March 28, 2018

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

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March 23, 2018

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 4, 2018

Events and jobs

Phd position in antimicrobial resistance development in biofilm communities – University of Leuven

Professor in Microbiome/Microbiota-Host Interactions – University of Alabama

Microbiology Lab Scientist – Lyneer Staffing

General microbiome

Impact of Brazilian microbiome for boosting agriculture, animal husbandry and human being: a book review – Arthur Prudêncio de Araujo Pereira, Journal of Cleaner Production

Are animals a source of Stenotrophomonas maltophiliain human infections? Contributions of a nationwide molecular study – Aurélie Jayol, European Journal of Clinical Microbiology & Infectious Diseases

The organization of bacterial genomes: Towards understanding the interplay between structure and function – Daan J.W. Brocken, Current Opinion in Systems Biology

Pregnancy and early life

Selective maternal seeding and environment shape the human gut microbiome – Katri Korpela, Genome Research

Ecological Shifts of Supragingival Microbiota in Association with Pregnancy – Wenzhen Lin, Frontiers in Cellular and Infectious Microbiology

Human respiratory microbiome

Impaired diversity of the lung microbiome predicts progression of idiopathic pulmonary fibrosis – Youhei Takahashi, Respiratory Research

Human gut microbiome

Methanogens in humans: potentially beneficial or harmful for health – Prem Prashant Chaudhary, Applied Microbiology and Biotechnology

Gut microbiota alterations and dietary modulation in childhood malnutrition – The role of short chain fatty acids – Ceyda Tugba Pekmez, Clinical Nutrition

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A. Rosa, Microbiome

Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development – Keaton Stagaman, mSystems

A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies – Bruno K. Rodiño-Janeiro, Advances in Therapy

Characterizing the metabolic phenotype of intestinal villus blunting in Zambian children with severe acute malnutrition and persistent diarrhea – Marta Farràs, PLOS one

Animal experiments

Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios – Zhen Tan, Antonie van Leeuwenhoek

Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice – Ling Xiao, Scientific Reports

TRIM31 Deficiency Is Associated with Impaired Glucose Metabolism and Disrupted Gut Microbiota in Mice – Jing Cheng, Frontiers in Physiology

Animal microbiome

Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota – Jinbo Xiong, Applied Microbiology and Biotechnology

Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities – Élise Lacoste, Marine Environmental Research

Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese – Sergei V. Drovetski, Scientific Reports

Skin microbiomes of California terrestrial salamanders are influenced by habitat more than host phylogeny – Alicia K. Bird, Frontiers in Microbiology

Plant, root, and soil microbiome

Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions – Antonietta Mello, Frontiers in Microbiology

Micro-decomposer communities and decomposition processes in tropical lowlands as affected by land use and litter type – Valentyna Krashevska, Oecologia

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Size-Controlled Production of Gold Bionanoparticles Using the Extremely Acidophilic Fe(III)-Reducing Bacterium, Acidocella aromatica – Intan Nurul Rizki, Minerals

Nematicidal protease genes screened from a soil metagenomic library to control Radopholus similismediated by Pseudomonas fluorescens pf36 – Deqiang Chen, Applied Microbiology and Biotechnology

The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting – Xiangyun Zang, Biotechnology for Biofuels

Diversity and contributions to nitrogen cycling and carbon fixation of soil salinity shaped microbial communities in Tarim Basin – Min Ren, Frontiers in Microbiology

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling – Ruben López-Mondéjar, The ISME Journal

Soil bacterial community shifts driven by restoration time and steppe types in the degraded steppe of Inner Mongolia – Minjie Yao, CATENA

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Enumeration of Culturable Endophytic Bacterial Population of Different Lycopersicum esculentum L. Varieties – Monika Singh, International Journal of Current Microbiology and Applied Sciences

Isolation and Characterization of Methanol Utilizing Microorganisms from Leguminous Crops – Umang Ahlawat, International Journal of Current Microbiology and Applied Sciences

Isolation of Mercury-Resistant Fungi from Mercury-Contaminated Agricultural Soil – Reginawanti Hindersah, Agriculture

Root-associated fungi shared between arbuscular mycorrhizal and ectomycorrhizal conifers in a temperate forest – Hirokazu Toju, Frontiers in Microbiology

Antagonistic Potential and Molecular Characterization of Trichoderma spp. against Rhizoctonia solani Infecting Ghost Pepper in Manipur, India – Khedarani Koijam, International Journal of Current Microbiology and Applied Sciences

Isolation of Biocontrol (Bacterial) Agents from Chickpea (Cicer arietinum linnaeus) – S. Vijaya Kumar, International Journal of Current Microbiology and Applied Sciences

Potentiality of Native Pseudomonas spp. in Promoting Sugarcane Seedling Growth and Red Rot (Colletotrichum falcatum went) Management – P. Kishore Varma, International Journal of Current Microbiology and Applied Sciences

Interactions between isolates of the fungus Beauveria bassiana and Zea mays – Aimee McKinnon, Lincoln University (thesis)

Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Soils of the Odiel Salt Marshes in Huelva, Southwestern Spain – Blanca Vera-Gargallo, Genome Anouncements

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau – Yunfu Gu, Scientific Reports

Water and extremophile microbiome

Survival of Listeria monocytogenes and Staphylococcus aureus in Synthetic Brines. Studying the Effects of Salt, Temperature and Sugar through the Approach of the Design of Experiments – Antonio Bevilacqua, Frontiers in Microbiology

Saccharolobus caldissimus gen. nov., sp. nov., a facultatively anaerobic iron-reducing hyperthermophilic archaeon isolated from an acidic terrestrial hot spring, and reclassification of Sulfolobus solfataricus as Saccharolobus solfataricus comb. nov. and Sulfolobus shibatae as Saccharolobus shibatae comb. nov. – Hiroyuki D. Sakai,  International Journal of Systematic and Evolutionary Microbiology

Distinct Osmoadaptation Strategies in the Strict Halophilic and Halotolerant Bacteria Isolated from Lunsu Salt Water Body of North West Himalayas – Shivani Vaidya, Current Microbiology

Archaeal Viruses from High-Temperature Environments – Jacob H. Munson-McGee, Genes

Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations – Nina Gunde-Cimerman, FEMS Microbiology Reviews

Tertiary treatment and dual disinfection to improve microbial quality of reclaimed water for potable and non-potable reuse: A case study of facilities in North Carolina – Emily S. Bailey, Science of The Total Environment

The Early Earth Geochemical and Isotope Record of Serpentinizing Environments from Archean Stichtite (Mg6Cr2(OH)16[CO3] · 4H2O) – Erik B. Melchiorre, Precambrian Research

Process performance and population dynamics of ammonium tolerant microorganisms during co-digestion of fish waste and manure – Linn Solli, Renewable Energy

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure – I.A. Vasiliadou, Science of The Total Environment

Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu, Bioresource Technology

Pretreatment of saline antibiotic wastewater using marine microalga – Xueqing Shi, Bioresource Technology

Bioinformatics

Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9Agene of Clostridium thermocellum – Wolfgang H. Schwarz, World Journal of Microbiology and Biotechnology

Techniques

Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench – Wei-Kai Wu, Journal of the Formosan Medical Association

The Application of Omics Data to the Development of AOPs – Mary T. McBride, A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment

From correlation to causation: analysis of metabolomics data using systems biology approaches – Antonio Rosato, Metabolomics

Application of ensemble deep neural network to metabolomics studies – Taiga Asakura, Analytica Chimica Acta

Genome-reconstruction for eukaryotes from complex natural microbial communities – Patrick T West, Genome Research

Microbes in the news

Magnetic bacteria cause a stir – Christian Harding, Chemistry World

Federal Panel Passes Antibiotic-Resistant Bacteria Resolutions – Troy Brown, MedScape

Dangerous bacteria found in raw milk from Pennsylvania dairy – Coral Beach, Food Safety Network

 

February 24, 2018

100+ alerts today with interesting papers across every category. Some highlights include choosing FMT donors, viral insulin-like peptides, and 2 papers on detecting duplicated figures.

General microbiome
Review: The microbiome in precision medicine: the way forward. – Joseph F Petrosino – Genome Medicine

Motivations of participants in the citizen science of microbiomics: data from the British Gut Project. – Lorenzo Del Savio – Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Pregnancy and early life
The Role of the Genitourinary Microbiome in Pediatric Urology: a Review. – Daniel Gerber – Current Urology Reports

Review: Reproductive outcome of patients undergoing in vitro fertilization treatment and diagnosed with bacterial vaginosis or abnormal vaginal microbiota: a systematic PRISMA review and meta-analysis. – Thor Haahr – Bjog : An International Journal Of Obstetrics And Gynaecology

Multi-site human microbiome
Review: The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis. – Bruno Bonaz – Frontiers In Neuroscience

Human vaginal microbiome
Protein Content of Cervicovaginal Fluid Is Altered During Bacterial Vaginosis. – Carolina Sanitá Tafner Ferreira – Journal Of Lower Genital Tract Disease

Human nearly-sterile sites
Microbiome-Host Interactions in Hematopoietic Stem-Cell Transplant Recipients. – Tessa Andermann – Biology Of Blood And Marrow Transplantation : Journal Of The American Society For Blood And Marrow Transplantation

Human gut microbiome
** Competitively Selected Donor Fecal Microbiota Transplantation: Butyrate Concentration and Diversity as Measures of Donor Quality. – Danielle Barnes – Journal Of Pediatric Gastroenterology And Nutrition

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients. – Federica Gigliucci – Frontiers In Cellular And Infection Microbiology

ReviewHuman Gut Microbiota and Gastrointestinal Cancer. – Changting Meng – Genomics, Proteomics & Bioinformatics

Review: Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism. – Jing Gao – Frontiers In Cellular And Infection Microbiology

Microbial interactions
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia. – Ross P Carlson – Biochemical Society Transactions

Worlds Apart – Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions. – Zhi-Luo Deng – Frontiers In Microbiology

Using niche breadth theory to explain generalization in mutualisms – Rebecca T. Batstone – Ecology

Metabolic division of labor in microbial systems – Ryan Tsoi – PNAS

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle – Karthik Anantharaman – ISME

Review: Bacterial – Fungal Interactions: ecology, mechanisms and challenges. – A Deveau – Fems Microbiology Reviews

Role of extracellular polymeric substances in polymicrobial biofilm infections of Staphylococcus epidermidis and Candida albicans modelled in the nematode Caenorhabditis elegans. – Jillian E Holt – Pathogens And Disease (older, from July 2017)

Animal experiments
Acute and repeated exposure to social stress reduces gut microbiota diversity in Syrian hamsters. – Katherine A Partrick – Behavioural Brain Research

1H NMR based identification of intestinally-absorbed metabolites by Ussing chamber analysis of the rat cecum. – Meredith Dinges – Analytical Chemistry

Influence of gemcitabine chemotherapy on the microbiota of pancreatic cancer xenografted mice. – Concetta Panebianco – Cancer Chemotherapy And Pharmacology

Grape seed proanthocyanidins influence gut microbiota and enteroendocrine secretions in female rats. – Àngela Casanova-Martí – Food & Function

Combined Dietary Anthocyanins, Flavonols, and Stilbenoids Alleviate Inflammatory Bowel Disease Symptoms in Mice. – Aurelia Scarano – Frontiers In Nutrition

Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion. – Jörn Karhausen – Laboratory Investigation; A Journal Of Technical Methods And Pathology

Glucocorticosteroids and ciclosporin do not significantly impact canine cutaneous microbiota. – Giovanni Widmer – Bmc Veterinary Research

The effects of high dose of two manganese supplements (organic and inorganic) on the rumen microbial ecosystem. – Svetlana Kišidayová – Plos One

Hydrogen peroxide production by lactobacilli promotes epithelial restitution during colitis. – Ashish K Singh – Redox Biology

Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson’s disease mice: gut microbiota, glial reaction and TLR4/TNF-α signaling pathway. – Meng-Fei Sun – Brain, Behavior, And Immunity

Rotenone induces gastrointestinal pathology and microbiota alterations in a rat model of Parkinson’s disease. – Michaela E Johnson – Neurotoxicology

Prenatal Androgen Exposure Causes Hypertension and Gut Microbiota Dysbiosis. – Shermel Sherman – Gut Microbes

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome – Claudia Pogoreutz – Ecology And Evolution

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. – Mireia Uribe-Herranz – Jci Insight

Animal microbiome
Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract. – Li Zhang – Frontiers In Microbiology

Characterization of gut bacterial flora of Apis mellifera from north-west Pakistan – Syed Ishtiaq Anjum – Saudi Journal Of Biological Sciences

A Member of the Roseobacter Clade, Octadecabacter sp., is the Dominant Symbiont in the Brittle Star Amphipholis squamata. – Kathleen M Morrow – Fems Microbiology Ecology

Alimentary microbes of winter-form Drosophila suzukii. – M T Fountain – Insect Molecular Biology

The development of gut microbiota in ostriches and its association with juvenile growth – Elin Videvall – bioRxiv

Review: Regulation of intestinal health by branched-chain amino acids. – Hua Zhou – Animal Science Journal = Nihon Chikusan Gakkaiho

Book chapter: Termite Gut Microbiome – Navodita Maurice – Sustainability in Plant and Crop Protection

Plant, root, and soil microbiome
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. – Joseph A Edwards – Plos Biology

Quantitative Genetic Analysis of the Maize Leaf Microbiome – Jason G. Wallace – bioRxiv

 

Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation. – Miriam B Herold – Fems Microbiology Letters

Landscape topography structures the soil microbiome in arctic polygonal tundra. – Neslihan Taş – Nature Communications

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China. – Xiaodong Yao – The Science Of The Total Environment

Seasonal dynamics in the community structure and trophic structure of testate amoebae inhabiting the Sanjiang peatlands, Northeast China. – Lihong Song – European Journal Of Protistology

Investigation of rhizospheric microbial communities in wheat, barley and two rice varieties at the seedling stage. – Tao Lu – Journal Of Agricultural And Food Chemistry

Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy warrants ecosystem function. – Witoon Purahong – Environmental Microbiology

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems. – Qisong Li – International Journal Of Molecular Sciences

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. – Liesje Mommer – The New Phytologist

Isolation and characterization of N2 -fixing bacteria from giant reed and switchgrass for plant growth promotion and nutrient uptake – Jia Xu – Journal of Basic Microbiology

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks – Hirokazu Toju – bioRxiv

Water and extremophile microbiome
Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation. – Ian Salter – Plos One

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. – Jeremiah J Minich – Plos One

Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge. – Blake D Ramsby – Molecular Ecology

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems – Navdeep K Dhami – Frontiers In Microbiology

Microbial Community Structure and Function Indicate the Severity of Chromium Contamination of the Yellow River. – Yaxin Pei – Frontiers In Microbiology

Assessing the microbial communities inhabiting drinking water networks and nitrifying enrichments with special respect on nitrifying microorganisms. – Zsuzsanna Nagymáté – Acta Microbiologica Et Immunologica Hungarica

Microbial community composition along a 50,000 year lacustrine sediment sequence. – Aurèle Vuillemin – Fems Microbiology Ecology

Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems. – Eléonore Frouin – Frontiers In Microbiology

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition – Alescia A. Roberto – Water Research

Built environment
Dog introduction alters the home dust microbiota. – Alexandra Sitarik – Indoor Air

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors. – Anirudra Parajuli – Frontiers In Microbiology

Removal of artificial sweeteners and their effects on microbial communities in sequencing batch reactors. – Shaoli Li – Scientific Reports

Microbes in space
Soil microbial habitats in an extreme desert Mars-analogue environment – Kimberley Warren-Rhodes – bioRxiv

Food microbiology
** Editorial: Microbiome Yarns: human milk oligosaccharides, Bifidobacterium and immunopowergames. – Kenneth Timmis – Microbial Biotechnology

Detection of Bacterial DNA During the Process of Sake Production Using Sokujo-Moto. – Momoka Terasaki – Current Microbiology

A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial. – Charlotte Bamberger – Nutrients

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity. – Rocío Escribano-Viana – Frontiers In Microbiology

Review: The Promising Pharmacological Effects and Therapeutic/Medicinal applications of Punica Granatum L. (Pomegranate) as a Functional Food in Humans and Animals. – Kuldeep Dhama – Recent Patents On Inflammation & Allergy Drug Discovery

Probiotics / prebiotics / antibiotics
Bile-Salt-Hydrolases from the Probiotic Strain – Thibault Allain – Frontiers In Microbiology

** A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. – Marc W Van Goethem – Microbiome

PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community. – Jing Wang – Environmental Pollution (Barking, Essex : 1987)

Short-term Oral Antibiotics Treatment Promotes Inflammatory Activation of Colonic Invariant Natural Killer T and Conventional CD4 – Claudia Burrello – Frontiers In Medicine

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3 – François P. Douillard – Plos One

A probiotic complex, rosavin, zinc, and prebiotics ameliorate intestinal inflammation in an acute colitis mouse model. – Jin-Sil Park – Journal Of Translational Medicine

Phages and viruses
** Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host-microbe interactions. – Emrah Altindis – Proceedings Of The National Academy Of Sciences Of The United States Of America

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. – Mitsuhiro Yoshida – Frontiers In Microbiology

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments. – Jacob H Munson-McGee – The Isme Journal

Bioinformatics
MUGAN: Multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment. – Byunghan Lee – Bioinformatics (Oxford, England)

Techniques
Time Radically Alters Ex Situ Evidentiary Soil 16S Bacterial Profiles Produced Via Next-Generation Sequencing – Alyssa J. Badgley – Forensic Sciences

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data – Jonathan M Palmer – bioRxiv

Genomes
Complete Genome Sequence and Genomic Characterization of – Won-Hyong Chung – Frontiers In Pharmacology

Luteimonas rhizosphaerae sp. nov., isolated from the rhizosphere of Triticum aestivum L. –  Guo-Yan Zhao – International Journal of Systematic and Evolutionary Microbiology

Science, publishing, and career
Testing Hypotheses on Risk Factors for Scientific Misconduct via Matched-Control Analysis of Papers Containing Problematic Image Duplications – Daniele Fanelli – Scientific and Engineering Ethics

Bioscience-scale automated detection of figure element reuse – Daniel E Acuna – bioRxiv

February 18, 2018

Quite a few articles with alerts from today and the day before. Many interesting articles on microbe/microbe and microbe-host interactions, enjoy!

Events and jobs
Senior Bioinformatician – Host Microbiota Interactions – Wellcome Trust Sanger Institute

Postdoctoral Fellow – ‘Microbiome of intestinal tract cancers’ – Centre for Molecular and Biomolecular Informatics (CMBI)

Department Chair – Department of Microbiology and Immunology – College of Veterinary Medicine Cornell University, Ithaca, New York

Associate Scientist- Microbiology – Aerotek, Los Angeles, CA

Multi-site human microbiome
Differential contributions of specimen types, culturing, and 16S – Lone Heimann Larsen – Journal Of Clinical Microbiology

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females – Yu-Feng Huang – BMC Medical Genomics

Human oral microbiome
Bacterial microleakage at the abutment-implant interface, in vitro study. – Carlos Larrucea – Clinical Implant Dentistry And Related Research

Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis. – Sébastien Boutin – Mediators Of Inflammation

Human vaginal microbiome
Review: Cervicovaginal Microbiota and Reproductive Health: The Virtue of Simplicity. – Melis N Anahtar – Cell Host & Microbe

Human gut microbiome
The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea-dominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. – Yi-Yuan Sun – Scientific Reports

Association of gut microbial communities with plasma lipopolysaccharide-binding protein (LBP) in premenopausal women – Jessica S Citronberg – ISME

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model – Andrew J Hryckowian – bioRxiv

Review: Gut Microbiota-Based Therapies for Irritable Bowel Syndrome. – Emily K Stern – Clinical And Translational Gastroenterology

Review: A neuroscience perspective of the gut theory of Parkinson’s disease. – Lisa M Smith – The European Journal Of Neuroscience

Microbial-microbial/host interactions
Interactions between predation and disturbances shape prey communities. – Canan Karakoç – Scientific Reports

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. – Damian W Rivett – Ecology Letters

Competition in biofilms between cystic fibrosis isolates of Pseudomonas aeruginosa is driven by R-pyocins – Olubukola Oluyombo – bioRxiv

Linking associations of rare low-abundance species to their environments by association networks – Tatiana V. Karpinets – Frontiers in Microbiology

Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease. – Denise N Bronner – Cell Host & Microbe

Goblet cell associated antigen passages are inhibited during Salmonella typhimur/cium infection to prevent pathogen dissemination and limit responses to dietary antigens. – Devesha H Kulkarni – Mucosal Immunology

Animal experiments
Cytosolic and secreted peptidoglycan-degrading enzymes in Drosophila respectively control local and systemic immune responses to microbiota – Bernard Charroux – Cell Host & Microbe

Differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus. – Mei-Zhou Huang – Plos One

Rumen-protected methionine during the peripartal period in dairy cows and its effects on abundance of major species of ruminal bacteria. – Mohamed K Abdelmegeid – Journal Of Animal Science And Biotechnology

Impact of Chestnut and Quebracho Tannins on Rumen Microbiota of Bovines. – Juan María Díaz Carrasco – Biomed Research International

Starvation influences the microbiota assembly and expression of immunity-related genes in the intestine of grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – Aquaculture

Animal microbiome
The Dynamic Distribution of Small-Tail Han Sheep Microbiota across Different Intestinal Segments. – Hao Zhang – Frontiers In Microbiology

Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. – H Pieter J van Veelen – The Isme Journal

Plant, root, and soil microbiome
Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts. – Stefanie Maier – The Isme Journal

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. – Radomir Schmidt – Plos One

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. – Corina Diana Ceapă – Plos One

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments – Liana T. Burghardt – PNAS

Microbial Flora Associated with the Halophyte- – Fehmida Bibi – Frontiers In Microbiology

Root growth improvement of mesquite seedlings and bacterial rhizosphere and soil community changes are induced by inoculation with plant growth-promoting bacteria and promote restoration of eroded desert soil – Cristina Galaviz – Land Degradation and Development

Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions – Marketa Polivkova – Applied Soil Ecology

Succession of the functional microbial communities and the metabolic functions in maize straw composting process – Huawei Wei – Bioresource Technology

Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality – Linlin Dong – Acta Pharmaceutica Sinica B

Review: Soil protists: a fertile frontier in soil biology research. – Stefan Geisen – Fems Microbiology Reviews

Water and extremophile microbiome
Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake. – Christian F Edwardson – Frontiers In Microbiology

Phosphorus Solubilizing and Releasing Bacteria Screening from the Rhizosphere in a Natural Wetland – Ying Cao – Water

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands – Bing Han – Scientific Reports

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities – Eric M Bottos – bioRxiv

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants – Marco A. Molina-Montenegro – PeerJ Preprints

Built environment
Liquid co-substrates repower sewage microbiomes – Justus Hardegen – bioRxiv

Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas – Edina Szekeres – Environmental Pollution

Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers – Huan Li – Water Research

Review: A review on the applications of microbial electrolysis cells in anaerobic digestion. – Zhengsheng Yu – Bioresource Technology

Probiotics / prebiotics / antibiotics
Tacrolimus concentration to dose ratio in solid organ transplant patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. – Michael H Woodworth – Transplant Infectious Disease : An Official Journal Of The Transplantation Society

Techniques
Functional imaging of the interaction between gut microbiota and the human host: A proof-of-concept clinical study evaluating novel use for 18F-FDG PET-CT. – Ben Boursi – Plos One

A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories? – Elisabeth Nagy – Clinical Microbiology and Infection

Microbes in the news
A trip to ‘the poopy lab’ in the interest of drug development – Eric Boodman – STAT News

Probe provides rapid lung investigation – Pallab Ghosh – BBC News

January 5, 2018

Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

December 22, 2017

As the end of this year approaches, we have a post filled with plant/soil microbiome papers, as well as a few interesting food microbiology papers — enjoy!

General microbiome

A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis – Romain Savary, ISME

Pregnancy and early life

Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan, Acta Obstetricia et Gynecologica Scandinavica

Liver microbiome

Environmental peer pressure: CD4+ T cell help in tolerance and transplantation – Dana Tedesco, Liver Transplantation

Skin microbiome

Food allergy and atopic dermatitis: Prediction, progression, and prevention – Carla Mastrorilli, Pediatric Allergy and Immunology

Respiratory microbiome

The Lung Microbiome in Idiopathic Pulmonary Fibrosis: A Promising Approach for Targeted Therapies – Fastrès Aline, International Journal of Molecular Sciences

Allergy – European Journal of Allergy and Clinical Immunology

Plant, root, and soil microbiome

Microbial and organic matter patterns in a prescribed burned and thinned managed forest ecosystem – Dessy A. Owiti, Ecosphere

Microbial Interactions and Perspectives for Bioremediation of Pesticides in the Soils – Ratna Prabha, Plant-Microbe Interactions in Agro-Ecological Perspectives

Fungi: An Effective Tool for Bioremediation – Sachin Gupta, Plant-Microbe Interactions in Agro-Ecological Perspectives

Arbuscular Mycorrhizal Fungi Improve Tolerance of Agricultural Plants to Cope Abiotic Stress Conditions – Pablo Cornejo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Assessment of bacterial communities of black soybean grown in fields – Akifumi Sugiyama, Communicative & Integrative Biology

Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community – S. Hortal, Scientific Reports

Trichoderma and Its Potential Applications – Monika Jangir, Plant-Microbe Interactions in Agro-Ecological Perspectives

Bacterial Rhizoremediation of Petroleum Hydrocarbons (PHC) – Jai Godheja, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential of Beneficial Bacteria as Eco-friendly Options for Chemical-Free Alternative Agriculture – Ch. Srinivasarao, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential Microbiological Approaches for the Remediation of Heavy Metal-Contaminated Soils – R. Krishnamoorthy, Plant-Microbe Interactions in Agro-Ecological Perspectives

Commercial Microbial Products: Exploiting Beneficial Plant-Microbe Interaction – Pallavi, Plant-Microbe Interactions in Agro-Ecological Perspectives

Interaction Between Beneficial Bacteria and Sugarcane – Guilherme Grodzki Oliveira Figueiredo, Plant-Microbe Interactions in Agro-Ecological Perspectives

Potential for Developing Low-Input Sustainable Agriculture in the Tropical Andes by Making Use of Native Microbial Resources – Luis Andrés Yarzábal, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant-Microbe Interactions in the Rhizosphere: Mechanisms and Their Ecological Benefits – Kulandaivelu Velmourougane, Plant-Microbe Interactions in Agro-Ecological Perspectives

Plant Interaction with Methylotrophic Communities – Manish Kumar, Plant-Microbe Interactions in Agro-Ecological Perspectives

Toward an Integrated Resource Management: Harnessing Trichoderma for Sustainable Intensification in Agriculture – Sumita Pal, Plant-Microbe Interactions in Agro-Ecological Perspectives,

Harnessing the Plant Microbiome: A Key Towards Sustainable Agriculture – Sanjana Kaul, Plant-Microbe Interactions in Agro-Ecological Perspectives

Rhizoremediation of Environmental Contaminants Using Microbial Communities – Ashish A. Prabhu, Plant-Microbe Interactions in Agro-Ecological Perspectives

Role of Plant Growth-Promoting Rhizobacteria for Improving Crop Productivity in Sustainable Agriculture – Abhijeet S. Kashyap, Plant-Microbe Interactions in Agro-Ecological Perspectives

Molecular evidence strongly supports deadwood-inhabiting fungi exhibiting unexpected tree species preferences in temperate forests – Witoon Purahong, ISME

Animal microbiome

Rare symbionts may contribute to the resilience of coral–algal assemblages – Maren Ziegler, ISME

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton – Anny Cárdenas, ISME

Evidence for a primate origin of zoonotic Helicobacter suis colonizing domesticated pigs – Bram Flahou, ISME

Water and extremophile microbiome

Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates – Jürgen F H Strassert, ISME

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters – Vincent Hervé, ISME

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment – Kohei Ino, ISME

Food microbiome

Evaluation of the use of malic acid decarboxylase-deficient starter culture in NaCl-free cucumber fermentations to reduce bloater incidence – Y. Zhai, Journal of Applied Microbiology

Effect of phenolic compounds on the growth of selected probiotic and pathogenic bacteria – R. Pacheco-Ordaz, Letters in Applied Microbiology

Recent advances in the microencapsulation of omega-3 oil and probiotic bacteria through complex coacervation: A review – Divya Eratte, Trends in Food Science & Technology

Q fever and prevalence of Coxiella burnetii in milk – Andreana Pexara, Trends in Food Science & Technology

Microbes and art

Bioessays Cover Art