July 22, 2018

Soil microbial community structure during pedogenesis; microbes in forest ecosystem; microbes of turbid Korean wines, of Mexican cheese; evaluating genomic diversity of viruses using a common bioinformatics platform and a lot more for today’s digest.

General microbiome

Nature’s conductors: what can microbial multi-heme cytochromes teach us about electron transport and biological energy conversion? – Grace W Chong – Current Opinion in Chemical Biology

Proteins of generalist and specialist pathogens differ in their amino acid composition – Luz P Blanco – Life Science Alliance

Human gut microbiome

Inhibiting Growth of Clostridioides difficile by Restoring Valerate, Produced by the Intestinal Microbiota – Julie A.K. McDonald – Gastroenterology

Animal experiments 

Bifidobacterium pseudolongum in the Ceca of Rats Fed Hi-Maize Starch Has Characteristics of a Keystone Species in Bifidobacterial Blooms – Manuela Centanni – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial Compositions and Enzymes of a Forest Ecosystem in Alabama: Initial Response to Thinning and Burning Management Selections – Fritz A. Ntoko – Open Journal of Forestry

Changes in soil microbial community structure in relation to plant succession and soil properties during 4000 years of pedogenesis – Shankar G. Shanmugam – European Journal of Soil Biology

Microbial Diversities and Potential Hazards of Korean Turbid Rice Wines (makgeolli): Multivariate Analyses – Nam Hee Kim – Food Microbiology

Impact of the South-to-North water diversion on the soil microbial community structure in the Miyun Reservoir riparian zone – Jiangqi Qu – IOP Science

The soil microbial foodweb revisited with metatranscriptomics – predatory Myxobacteria as keystone taxon? – Sebastian Petters – bioRxiv

Built environment 

Black water collected from the septic tank treated with a living machine system: HRT effect and microbial community structure – Zhan Jin – Chemosphere

Microbial communities and functional genes of nitrogen cycling in an electrolysis augmented constructed wetland treating wastewater treatment plant effluent – Pengfei Zhang –  Chemosphere

Food microbiology

Profiling of bacterial and fungal communities of Mexican cheeses by high throughput DNA sequencing – Selvasankar Murugesan – Food Research International

Phages and viruses

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy – Pakorn Aiewsakun -Journal of General Virology

Techniques

Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus – Chan Yeong Kim – Scientific Reports

Environmental proteomic studies: closer step to understand bacterial biofilms – Anupama Rani – World Journal of Microbiology and Biotechnology

Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments – Muhammad Bilal – Applied Microbiology and Biotechnology

A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities – Mehreen Anjum – Journal of Microbiological Methods

 

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July 5, 2018

Today’s microbiology picks have articles on sampling source effect on the gut microbial diversity, whether resistant starch in mothers could benefit the offsprings, protective role of the gut bacteria of firebugs, microbial community shift during different stages in anaerobic membrane bioreactor, NanoAmpli-Seq as well as articles from plant-root-soil microbiome. Precision medicine, genetics of social interaction and isolation, “ethics dumping ” among our non-microbiology picks.

 

Events and jobs

John Maddox Prize 2018 nomination – Deadline: 13th August 2018 – Check their website for more details

General microbiome

Human-associated microbial populations as evidence in forensic casework – Frederike C.A. Quaak – Forensic Science International: Genetics

The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy.  – U Desselberger – MDPI

244 Analysis of microbiome prostatic secretion in depending of levels total testosterone in blood serum – M.I. Kogan – The Journal of Sexual Medicine

Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention – Catherine Ley – PLoS One

 

Human skin microbiome

Microbiome analysis of forehead skin in patients with atopic dermatitis and healthy subjects: Implication of Staphylococcus and Corynebacterium –  Masutaka Furue – The Journal of Dermatology

Human vaginal microbiome

Trichomonas vaginalis: Pathogenesis, Symbiont Interactions, and Host Cell Immune Responses – Frances Mercer – Trends in Parasitology

Human gut microbiome

More of the Gut in the Lung: How Two Microbiomes Meet in ARDS – Samiran Mukherjee – Yale Journal of Biology and Medicine

The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Severe Defects in the Macrophage Barrier to Gut Microflora in Inflammatory Bowel Disease and Colon Cancer. – Carlos A. Rubiro – Anticancer Research

Animal experiments 

Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny – Julie Leblois – PLoS One

Animal microbiome

The cotton stainer’s gut microbiota suppresses infection of a co‐transmitted trypanosomatid parasite – Thomas O Onchuru – Molecular Ecology

Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources – Haonan Wu – Microbiology Open

Evidence for multiple ecological roles of Leptographium abietinum, a symbiotic fungus associated with the North American spruce beetle – Thomas S Davis – Fungal Ecology

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon – Evan P Starr – Microbiome

Swift Acid Rain Sensing by Synergistic Rhizospheric Bioelectrochemical Responses – Tian Li – ACS Sensors

Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays – Saarah A Maarastawi – Frontiers in Microbiology

Plant growth promoting bacteria associated with corm of Crocus sativus during three growth stages – Ranjit Kour – Letters in Applied Microbiology

Fungal Diversity of Rhizosphere Soil from 11 Varieties of Grapevines at Maturity Stage from Two Vineyards in China – Ping Zhao – Journal of Biobased Materials and Bioenergy

Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates – Meike Siebers – PLoS One

The value of wet leaves – Todd E. Dawson – New Phytologist

Water and extremophile microbiome 

Biofilm and planktonic bacterial communities in a drinking water distribution system supplied with untreated groundwater – Jianfei Chen – Archives of Microbiology

Marine Environmental Epigenetics – Jose M. Eirin-Lopez – Annual Reviews

Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration ratesDisentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates – Oliver Müller – Environmental Microbiology

Effect of different carbon sources on denitrification performance, microbial community structure and denitrification genes – Zhongshuo Xu – Science of The Total Environment

Built environment 

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor –  Nsanzumukiza Martin Vincent – MDPI

Food microbiology

Inactivation of Escherichia coli O157:H7 and Salmonella and Native Microbiota on Fresh Strawberries by Antimicrobial Washing and Coating – Mingming Guo – Journal of Food Protection

Microbial quality of ice cream sold by retail outlets in Erzurum. –  S Çubukçı – CAB Direct

 

Techniques

Preprint: NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Preprint: Genetic insight into zinc and antimicrobial toxicity uncovers a glycerol phosphate modification on streptococcal rhamnose polysaccharides – Rebecca J. Edgar – bioRxiv

Preprint: Nano-particles from Chaetomium against Rice Blast – Jiao Jiao Song – bioRxiv

Seamless assembly of recombinant adenoviral genomes from high-copy plasmids – Jessica J. Miciak – PLoS One

Twenty-seven years of screening for Shiga toxin-producing Escherichia coli in a university hospital. Brussels, Belgium, 1987-2014 – Klara De Rauw – PLoS One

Microbes in the news

Bacteria Fight Competitors by Turning them Against Each Other – Technology Networks

Non-microbiology Picks

Personalized medicine should not be restricted to the wealthy – Nature

Elucidating the genetic basis of social interaction and isolation – Nature Communications

Evaluation woes: we’re on it, responds DORA – Nature

Italy is squeezing out wet biology research – Nature

Europe’s biggest research fund cracks down on ‘ethics dumping’ – Nature

 

June 7, 2018

 

Today’s microbiology highlights: Microbiome in pregnancies, microbiome of SLE, Mycobacteria of a karst region, skin microbiome of non-human mammals. And lab diversity, potential problem in big data, Paris climate agreement of 1.5⁰C increase among the non-microbe highlights.

 

General microbiome

Biochemical, molecular and antibiotic resistance profile of multi-potential toluene metabolizing bacteria isolated from tannery effluents – F Muccee – bioRxiv

Pregnancy and early life

Review: Microbiome in normal and pathological pregnancies: A literature overview – CR Taddei – AJRI

Multi-site human microbiome

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells – AP Chan – Scientific Reports

 

Human gut microbiome

Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis – JS Bajaj – AJG

Review: Early-Life Food Nutrition, Microbiota Maturation and Immune Development Shape Life-Long Health – X Zhou – Critical Reviews in Food Science and Nutrition

Animal experiments

Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota – F Cignarella – Cell Metabolism

The Microbiome and Systemic Lupus Erythematosus – JT Rosenbaum – The New England Journal of Medicine

Review: The probiotic effectiveness in experimental colitis is correlated with gut microbiome and host genetic features – S Suwal – bioRxiv

Animal microbiome 

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia – AA Ross – PNAS

Alterations in the gut (Gallus gallus) microbiota following the consumption of zinc biofortified wheat (Triticum aestivum) -based diet – S Reed – ACS

Water and extremophile microbiome 

Nontuberculous mycobacteria in the environment of Hranice Abyss, the world’s deepest flooded cave (Hranice karst, Czech Republic) – I Pavlik – Environmental Science and Pollution Research

Built environment 

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

Food microbiology

Effect of herbal feed additives on performance parameters, intestinal microbiota, intestinal morphology and meat lipid oxidation of broiler chickens – I Giannenas – British Poultry Science

 

Techniques

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research – PD Schloss – mBio

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens – L Guo – bioRxiv

Microbes in the news

Media Advisory: Live exhibit of dance and song on tiny world of bacteria inside us comes to Buffalo Museum of Science – UB News Center

Non-microbiology picks

These labs are remarkably diverse — here’s why they’re winning at science – Nature

Big data little help in megafauna mysteries – Nature

What does it take to make an institution more diverse? – Nature

The many possible climates from the Paris Agreement’s aim of 1.5 °C warming – Nature

 

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