October 26, 2019

Highlights: Bacterial communities in aquaculture, crocodiles, tadpoles, mushrooms, coasts, sports facilities; viruses; standardization issues of human microbiome research; some cool events and news hot off the press!

 

Events and jobs

2019 Genome Center Halloween Symposium – 31/10/2019 – UCD, USA

MB Seminar: Marine Host-Microbiome Interactions: Challenges and Opportunities (Dr. Jonathan Eisen, UC Davis) – 22/11/2019 – UCSD, USA

General microbiome 

Metabolic specializations within a bacterial community to create living rocks – Samantha C Waterworth – bioRxiv

Analysis of bacterial microbiome associated with nylon and copper nets in an aquaculture context – Paula Canada – Aquaculture

The gut-eye-lacrimal gland-microbiome axis in Sjögren Syndrome – Claudia M. Trujillo-Vargas – The Ocular Surface

Multi-site human microbiome

DNA extraction for human microbiome studies: the issue of standardization  – K. Leigh Greathouse Genome Biology

Storage media and not extraction method has the biggest impact on recovery of bacteria from the oral microbiome – Xiaoyan Zhou – Nature

Factors contributing to interindividual variation in retronasal odor perception from aroma glycosides: the role of odorant sensory detection threshold, oral microbiota and hydrolysis in saliva – Mango Parker – ACS

Animal experiments 

Contribution of fungal microbiome to intestinal physiology, early-life immune development and mucosal inflammation in mice – Erik van Tilburg Bernardes – bioRxiv

Animal microbiome 

Gut microbiota structure differs between honey bees in winter and summer – Lucie Kešnerová – bioRxiv

Characterisation of the intestinal microbiota of commercially farmed saltwater crocodiles, Crocodylus porosus – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Changes in intestinal microbial community of Rana chensinensis tadpoles during metamorphosis – Hongyu Yang – Aquaculture

Plant, root, and soil microbiome

Impact of agro-farming activities on microbial diversity of acidic red soils in a Camellia Oleifera Forest – Jun Li – Revista Brasileira de Ciência do Solo

A horizon scan of priorities for coastal marine microbiome research – Stacey M. Trevathan-Tackett – Nature

Water and extremophile microbiome 

Effects of disinfection efficiency on microbial communities and corrosion processes in drinking water distribution systems simulated with actual running conditions – Ying Zhu – Journal of Environmental Sciences

Built environment 

Microbial diversity of bioaerosol inside sports facilities and antibiotic resistance of isolated Staphylococcus spp. – Marta Małecka-Adamowicz – Aerobiologia

Food microbiology

Comparing approaches for capturing bacterial assemblages 2 associated with symptomatic (bacterial blotch) and asymptomatic 3 mushroom (Agaricus bisporus) caps – Samuel J. Martins – APS

Comprehensive Understanding of the Bacterial Populations and Metabolites Profile of Fermented Feed by 16S rRNA Gene Sequencing and Liquid Chromatography–Mass Spectrometry – Wei Jin – MDPI Metabolites

Phages and viruses

Viruses RIG up intestinal immunity – Sanghyun Lee – Nature Immunology

Gut DNA Virome Diversity and Its Association with Host Bacteria Regulate Inflammatory Phenotype and Neuronal Immunotoxicity in Experimental Gulf War Illness – Ratanesh K Seth – MDPI Viruses

Viral quasispecies – Esteban Domingo – PLoS Genetics

Techniques

Effective application of machine learning to microbiome-based classification problems – Begüm D. Topçuoğlu – bioRxiv

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey – bioRxiv

Microbes in the news

Even the Fetus Has Gut Bacteria, Study Shows – News Wise

Tropical Air Microbiome Analysis Reveals Daily Cycle, Environmental Drivers – genomeweb

Global Microbiome Sequencing Market – Yahoo

How our day-to-day food intake shapes our gut microbiota – Gut microbiota for health

Tracking down the functions of the microbiome – phys.org

Unhealthy gut microbiome reduces brain synaptic pruning, impairs learning – News Medical

Harnessing the Power of Microbes to Fight Cancer – Medscape.com

October 5, 2019

This weekend, read about how cooking food modifies the microbiome, how bacteria ‘strip off’ to evade antibiotics, and more. Check out an interesting pilot study looking at potential inclusion and exclusion criteria of donors for safe vaginal microbiota transplant. Enjoy!

Events

Bioinformatics for the Microbiome Symposium 2019, Stanford University, Monday October 28.
Some tickets are still available!

General microbiome

Mobile phones as fomites for potential pathogens in hospitals: microbiome analysis reveals hidden contaminants – Rebecca Simmonds – Journal of Hospital Infection

Review: Microbiomes as sources of emergent host phenotypes – J. B. Lynch and E. Y. Hsiao – Science

Vaginal microbiome

*Conceptual Design of a Universal Donor Screening Approach for Vaginal Microbiota Transplant – Kevin DeLong – Frontiers in Cellular and Infection Microbiology

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia – Joan T. Price – PlosOne

Urinary microbiome

*Possible role of L-form switching in recurrent urinary tract infection – Katarzyna M. Mickiewicz – Nature Communications

Aerococcus urinae and Globicatella sanguinis Persist in Polymicrobial Urethral Catheter Biofilms Examined in Longitudinal Profiles at the Proteomic Level – Yanbao Yu – Biochemistry Insights

Gut microbiome

*Cooking shapes the structure and function of the gut microbiome – Rachel N. Carmody – Nature Microbiology

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma – Wen Fong Ooi – Gut

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial – Selina R.Cox – Gastroenterology

Water microbiome

Trophic networks improve the performance of microbial anodes treating wastewater – Christin Koch – npj Biofilms and Microbiomes

Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge – Luong N.Nguyen – Journal of Environmental Management

Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus – Ragnhildur Guðmundsdóttir – PlosOne

Animal microbiome

Looking like the locals – gut microbiome changes post-release in an endangered species – Rowena Chong – Animal microbiome

Animal experiment

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Pablo Arroyo – PlosOne

Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection – Ashley D. Smith – PlosOne

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model – Yoshitomo Morinaga – PlosOne

Plant microbiome

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae) – Suresh J. Gawande – PlosOne

Food

Comparison of the microbial composition of African fermented foods using amplicon sequencing – Maria Diaz – Scientific Reports

The impact of grape processing and carbonic maceration on the microbiota of early stages of winemaking – Raffaele Guzzon – Journal of Applied Microbiology

Fungi

Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa – Tamara Janakiev – Frontiers in Microbiology

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses – Gian Maria Niccolò Benucci – PeerJ

Viruses

The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches – Federica Ungaro – United European Gastroenterology Journal

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – Obstetrics and Gynaecology

Bioinformatics

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database – João L. Reis-Cunha – PlosOne

February 23, 2019

Highlights: Today’s digest has articles on microbes associated with infants, vagina, gut, water and many more.

Events and jobs

Postdoctoral Researcher in mathematical modelling of the impact of host restriction on the transmission of bacteria – Amsterdam – Closing date: February 28, 2019

Pregnancy and early life

A role for the microbiome in mother–infant interaction and perinatal depression – Amanda Sanders – The International Review of Psychiatry

Multi-site human microbiome

Surgical site infections and the microbiome: An updated perspective – Richard P. Wenzel – Infection Control & Hospital Epidemiology

Human vaginal microbiome

The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls – Baris Ata – Scientific Reports

Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions – Cameron Klein – mBio

Human nearly-sterile sites 

Microbiome-based body fluid identification of samples exposed to indoor conditions – Akos Dobay – FSI Genetics

Human gut microbiome

Arabinoxylan oligosaccharides and polyunsaturated fatty acid effects on gut microbiota and metabolic markers in overweight individuals with signs of metabolic syndrome: a randomized cross-over trial – Louise Kjølbæk – Clinical Nutrition

The human microbiota and infection prevention – R. Araos – Infection Control & Hospital Epidemiology

Gut pathobionts as triggers for liver diseases – Peter Fickert – Nature Microbiology

Man and the Microbiome: A New Theory of Everything? – Mary I. Butler –  Annual Review of Clinical Psychology

Is it true that gut microbiota is considered as panacea in cancer therapy? – Amir Salek Farrokhi –  Journal of Cellular Physiology

Composition of gut microbiota in patients with toxigenic Clostridioides (Clostridium) difficile: Comparison between subgroups according to clinical criteria and toxin gene load – Sung-Hee Han – PLoS ONE

Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomised controlled-feeding trial – Yi Wan – Gut

The Intestinal Microbiome, Plasma Metabolome and Liver Transcriptome‐ A Conspiracy Driving Hepatic Steatosis – Wajahat Z Mehal – Hepatology

A possible link between polyunsaturated fatty acids and uremic toxins from the gut microbiota in hemodialysis patients: A hypothesis – Julie Ann Kemp – Hemodialysis International 

Animal experiments 

Alterations of the mice gut microbiome via Schistosoma japonicum ova-induced granuloma – Yanqing Zhao – Frontiers in Microbiology

The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans – Johannes Zimmermann – bioRxiv

Helminth-Based Product and the Microbiome of Mice with Lupus – Hadar Neuman – mSystems

Gut microbiota regulates lacteal integrity by inducing VEGF-C in intestinal villus macrophages. – SH Suh – EMBO Reports

Animal microbiome

Gut Microbiome Analysis In Adult Tropical Gars (Atractosteus tropicus) – Roberto Mendez-Perez – bioRxiv

Moderate plant water stress improves larval development, and impacts immunity and gut microbiota of a specialist herbivore – Elena Rosa -PLoS ONE

Plant, root, and soil microbiome

Chinese white truffles shape the ectomycorrhizal microbial communities of Corylus avellana – Mei Yang – Annals of Microbiology

Narrow safety margin in the phyllosphere during thermal extremes – Sylvain Pincebourde – PNAS

Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles – Antoine P. Pagé – PLoS ONE

Water and extremophile microbiome 

Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California – Sabah Ul-Hasan – PLoS ONE

Editorial: Thermophilic and Halophilic Extremophiles in Eurasian Environments – Hongchen Jiang – Frontiers in Microbiology

Marine deep biosphere microbial communities assemble in near-surface sediments in Aarhus Bay – Caitlin Petro – bioRxiv

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O – Ömer K. Coskun – The ISME Journal

Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard) – Xiao-Mei Fang – Antonie van Leeuwenhoek

Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover – Lorrie Maccario – Scientific Reports

Bacterial community composition shaped by water chemistry and geographic distance in an anthropogenically disturbed river – Peng Wang – Science of The Total Environment

Built environment 

Cell factories converting lactate and acetate to butyrate: Clostridium butyricum and microbial communities from dark fermentation bioreactors – Anna Detman – Microbial Cell Factories

Phages and viruses

Discovery of several thousand highly diverse circular DNA viruses – Michael J Tisza – bioRxiv

Techniques

Spatial metabolomics of in situ, host-microbe interactions – Benedikt K Geier – bioRxiv

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass – Vincent Caruso – mSystems

 

 

November 19, 2018

Today’s digest features shallow shotgun sequencing as a useful alternative to 16S sequencing, soil metaproteomics, virus genomes from deep sea sediments, and more. And there’s an important news: the MicroMundo has been launched in Portugal! Happy reading!

Events and jobs

Open Rank Faculty Position in Microbiome or Microbial Systems Research, Baylor College of Medicine in Houston, TX

Physalia courses: 16S/ITS Metabarcoding of microbial communities (Berlin, 1-5 April 2019) Instructors: Anna Sandionigi, Antti Karkman, Bruno Fosso

Physalia courses: Metagenomics (Berlin, 27-31 May 2019) Instructors: Dr. Curtis Huttenhower, Melanie Schirmer, Cesar Arze

Gut microbiome

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn’s Disease Patient – Xin Fang – Front. Microbio.

Preprint: Microbial Dysbiosis and polyamine metabolism as predictive markers for early detection during progression of pancreatic adenocarcinoma in spontaneous mouse model – Roberto Mendez – bioRxiv

Oral microbiome

Preprint: Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study – Francesco Beghini – bioRxiv

Preprint: Sociodemographic patterning in the oral microbiome of a diverse sample of New Yorkers – Audrey Renson – bioRxiv

Soil microbiome

*Review: Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics – Robert Starke – Journal of Proteomics

Phages and viruses

Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters  – Yanze Li – Viruses

*Preprint: Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism – Disa Backstrom – bioRxiv

Bioinformatics

*Evaluating the Information Content of Shallow Shotgun Metagenomics – Benjamin Hillmann – MySystems

A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series – Fang Zhang – Stat Appl Genet Mol Biol.

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts – Breitwieser Florian – Genome Biol.

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data –Simon Lucas – Gigascience

Svetlana’s microbiology pick

* Last week was World Antibiotic Awareness Week and the MicroMundo project has been launched in Portugal:
Initially created in the USA (2012) as Small World Initiative, the MicroMundo is an innovative Citizen Science project where professors and researchers from the University of Porto encourage students to pursue career in science while addressing a worldwide health threat – antibiotic resistance.

October 23, 2018

Here comes today’s Microbiome Digest featuring the recent articles on microbial methane oxidizers, sulfidic waters, PM exposure effect on airway microbiome, dysbiotic state of spring fever, diets targeting microbiome and be a cure, peri-implantitis, effect of age and inflammation on mice microbiome, diet effect on monkeys microbiome, fecal microbial transplant in UC patients, cervical microbiome, functional repertoire of ETEC and Bifidobacterium, bile duct inflammation causing microbes, role of probiotics. HAPPY READING.

EVENTS, JOBS, SCHOLARSHIPS:

Commonwealth PhD Scholarships – Study at UK University

ENVIRONMENTAL MICROBIOME:

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers – He Z – Environ Pollut

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters – Deja-Sikora E – Microb Ecol

HUMAN RESPIRATORY MICROBIOME:

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure – Wang L – Ecotoxicol Environ Saf

ORAL MICROBIOME:

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children – Chen B – Int Immunopharmacol

The Severity of Human Peri-Implantitis Lesions Correlates with the Level of Submucosal Microbial Dysbiosis – Kröger A – J Clin Periodontol

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis – Boyer E – Sci Rep

Effects of antimicrobial peptide GH12 on the cariogenic properties and composition of a cariogenic multispecies biofilm – Jiang W – Appl Environ Microbiol
GUT MICROBIOME:

Review: Natural polysaccharides exhibit anti-tumor activity by targeting gut microbiota – Liu L – Int J Biol Macromol

Polysaccharides from Laminaria japonica alleviated metabolic syndrome in BALB/c mice by normalizing the gut microbiota – Duan M – Int J Biol Macromol.

Gut microbiota translocation promotes autoimmune cholangitis – Ma HD – J Autoimmun

Competitive lottery-based assembly of selected clades in the human gut microbiome – Verster AJ- Microbiome

Mini-Review : Leaky Gut, Leaky Brain? – Obrenovich MEM – Microorganisms

REPRODUCTIVE MICROBIOME:

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study – Arokiyaraj S –
Sci Rep

ANIMAL MODEL MICROBIOME:

Long-term intake of Lactobacillus paracasei KW3110 prevents age-related chronic inflammation and retinal cell loss in physiologically aged mice – Morita Y – Aging

Targeted Diet Modification Reduces Multiple Sclerosis-like Disease in Adult Marmoset Monkeys from an Outbred Colony – Kap YS – J Immuno

FUNCTIONAL REPERTOIRE INSIGHTS:

Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3+ regulatory T cells – Verma R – Sci Immunol.

De-O-Acetylation of mucin-derived sialic acids by recombinant NanS-p esterases of Escherichia coli O157:H7 strain EDL933 – Feuerbaum S – Int J Med Microbiol.

PLANT MICROBIOME:

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales – Li HY- Microbiome

METHODS:

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study – Jitsumura M – BMJ Open

PROBIOTICS:

Probiotics in Autoimmune and Inflammatory Disorders – Liu Y – Nutrients

NON-MICROBIOME PICK:

Preprint: Segregational drift and the interplay between plasmid copy number and evolvability – Judith Ilhan- Biorxiv

September 25, 2018

Events and jobs

4th Annual European Microbiome Congress – London UK – November 14-15 2018

*****************************

General microbiome

Review: “Under the Skin” and into the Gut: Social Epidemiology of the Microbiome – Jennifer Beam Dowd – Current Epidemiology Reports

Review: Concurrent cross‐reactivity of microbiota‐derived epitopes to both self and pathogens may underlie the “Hygiene hypothesis” – David Usharauli – Scandinavian Journal of Immunology

Pregnancy and early life

Influence of non-polio enteroviruses and the bacterial gut microbiota on oral poliovirus vaccine response: a study from south India – Ira Praharaj – The Journal of Infectious Diseases

A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space – Samanta Michelini – Microbiome

Human respiratory microbiome

Review: Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma – Elliot Mathieu – Frontiers in Physiology

Different Upper Airway Microbiome and Their Functional Genes Associated with Asthma in Young Adults and Elderly Individuals – Jin‐Jae Lee – Allergy

Human oral microbiome

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption – Annette Carola Anderson – Scientific Reports

Human gut microbiome

Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects – Mireia Lopez-Siles – Frontiers in Cellular and Infection Microbiology

Influence of gender and menopausal status on gut microbiota – Jose A.Santos-Marcos – Maturitas

Review: High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group – François Blachier – Clinical Nutrition

Review: Review of the effects of sliver nanoparticle exposure on gut bacteria – Jiangyan Li – Journal of Applied Toxicology

Review: Interactions between Bitter Taste, Diet and Dysbiosis: Consequences for Appetite and Obesity – Alexandria Turner – Nutrients

Review: Progress in characterizing the linkage between Fusobacterium nucleatum and gastrointestinal cancer – Yang Liu – Journal of Gastroenterology

The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome – Keisuke Kosumi – The American Journal of Pathology

*****************************

Animal experiments

Commensal microbiota induces colonic barrier structure and functions that contribute to homeostasis – Christina L. Hayes – Scientific Reports

Palmatine ameliorated murine colitis by suppressing tryptophan metabolism and regulating gut microbiota – Xiao-Jun Zhang – Pharmacological Research

Behavioral response to fiber feedingis cohort-dependent and associated with gut microbiota composition in mice – Lucy J.Mailing – Behavioural Brain Research

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Goji Berry Modulates Gut Microbiota and Alleviates Colitis in IL‐10‐Deficient Mice – Yifei Kang – Molecular Nutrition and Food Research

Konjaku flour reduces obesity in mice by modulating the composition of the gut microbiota – Yongbo Kang – International Journal of Obesity

Polysaccharide from fermented Momordica charantia L. with Lactobacillus plantarum NCU116 ameliorates type 2 diabetes in rats – He Gao – Carbohydrate Polymers

Allergen Immunization Induces Major Changes in Microbiota Composition and Short-Chain Fatty Acid Production in Different Gut Segments in a Mouse Model of Lupine Food Allergy – Andreassen M – Allergy and Immunology

In vitro experiments

Dietary fatty acids sustain growth of human gut microbiota – Richard Agans – Applied and Environmental Microbiology

Animal microbiome

Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri) – Xiao-Ling Wan – Scientific Reports

Differences in the Gut Microbiota Establishment and Metabolome Characteristics Between Low- and Normal-Birth-Weight Piglets During Early-Life – Na Li – Frontiers in Microbiology

Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves – Bridget E. Fomenky – Scientific Reports

Evaluation of microbial communities associated with the liquid and solid phases of the rumen of cattle offered a diet of perennial ryegrass or white clover – Jenna M. Bowen – Frontiers in Microbiology

Possibilities of early life programming in broiler chickens via intestinal microbiota modulation – Luis A Rubio – Poultry Science

A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms – Alejandra Hernandez-Agreda – Frontiers in Microbiology

Plant, root, and soil microbiome

Interactions of mycorrhiza and protists in the rhizosphere systemically alter microbial community composition, plant shoot-to-root ratio and within-root system nitrogen allocation – Gunnar J. Henkes – Frontiers in Environmental Science

Combined effects of biochar addition and nitrogen fertilizer reduction on the rhizosphere metabolomics of maize (Zea mays L.) seedlings – Nan Cheng – Plant and Soil

Does sulfur fertilizer influence Cu migration and transformation in colloids of soil pore water from the rice (Oryza sativa L.) rhizosphere? – Lijuan Sun – Environmental Pollution

The Alleopathic Compound Luteolin from Peanut Litter Affects Peanut Nodule Formation and the Rhizosphere Microbial Community – Hong-Wei Wang – Agronomy Journal

Seasonal comparison of bacterial communities in rhizosphere of alpine cushion plants in the Himalayan Hengduan Mountains – Shuai Chang – Plant Diversity

The effect of a medic-wheat rotational system and contrasting degrees of soil disturbance on nematode functional groups and soil microbial communities – Johan Habig – Agriculture, Ecosystems & Environment

Soil-microbial communities indexing from mangroves rhizophere and barren sandy habitats – Kandasamy Saravanakumar – Physiological and Molecular Plant Pathology

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil – Boxi Wang – PLOS One

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – FEMS Microbiology Ecology

Responses of arbuscular mycorrhizal fungi to long-term inorganic and organic nutrient addition in a lowland tropical forest – Merlin Sheldrake – The ISME Journal

Genetic correlation network prediction of forest soil microbial functional organization
Bin Ma – The ISME Journal

Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach – M. H. Hemmat-Jou – Ecotoxicology

Water and extremophile microbiome

Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs – Nathaniel W. Fortney – Frontiers in Microbiology

Methanogens and iron-reducing bacteria: the overlooked members of mercury methylating microbial communities in boreal lakes – Andrea G. Bravo – Applied and Environmental Microbiology

Metagenomics reveals microbial diversity and metabolic potentials of seawater and surface sediment from a hadal biosphere at the Yap Trench – Xinxu Zhang – Frontiers in Microbiology

Dynamics and determinants of amoeba community, occurrence and abundance in subtropical reservoirs and rivers – Kexin Ren – Water Research

Microbial Ecology

Review: A coexistence theory in microbial communities – Marina Dohi – Royal Society Open Science

Inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier – Data in Brief

Resistome

Selection for increased quorum-sensing cooperation in Pseudomonas aeruginosa through the shut-down of a drug resistance pump – Ron D. Oshri – The ISME Journal

*****************************

Fecal Transplants

A Systematic Review of the Efficacy and Safety of Fecal Microbiota Transplant for Clostridium difficile Infection in Immunocompromised Patients – Oluwaseun Shogbesan – Canadian Journal of Gastroenterology and Hepatology

Faecal microbiota transplantation as a treatment for inflammatory bowel disease: a national survey of adult and paediatric gastroenterologists in the UK – James Roger Mcilroy – Frontline Gastroenterology

Introduction to the joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) faecal microbiota transplant guidelines – Benjamin H. Mullish – The Journal of Hospital Infection

Phages and viruses

Detection of Viruses in Clinical Samples Using Metagenomic Sequencing and Targeted Sequence Capture – Kristine M. Wylie – Journal of Clinical Microbiology

Waste and Pollution

Pathogens, faecal indicators and human‐specific microbial source‐tracking markers in sewage – Cristina García‐Aljaro – Journal of Applied Microbiology

September 10, 2018

In the today’s digest: an article on detection limits and bias with DNA extraction kits and primer choice, a novel R package to analyze timeseries in the 16S microbiome data in perturbation studies, a study on how fecal microbiota transplantation induces changes in gut microbial and metabolomic profiles of pediatric ulcerative colitis patients, plus an invitation for the first worldwide online open access course via Twitter about science and microbiology starting October 2.

Event

Third Annual Microbiome Symposium at Stanford, September 24 at the Stanford Faculty Club, Palo Alto, CA.

Human gut microbiome

*Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients – David J Nusbaum – FEMS Microbiology Ecology

Review: Sample preparation and recent trends in volatolomics for diagnosing gastrointestinal diseases – Tomasz Majchrzak – TrAC Trends in Analytical Chemistry

Special Report: The role of gut microbiota in lupus: what we know in 2018? – Lorena Ruiz – Expert Review of Clinical Immunology

Human gut virome

The Intestinal Virome and Immunity – Jessica A. Neil and Ken Cadwell – J Immunology

Human lung microbiome

The Human Respiratory Microbiome: The End of the Beginning? – Alicia B. Mitchell and Allan R. Glanville – Essentials in Lung Transplantation

Human oral microbiome

Review: The oral microbiome – friend or foe? – Kilian Mogens – Eur J Oral Science

Animal microbiome

Ultrahigh-throughput functional profiling of microbiota communities – Stanislav S. Terekhova – PNAS

Water microbiome

*Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing – Jakob Brandt and Mads Albertsen – Frontiers in Microbiology

Application of untargeted metabolomics for the detection of pathogenic Naegleria fowleri in an operational drinking water distribution system – Zhihao Yu – Water Research

Soil microbiome

Investigation on microbial community in remediation of lead-contaminated soil by Trifolium repensL. – Chenjing Liu – Ecotoxicology and Environmental Safety

Bioinformatics

*The Block Bootstrap Method for Longitudinal Microbiome Data – Pratheepa Jeganathan – arXiv

*Course

#EUROmicroMOOC: Trends in Microbiology [The first worldwide online open access microbiology course via Twitter]