor-α secretion – Derek A. Martin et al. – Journal of Functional Foods

Mouse: Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka et al. – Cell Reports

Animal microbiome

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil – Tiago F. Moreira et al. – PLoS One

Food microbiology

The potential use of leaf extracts of two Newtonia (Fabaceae) species to treat diarrhoea – K.E. Motlhatlego et al. – South African Journal of Botany

Editorial: The interactions between food components and human nutrition – Charles Brennan – International Journal of Food Science & Technology

Plant, root and soil microbiome

** The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites – G. Rodríguez-Caballero et al. – Science of the Total Environment

Review: Environmental and public health related risk of veterinary zinc in pig production – Using Denmark as an example – John Jensen et al. – Environment International

Hydrophobins contribute to root colonization and stress responses in the rhizosphere-competent insect pathogenic fungus Beauveria bassiana – Soumya Moonjely et al. – Microbiology

Perspective: Tracing the role of human civilization in the globalization of plant pathogens – Alberto Santini et al. – ISME

Water and extremophile microbiome

Review: Surface water flooding, groundwater contamination, and enteric disease in developed countries: A scoping review of connections and consequences – L. Andrade et al. – Environmental Pollution

Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration – Edson Baltazar Estrada-Arriaga et al. – Journal of Environmental Management

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches – Samuel P. Parker et al. – Ecosphere

Phages and viruses

Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India) – Vijayan Jasna et al. – PLoS One

Bioinformatics

A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data – Juhee Lee and Marilou Sison-Mangus – Frontiers in Microbiology

A systems pharmacology model for inflammatory bowel disease – Violeta Balbas-Martinez et al. – PLoS One

Microbes in the news

** Of Microbes and Men: Advancing Epidemiologic Research on the Human Microbiome – Victoria Fisher – National Cancer Institute

Opinion: Inflammatory bowel disease: complexity and variability need integration – Claudio Fiocchi – Frontiers in Medicine

Stress: How social conflict alters gut bacteria – Maria Cohut – Medical News Today

High-Fiber Generates Gut Bacteria Good for Type 2 Diabetes – Becky McCall – Medscape

New pathway may lead to improved probiotic products – Tim Lundeen – Feedstuffs

Probiotic potential: Specific gut microbes could cut severity of parasitic infections in developing countries – Nathan Gray – NUTRAingredients

Wandering Gut Bacteria Could Be Behind Conditions Like Lupus – Abby Norman – Futurism

Model Can Predict Which Bacteria will Engraft after FMT – Rachel Lutz – MD Magazine

Can Coral Microbes Protect Reefs From Climate Change? – Amelia Urry – NewsDeeply

Study: Several important vaginal metabolites elevated in smokers – Bob Kronemyer – Modern Medicine

Doctors collect viruses from pond and employ them to combat a man’s antibiotic resistance infection in man’s heart – Mark Kaufman – Mashable

Making good bacteria more resilient – Gali Weinreb – Globes

Study links decline of ‘good’ bacteria in infants to higher long-term increases in pH of poo – Tim Cutcliffe – NUTRAingredients

Microbes on the market

German biotech company wants to turn old PCs into gold – Jeremy Gray – Handelsblatt Global – European Business & Finance News

 

March 13, 2018

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In today’s digest it was quite hard to pick just few papers, since there are many, many interesting papers. From mentioned reviews I would recommend the one by H. Bokhari on the exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens and the one by J. R. Bober on engineering probiotics and microbes for biomedical applications. From other papers I would like to highlight the one by M. Mehrshad and enigmatic SAR202 cluster, the one by A. C. Lehours and biogeographic patterns of aerobic anoxygenic phototrophic bacteria and the one by E. M. Llufrio and how fluorescence activated cell sorting introduces oxidative stress and alters the metabolic state of cells. Don’t forget to check on news, where you can read about metagenomic clustering powered by supercomputers, while in general science section there is an interesting article by B. Barros on ‘scientific knowledge percolation process’ or how scientific information diffuse into the social sphere.

General microbiome

Review: Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens – Habib Bokhari – Critical Reviews in Microbiology

The aryl hydrocarbon receptor as a moderator of host-microbiota communication – Limin Zhang – Current Opinion in Toxicology

Pregnancy and early life

The Role of the Microbiome in the Developmental Origins of Health and Disease – Leah T. Stiemsma – Pediatrics

Human gut microbiome

 

Translocation of a gut pathobiont drives autoimmunity in mice and humans – S. Manfredo Vieira – Science

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome – Laura-Isobel McCall – PLOS One

How to Increase the Butyrate-Producing Capacity of the Gut Microbiome: Do IBD Patients Really Need Butyrate Replacement and Butyrogenic Therapy? – Stanislav Sitkin – Journal of Crohn’s and Colitis

Effect of Faecal Microbiota Transplantation for Treatment of Clostridium difficile Infection in Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis of Cohort Studies – Tuo chen –  Journal of Crohn’s and Colitis

Animal experiments 

Supplementation of Bacillus subtilis based probiotic reduces heat stress-related behaviors and inflammatory response in broiler chickens – W C Wang – Journal of Animal Science

Comparisons of bacterial and Archaeal Communities in the Rumen and a Dual-Flow Continuous Culture Fermentation System using Amplicon Sequencing – I J Salfer – Journal of Animal Science

The Microbiome Regulates Pulmonary Responses to Ozone in Mice – Youngji Cho – American Journal of Respiratory Cell and Molecular Biology

Bifidobacteria exert species-specific effects on constipation in BALB/c mice – Linlin Wang – Food & Function

Animal microbiome 

Comparative Analysis of the Gut Bacterial Community of Four Anastrepha Fruit Flies (Diptera: Tephritidae) Based on Pyrosequencing – Carmen Ventura – Current Microbiology

Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats’ rumen – Thi Huyen Do – The Journal of General and Applied Microbiology

Plant, root, and soil microbiome

Colonization of Eggplant by Endophytic Bacteria Antagonistic to Ralstonia solanacearum, the Bacterial Wilt Pathogen – Gauri A. Achari – Proceedings of the National Academy of Sciences, India Section B: Biological Sciences

Landscape scale factors affecting prevalence of Escherichia coli in surface soil include land cover type, edge interactions, and soil pH – Nicholas Dusek – Applied and Environmental Microbiology

Nigericin and grisorixin methyl ester from the Algerian soil-living Streptomyces youssoufiensis SF10 strain: a computational study on their epimeric structures and evaluation of glioblastoma stem cells growth inhibition – Nassima Leulmi – Natural Product Research

Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification – Haifeng Qian – Pesticide Biochemistry and Physiology

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás  – Frontiers in Microbiology

Resveratrol as a growth substrate for bacteria from the rhizosphere – Zohre Kurt – Applied and Environmental Microbiology

Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits – Jonathan W. Leff – The ISME Journal

Diversity of microbial communities potentially involved in mercury methylation in rice paddies surrounding typical mercury mining areas in China – Xin Liu – Microbiology Open

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology

Volatile compounds from beneficial or pathogenic bacteria differentially regulate root exudation, transcription of iron transporters, and defense signaling pathways in Sorghum bicolor – Erasto Hernández-Calderón –  Plant Molecular Biology

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root–rhizosphere interactome – Etienne Yergeau – The ISME Journal

Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community – Xi-Hui Xu – Journal of Hazardous Materials

Water and extremophile microbiome 

Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes – Anne-Catherine Lehours – Scientific Report

Mercury-methylating bacteria are associated with zooplankton: a proof-of-principle survey in the Baltic Sea –  Elena Gorokhova – bioRxiv

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community – Laura Gómez-Consarnau – bioRxiv

Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows – Songlin Liu – Microbiology Open

Chapter 17 – Rhizosphere Metabolite Profiling: An Opportunity to Understand Plant-Microbe Interactions for Crop Improvement -Amit Verma – Crop Improvement Through Microbial Biotechnology

Chapter 22 – Plant-Microbe Interaction and Genome Sequencing: An Evolutionary Insight – Krishna K. Sharma – Crop Improvement Through Microbial Biotechnology

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management – Domenico Savio – Wiley Interdisciplinary Reviews: Water

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments – Kathleen M. Scott – Environmental Microbiology

Data Article: Bioinformatics delimitation based on sequence data of the psychrophilic and psychrotolerant actinobacteria isolated from the Polar Frontal waters of the Antarctic Ocean – Palaniappan Sivasankar – Data in Brief

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity – Kai Tang – Frontiers in Microbiology

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling – Maliheh Mehrshad – The ISME Journal

The widespread dissemination of integrons throughout bacterial communities in a riverine system – Gregory C. A. Amos – The ISME Journal

Expression profiling of host and virus during a coccolithophore bloom provides insights into the role of viral infection in promoting carbon export – Uri Sheyn – The ISME Journal

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

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

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – The ISME Journal

Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef  – Michael P. Lesser – The ISME Journal

Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. – Mikhail A. Moldovan – Frontiers in Microbiology

Halotolerant Exiguobacterium profundum PHM11 Tolerate Salinity by Accumulating L-Proline and Fine-Tuning Gene Expression Profiles of Related Metabolic Pathways – Vikas K. Patel – Frontiers in Microbiology

The predictability of a lake phytoplankton community, over time-scales of hours to years – Mridul K. Thomas – Ecology Letters

Built environment

Anaerobic Ammonium-Oxidizing Bacteria in Cow Manure Composting – Tingting Wang – Journal of Microbiology and Biotechnology

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems – Krishnaveni Venkidusamy – Frontiers in Microbiology

Inhibitors degradation and microbial response during continuous anaerobic conversion of hydrothermal liquefaction wastewater – Buchun Sia – Science of The Total Environment

Food microbiology

Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation – Francesca De Filippis – Food Microbiology

Staphylococcus aureus undergoes major transcriptional reorganization during growth with Enterococcus faecalis in milk – Gabriela NogueiraViçosa – Food Microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts – Food Microbiology

Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Qian Li – Food Microbiology

Microbial diversity and chemical analysis of the starters used in traditional Chinese sweet rice wine – Haiying Cai –  Food Microbiology

Structure of association networks in food bacterial communities – Eugenio Parente – Food Microbiology

Shifts in spinach microbial communities after chlorine washing and storage at compliant and abusive temperatures – Ganyu Gu – Food Microbiology

Probiotics / prebiotics

Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay – Benedetta Bottari – Microbiology

Phages and viruses

A Holistic Assessment of the Risks and Benefits of the Synthesis of Horsepox Virus – Diane Di Euliis – mSphere

Biotechnology

Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting – Caihong Song – Bioresource Technology

Review: Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications – Josef R. Bober – Annual Review of Biomedical Engineering

Techniques

Sorting Cells Alters Their Redox State and Cellular Metabolome – Elizabeth M. Llufrio – Redox Biology

Microbes in the news 

Ibuprofen Counters Key Bacteria in Lungs of CF Patients, Study Shows

Bacteria in your intestines can trigger autoimmune diseases

A game changer: Metagenomic clustering powered by supercomputers

Science, publishing, and career

Scientific knowledge percolation process and social impact: a case study on the biotechnology and microbiology perceptions on Twitter – Beatriz Barros – Science and Public Policy