June 6, 2018

 

Today’s highlights: Microbes on aging flue-cured tobaccos, impact of gut microbes on neurological disease, gut microbiome of non-human microbiome, diet simplification selects for high gut microbial diversity.

General microbiome

Species Diversity and Functional Prediction of Surface Bacterial Communities on Aging Flue-Cured Tobaccos – F Wang – Current Microbiology

Oxygen restriction induces a viable but non-culturable population in bacteria – LA Kvich – bioRxiv

Human respiratory microbiome

Airway Microbiota Is Associated with Up-Regulation of the PI3K Pathway in Lung Cancer – J-C J Tsay – American Journal of Respiratory and Critical Care Medicine

Human skin microbiome

Role of anaerobes in polymicrobial communities and biofilms complicating diabetic foot ulcers – SL Percival – International Wound Journal

Human gut microbiome

Impact of gut microbiota on neurological diseases: Diet composition and novel treatments – A L-Garcia – Critical Reviews in Food Science and Nutrition

Composition and richness of the serum microbiome differ by age and link to systemic inflammation – TW Buford – GeroScience

Animal microbiome 

Review: The gut microbiome of nonhuman primates: Lessons in ecology and evolution – JB Clayton – American Journal of Primatology

Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions – N Akduman – PLoS One

Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas – H Li – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Rhizospheric bacterial isolates of grass pea (Lathyrus sativus L.) endowed with multiple plant growth promoting traits – A Mussa – Journal of Applied Microbiology

Diversity of culturable methylotrophic bacteria in different genotypes of groundnut and their potential for plant growth promotion – R. Krishnamoorthy – 3 Biotech

Environmental factors shaping the diversity of bacterial communities that promote rice production – Z Wu – BMC Microbiology

Water and extremophile microbiome 

Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay – MS Reza – Gene

Decay of sewage-associated bacterial communities in fresh and marine environmental waters and sediment – W Ahmed – Applied Microbiology and Biotechnology

 

May 28, 2018

 

In our short digest today, you could read articles on animal experiments and pre-prints on techniques!

Human gut microbiome

Preprint: Using molecular ecological network analysis to explore the effects of chemotherapy on intestinal microbial communities of colorectal cancer patients – J Cong – bioRxiv

Animal experiments 

Anti-diabetic effect of baicalein is associated with the modulation of gut microbiota in streptozotocin and high-fat-diet induced diabetic rats – B Zhang – Journal of Functional Foods

Effects of limestone inclusion on growth performance, intestinal microbiota, and the jejunal transcriptomic profile when fed to weaning pigs – L Blavi – Animal Feed Science and Technology

Plant, root, and soil microbiome

Soil microbiological attributes indicate recovery of an iron mining area and of the biological quality of adjacent phytophysiognomies – AO Silva – Ecological Indicators

Water and extremophile microbiome 

Response of microbial populations regulating nutrient biogeochemical cycles to oiling of coastal saltmarshes from the Deepwater Horizon oil spill – H-S Bae – Environmental Pollution

 

Techniques

Preprint: Using the Wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens – R Hernandez – bioRxiv

Preprint: Isolation and antibiotic profile of Vibrio spp. final effluents of two wastewater treatment plants in the Eastern Cape of South Africa – O Osuolale – bioRxiv

Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water – P Kulkarni – Science of The Total Environment

Effect of temperature and pH on the community dynamics of coagulase-negative staphylococci during spontaneous meat fermentation in a model system – DA Stavropoulou – Food Microbiology

 

May 27, 2018

Pharmacobiomics, liver-microbiome axis, starvation effect on gut microbiota of shrimp,  influence of gut microbiome on the larvae of a lepidopteran pest, microbiota of berries, building a local scientific community in data science and lots of articles for today’s digest.

General microbiome

Pharmacology in the age of the Holobiont – P Norvaisas – Current Opinion in Systems Biology

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production – D Gallagher – Bioresource Technology

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium – N Vardanyan – Environmental Technology

Variation in Electrode Redox Potential Selects for Different Microorganisms Under Cathodic Current Flow From Electrodes in Marine Sediments – BR Lam – Environmental Microbiology

Diurnal patterns of airborne algae in the Hawaiian Islands: a preliminary study – HW Singh – Aerobiologia

Novel human microbe-disease associations inference based on network consistency projection – S Zou – Scientific Reports

Multi-site human microbiome

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans – A Vanhatalo – Free Radical Biology and Medicine

Review: Biodiversity of the Human Oral Mycobiome in Health and Disease – HMHN Bandara – Oral Diseases

 

Human nearly-sterile sites 

Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation – D-L Vu – Clinical Microbiology and Infection

Human gut microbiome

Review: Liver–Microbiome Axis in Health and Disease – TE Adolph – Trends in Immunology

Preprint: Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis. – MM David – bioRxiv

Fecal and Mucosa-Associated Intestinal Microbiota in Patients with Diarrhea-Predominant Irritable Bowel Syndrome – N Maharshak – Digestive Diseases and Sciences

Prevention and treatment of Clostridium difficile associated diarrhea by reconstitution of the microbiota – N Eliakim-Raz – Human Vaccines & Immunotherapeutics

Animal experiments 

Bifidobacterium spp. reshaping in the gut microbiota by low dose of juçara supplementation and hypothalamic insulin resistance in Wistar rats – G Jamar – Journal of Functional Foods

Salvianolic acid B alters the gut microbiota and mitigates colitis severity and associated inflammation – X Wu – Journal of Functional Foods

Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model – X Zhang – Journal of Functional Foods

Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities – W-F Dai – Fish & Shellfish Immunology

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Z Ge – Scientific Reports

Animal microbiome 

Preprint: The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – MT Schwarz – bioRxiv

Plant, root, and soil microbiome

Review: High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota – A pilot study – J Lukša – Food Research International

Microbial functional responses to long-term anthropogenic impact in mangrove soils – L Cabral – Ecotoxicology and Environmental Safety

Foliage application of nitrogen has less influence on soil microbial biomass and community composition than soil application of nitrogen – X Huang – Journal of Soils and Sediments

Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments – Y Chen – Science of The Total Environment

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5 – J Gao – Ecotoxicology and Environmental Safety

Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+‐pumping pyrophosphatase in pepper plants – G Vigani – Environmental Microbiology

Defining plant growth promoting rhizobacteria molecular and biochemical networks in beneficial plant-microbe interactions – A Rosier – Plant and Soil

Roles of Plant-Associated Microbiota in Traditional Herbal Medicine – W Huang – Trends in Plant Science

Spatial structuring of soil microbial communities in commercial apple orchards – G Deakin – Applied Soil Ecology

Effects of root colonization by zinc-solubilizing bacteria on rice plant (Oryza sativa MR219) growth – NMI Othman – Agriculture and Natural Resources

Promising filamentous native fungi isolated from paddy soils for arsenic mitigation in rice grains cultivated under flooded conditions – FR Segura – Journal of Environmental Chemical Engineering

Soil respiration in Chinese tea gardens: autotrophic and heterotrophic respiration – LC Fan – European Journal of Soil Science

Water and extremophile microbiome 

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and ‘Candidatus Methanohalarchaeum thermophilum’, extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. – DY Sorokin – International Journal of Systematic and Evolutionary Microbiology

 

Food microbiology

The Genus Wallemia—From Contamination of Food to Health Threat – J Zajc- Microorganisms

Phages and viruses

Biological species in the viral world – L-M Bobay – PNAS

Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium – K Moon – Scientific Reports

 

Non-microbiology picks

Preprint: Building a local community of practice in scientific programming for Life Scientists – SLR Stevens – bioRxiv

 

May 12, 2018

Today’s highlights in our Microbiology picks: Antibacterial activity of nested concentric patterns, relationship between the microbiota epitopes and antigenic epitopes, a book chapter on N-Acetyl transferase microbes, core microbiota for de novo IBD, soil microbes and disease suppression, fungi of office dust, microbes of potable  water from the Himalayan region, articles from ‘Techniques’ section.

Today’s highlights in our non-microbes picks: Epidemiology is important, recent on-goings on harassment, mental health awareness in academia, mimicking the prebiotic chemistry using flow chemistry, step taken by Wellcome Trust against misconduct in academia including harassment, Horizon 2020 budget for 2021-27.

 

Events and jobs

Laboratory Manager : New York, NY, United States – Albert Einstein College of Medicine – Deadline: 18 May 2018

General microbiome

Supramolecular Kandinsky circles with high antibacterial activity – H Wang – Nature Communications

Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes – SC Pro – PLoS One

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia – JB Benoit – PLoS One

Book chapter: N-Acetyltransferases Microorganisms – S Boukouvala – Arylamine N-acetyltransferases in Health and Disease:From Pharmacogenetics to Drug Discovery and Diagnostics

 

Human vaginal microbiome

Preprint: Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Z-L Deng – bioRxiv

Human gut microbiome

Preprint: Variability of core microbiota in newly diagnosed treatment-naïve paediatric Inflammatory Bowel Disease patients – TGJ de Meij – bioRxiv

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Y Zhang – mBio

Animal experiments 

Preprint: Bottlenecks in the transmission of Porcine reproductive and respiratory syndrome virus (PRRSV1) to naïve pigs and quasi-species variation during infection in partially immune pigs – M Cortey – bioRxiv

Lactobacillus gasseri PA-3 utilizes the purines GMP and guanosine and decreases their absorption in rats – N Yamada – Nucleosides, Nucleotides & Nucleic Acids

An exclusive metabolic niche enables strain engraftment in the gut microbiota – ES Sheperd – Nature

Interleukin 1α-Deficient Mice Have an Altered Gut Microbiota Leading to Protection from Dextran Sodium Sulfate-Induced Colitis – M Nunberg – mSystems

Animal microbiome 

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – F Zepeda-Paulo – PeerJ

Plant, root, and soil microbiome

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression – BEA Dignam – PLoS One

Relations between bacterial communities and enzyme functions of two paddy soils – X Luo – European Journal of Soil Science

Nematophagus fungi increasing phosphorus uptake and promoting plant growth – TSA Monteiro – Biological Control

Water and extremophile microbiome 

Effect of elevated pressure on ferric iron reduction coupled to sulfur oxidation by biomining microorganisms – R Zhang – Hydrometallurgy

Halophilic & halotolerant prokaryotes in humans – EH Seck – Future Medicine

Preprint: Structural variability and functional association in the epiphytic bacteria assemblies of freshwater macrophytes (Myriophyllum spicatum) – L Xian – bioRxiv

Investigation of nutrients and faecal coliforms removal in wastewater using a hydroponic system – SF Ndulini – Physics and Chemistry of the Earth, Parts A/B/C

Built environment 

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – J-H Park – Indoor Air

 

Phages and viruses

Preprint: First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region – AK Singh – bioRxiv

Preprint: “In plaque-mass spectrometry imaging” reveals a major metabolic shift towards odd-chain fatty acid lipids induced by host-virus interactions – G Schleyer – bioRxiv

Preprint: Adventitious viruses persistently infect three commonly used mosquito cell lines – J Weger-Lucarelli – bioRxiv

Techniques

Preprint: High-resolution ISR amplicon sequencing reveals personalized oral microbiome – C Mukherjee – bioRxiv

Preprint: Transcriptome Analysis of Neisseria gonorrhoeae During Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants Between Men and Women – K Nudel – bioRxiv

Designer cells programming quorum-sensing interference with microbes – F Sedlmeyer – Nature Communications

A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum – A Roth – Nature Communications

Preprint: Detection and quantification of the heterogeneity of S. aureus bacterial populations to identify antibiotic-induced persistence – MH Hasan – bioRxiv

Rapid isolation of fast-growing methanotrophs from environmental samples using continuous cultivation with gradually increased dilution rates – J Kim – Applied Microbiology and Biotechnology

Microbes in the news

Stanley Falkow, Who Saw How Bacteria Cause Disease, Dies at 84 – NY Times

How the Bugs In Your Gut Could Affect Your Blood Vessels – Live Science

Faeces transplant: The best cure for severe diarrhoea may be more faeces – Times Live

Cancer-killing viruses show promise — and draw billion-dollar investment – Nature

Does where we live affect our skin microbiome? – Medical News Bulletin

Non-Microbiology Picks

Editorial: Epidemiology is a science of high importance – Nature Communications

Mimicking the surface and prebiotic chemistry of early Earth using flow chemistry – DJ Ritson – Nature Communications

I’d whisper to my student self: you are not alone – D Reay – Nature

Harassment should count as scientific misconduct – E Marín-Spiotta – Nature

€100-billion budget proposed for Europe’s next big research programme – I Vesper – Nature

Editorial: The #MeToo campaign is gaining ground in China – Nature

Editorial: What to do to improve postgraduate mental health – Nature

Report harassment or risk losing funding, says top UK science funder – H Else – Nature

78,000-year-old record of Middle and Later stone age innovation in an East African tropical forest – C Shipton – Nature Communications

KACST Impact – Nature Communications

 

May 6, 2018

Brassicaceae plants-fungi associations, a feature on PCR bias during microbiome analysis, a thesis about viruses; preprints about Mobile-CRISPRi system on bacteria, what may happen to the intestinal microbiota when Lactobacillus reuteri intervenes; few non-microbio picks covering mental health, conservation policy, stem cell policy; and a lot more for our digest from Sunday.

General microbiome

Preprint: Mobile-CRISPRi: Enabling Genetic Analysis of Diverse Bacteria – JM Peters – bioRxiv

Preprint: Effect of Lactobacillus reuteri on intestinal microflora and immune parameters: involvement of sex differences – J He – biorXiv

Review: The Interplay Between the Microbiome and Cardiovascular Risk – BA Minnifield – Current Genetic Medicine Reports

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria – KL Wyres – Current Opinion in Microbiology

Proteomic studies on lactic acid bacteria: A review – KS Vinusha – Biochemistry and Biophysics Reports

Multi-site human microbiome

Distinct shifts in the oral microbiota are associated with the progression and aggravation of mucositis during radiotherapy – J Hou – Radiotherapy and Oncology

Human skin microbiome

Skin microbiome changes in patients with interdigital tinea pedis – R  Wang – British Journal of Dermatology

Human vaginal microbiome

The Vaginal Eukaryotic DNA Virome and Preterm Birth  – KM Wylie – American Journal of Obstetrics and Gynecology

Systematic Review: The vaginal microbiota and its association with Human Papillomavirus, Chlamydia trachomatis, Neisseria gonorrhea and Mycoplasma genitalium infections: a systematic review and meta-analysis – J Tamarelle – Clinical Microbiology and Infection

Human gut microbiome

Review: Methods for studying gut microbiota: A primer for physicians – AN Sarangi – Journal of Clinical and Experimental Hepatology

Review: Effects of the Gut microbiota on Amygdalin and its use as an anti-cancer therapy: Substantial review on the key components involved in altering dose efficacy and toxicity – V Jaiswal – Biochemistry and Biophysics Reports

The ability of human intestinal anaerobes to metabolize different oligosaccharides: Novel means for microbiota modulation? – R Ose – Anaerobe

Clostridium difficile cure with fecal microbiota transplantation in a child with Pompe disease: a case report – DE Dow – Journal of Medical Case Reports

Association Between Bacteremia from Specific Microbes and Subsequent Diagnosis of Colorectal Cancer  – TNY Kwong – Gastroenterology

Animal experiments 

Tributyltin exposure induces gut microbiome dysbiosis with increased body weight gain and dyslipidemia in mice – H Guo – Environmental Toxicology and Pharmacology

Inhibition Effect of Glycyrrhiza Polysaccharide (GCP) on Tumor Growth through Regulation of the Gut Microbiota Composition – X Zhang – Journal of Pharmacological Sciences

Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy mice – D Ma – Scientific Reports

Preprint: Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota – W Yan – bioRxiv

Acute exposure to PBDEs at an environmentally realistic concentration causes abrupt changes in the gut microbiota and host health of zebrafish – L Chen – Environmental Pollution

Animal microbiome 

Integrated metatranscriptomics and metaproteomics for the characterization of bacterial microbiota in unfed Ixodes ricinus – A Hernández-Jarguín – Ticks and Tick-borne Diseases

Metatranscriptome analysis of the intestinal microorganisms in Pardosa pseudoannulata in response to cadmium stress – H Yang – Ecotoxicology and Environmental Safety

Plant, root, and soil microbiome

Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host–symbiont molecular mechanisms – K Hiruma – Current Opinion in Plant Biology

Cross-kingdom lipid transfer in arbuscular mycorrhiza symbiosis and beyond – A Keymer – Current Opinion in Plant Biology

Isolation of local Bacillus spp. from Afghanistan soils and their potential in suppressing the root-knot nematodes on tomato – AS Jamily – J-Stage

Effect of community-based soil and water conservation practices on arbuscular mycorrhizal fungi types, spore densities, root colonization, and soil nutrients in the northern highlands of Ethiopia – M Welemariam – Chemical and Biological Technologies in Agriculture

Biocontrol mechanisms of Bacillus sp., isolated from tomato rhizosphere, against Fusarium oxysporum f. sp. lycopersici – M Jangir – Biological Control

Root Exudates Dominate the Colonization of Pathogen and Plant Growth-Promoting Rhizobacteria – J Yuan – Root Biology

Unfolding the Role of Rhizomicrobiome Toward Sustainable Agriculture – S Kaul – Root Biology

Litter breakdown as a tool for assessment of the efficiency of afforestation and ash-aided phytostabilization on metal-contaminated soils functioning in Northern France – J Leclercq-Dransart – Environmental Science and Pollution Research 

Sugars en route to the roots. Transport, metabolism and storage within plant roots and towards microorganisms of the rhizosphere – N Hennion – Physiologia Plantarum

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient – A Angermeyer – PeerJ

Impact of slope exposure on chemical and microbiological properties of Norway spruce deadwood and underlying soil during early stages of decomposition in the Italian Alps – T Bardelli – CATENA

Built environment 

A comparative study of eubacterial communities by PCR-DGGE fingerprints in anoxic and aerobic biotrickling filters used for biogas desulfurization – A Valle – Bioprocess and Biosystems Engineering

Food microbiology

Microbial community dynamics of Dan’er barley grain during the industrial malting process – X Li – Food Microbiology

Physicochemical, microbiological and sensory acceptance alterations of strawberries caused by gamma radiation and storage time – M de Jesus Filho – Scientia Horticulturae

Evaluation of critical points of mould growth and mycotoxin production in the stored barley ecosystem with a hazardous initial microbiological state of grain – J Wawrzyniak – Journal of Stored Products Research

Viruses and phages

Thesis: Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology – G Mahmoudabadi – Caltech THESIS

 

Techniques

Microbiology: making the best of PCR bias – M  Eisenstein – Nature

Anton Chekhov and Robert Koch Cheek to Cheek: A Proteomic Study – A D’Amato – Proteomics

Microbes in the news

Future of Microbiome Drugs Market including key players Pfizer, Second Genome, Seres Therapeutics – Technical Progress News

Pattern hair loss could be due to gut bacteria – Science Nordic

Legionella bacteria has been detected at the problem-plagued Perth Children’s Hospital. – SBS News

Connections Between Art And Science Explored – The Enterprise

Non-microbiology picks

Arctic ice carries heavy freight of plastic – Nature

Brazil’s lawmakers renew push to weaken environmental rules – Nature

Feeling overwhelmed by academia? You are not alone – Nature

Real-world illness requires medical multitasking – Nature

Announcement: stem-cell policy – Nature

May 5, 2018

 

For the Saturday digest the theses on making pipelines of microbial communities available and microbes of butterflies; plus the whole section of animal microbiome would be my choice for reading.

General microbiome

Thesis: Making Pipelines and Large Processing Microbial Community Studies Available to Any User, Any Time, Any Place – JAN Molina – ProQuest

Multi-site human microbiome

Social networks, cooperative breeding, and the human milk microbiome – CL Meehan  – American Journal of Human Biology

 

Human gut microbiome

Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals – CP Neff – EBioMedicine

Animal microbiome 

Thesis: Evolution of Microbial Communities and Chemosensory Genes in Passion-Vine Butterflies – B van Schooten – ProQuest

Microbial community and diversity in the feces of Sichuan takin (Budorcas taxicolor tibetana) as revealed by Illumina Miseq sequencing and quantitative real-time PCR – H Zhu – AMB Express

Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi) – J Kylie – BMC Veterinary Research

Plant, root, and soil microbiome

Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola) and characterization of osmoregulatory genes in halophilic Bacilli – S Mukhtar – Canadian Journal of Microbiology

Contrasting beneficial and pathogenic microbial communities across consecutive cropping fields of greenhouse strawberry – Y Huang – Applied Microbiology and Biotechnology

Reanalysis of microbiomes in soils affected by apple replant disease (ARD): Old foes and novel suspects lead to the proposal of extended model of disease development – L Nicola – Applied Soil Ecology

Root–Microbe Interactions: Understanding and Exploitation of Microbiome – A Sharma – Root Biology

Biodegradation of pyraclostrobin by two microbial communities from Hawaiian soils and metabolic mechanism – X Chen – Journal of Hazardous Materials

Water and extremophile microbiome 

Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine – JO Bonilla – Extremophiles

 

Techniques

Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation – Q Zeng – Microbiome

DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces – PB Shridhar – PLoS One

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay – MS Reza – Gene

 

 

April 30, 2018

 

Articles from the section ‘Techniques’ are my suggested reads for today’s short digest!

General microbiome

Microbial interactions trigger the production of antibiotics – T Netzker – Current Opinion in Microbiology

 

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

Preprint: Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia – LMO Loohuis – bioRxiv

 

Plant, root, and soil microbiome

Effectiveness of bacterial inoculation in alleviation of salinity on water status, mineral content, gas exchange and photosynthetic parameters of Viburnum tinus L. plants – MJ Gómez-Bellot – Scientia Horticulturae

Review: Where are we going with genomics in plant pathogenic bacteria? – J Xu – Genomics

Water and extremophile microbiome 

Preprint: Illuminating microbial metabolic activities in the dark deep ocean with metaproteomics – Z-X Xie – bioRxiv

 

Phages and viruses

Comparison of Staphylococcus Phage K with Close Phage Relatives Commonly Employed in Phage Therapeutics – J Ajuebor – Antibiotics

Techniques

Preprint: DivNet: Estimating diversity in networked communities – AD Willis – bioRxiv

A synthetic bacterial information transfer system functions in the mammalian gut – S Kim – bioRxiv

Microbes in the news

A population that pollutes itself into extinction – NY Times

Why veterinarians say you shouldn’t feed your dog raw meat – Western Mass News

Soil protists: a fertile frontier in biology research – OUP Blog

China Industrial Microbiology market Research Report Released with growth, latest trends & forecasts till 2022 – bitzArena

Global Microbiome Therapeutics Market 2018 | Major Companies, Industry Dynamics and Growth Factors 2025 – The Expert Consulting