December 14, 2018

The microbiota of chigger mites and praying mantids, the prevalence of thermophiles in domestic water heaters, the bacteria that colonize and degrade centuries-old art.

General microbiome

Migration alters oscillatory dynamics and promotes survival in connected bacterial populations – Shreyas Gokhale – Nature Communications

Pre-print: A probabilistic model to identify the core microbial community – Thiago Gumiere – bioRxiv

Human oral microbiome

Pre-print: Correlation between the oral microbiome and brain resting state connectivity in smokers – Dongdong Lin – bioRxiv

Animal experiments

Host-targeted niclosamide inhibits C. difficile virulence and prevents disease in mice without disrupting the gut microbiota – John Tam – Nature Communications

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Ann-Sofie Riis Poulsen – PLOS ONE

Animal microbiome

Bacterial microbiome of the chigger mite Leptotrombidium imphalum varies by life stage and infection with the scrub typhus pathogen Orientia tsutsugamushi – Loganathan Ponnusamy – PLOS ONE

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes – Kara A Tinker – PLOS ONE

Plant, root, and soil microbiome

Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient – Max E. Schön – PLOS ONE

Treating wheat seeds with neonicotinoid insecticides does not harm the rhizosphere microbial community – Yaofa Li – PLOS ONE

Water and extremophile microbiome

Pre-print: An archaeal symbiont-host association from the deep terrestrial subsurface – Katrin Schwank – bioRxiv

Marine-Derived Fungi: Promising Candidates for Enhanced Bioremediation – Anjana K Vala – Approaches in Bioremediation

Built environment

Biogeography of thermophiles and predominance of Thermus scotoductus in domestic water heaters – Regina L Wilpiszeski – Extremophiles

Probiotics/prebiotics

Dopamine production in Enterococcus faecium: A microbial endocrinology-based mechanism for the selection of probiotics based on neurochemical-producing potential – Daniel Villageliú – PLOS ONE

Phages and viruses

A chemical defence against phage infection – Sarah Kronheim – Nature

Bioinformatics

Pre-print: Metagenome-wide measurement of protein synthesis in the human fecal microbiota using MetaRibo-Seq – Brayon J Fremin – bioRxiv

Pre-print: Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions – Hila Sberro – bioRxiv

Metabolomics

Rumen and plasma metabolomics profiling by UHPLC-QTOF/MS revealed metabolic alterations associated with a high-corn diet in beef steers – You Yang – PLOS ONE

More microbes

Pre-print: Real-time capture of horizontal gene transfers from gut microbiota by engineered CRISPR-Cas acquisition – Christian Munck – bioRxiv

Bacteria art

A detailed look at the microorganisms that colonize, and degrade, a 400-year-old painting – ScienceDaily

Inside SAIC’s Bio Art Lab, where art is life—literally – Paul Dailing – Chicago Reader

Across China: Medical students paint “Mona Lisa” with bacteria – Xinhua Net

Science, career, and publishing

Pre-print: Non-academic employability of life science PhDs: the importance of training beyond the bench – Sohyoung Her – bioRxiv

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November 27, 2018

Microbial communities of IBS patients after fecal microbiota transplantation, the shipworm gill-associated microbiota, a profile of bioartist Ani Liu in our “bacteria art” section.

Human skin microbiome

The Microbiome in Atopic Dermatitis – Amy S Paller – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Microbiome dynamics in obesity – Christoph A Thaiss – Science

The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation – Tarek Mazzawi – PLOS ONE

Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential – Christopher Bulow – mSphere

Comparison of the gut microbiota of obese individuals from different geographic origins – Emmanouil Angelakis – New Microbes and New Infections

Review: Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome – Manosha Perera – International Journal of Medical Reviews

Animal experiments

Proteomic Analysis of Microbial Induced Redox-Dependent Intestinal Signaling – Jason D Matthews – Redox Biology

Population and Culture Age Influence the Microbiome Profiles of House Dust Mites – Jan Hubert – Microbial Ecology

Animal microbiome

Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans – Francesca Scolari – BMC Microbiology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Thais L Brito – PLOS ONE

Plant, root, and soil microbiome

Host-specific signatures of the cell wall changes induced by the plant parasitic nematode, Meloidogyne incognita – Refik Bozbuga – Scientific Reports

The effects of struvite and sewage sludge on plant yield and the microbial community of a semiarid Mediterranean soil – F Bastida – Geoderma

Review: Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review – Tong Yu – Science of the Total Environment

Water and extremophile microbiome

Combining fish and benthic communities into multiple regimes reveals complex reef dynamics – Mary K Donovan – Scientific Reports

Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China – Shilei Sang – Scientific Reports

Bioinformatics

Pre-print: Naught all zeros in sequence count data are the same – Justin D Silverman – bioRxiv

Microbes in the news

A bacterium’s enemy isn’t your friend – Michael S. Gilmore – Nature

Bacteria art

Portrait of the Artist as a Microbial Growth – Kevin Litman-Navarro – The Outline

September 18, 2018

Quite a few articles of interest today:

  1. Foods that are protective of the gut microbiome: Specific oligosaccharides in breast milk can compensate for the effects of C-section births, and cranberries can compensate for the effects of dietary changes in mice.
  2. A possible bi-directional relationship between the gut microbiome and high altitudes: Specific differences in the gut microbiome are associated with differences in tolerance to high altitudes in males, and exposure to high altitudes can alter the gut microbiome in mice.
  3. Microbes in Space: Nitrogen cycle nicroorganisms that may be able to produce food, water and O2 in space, and exposing desert extremophiles to Martian conditions to learn about the kinds of bacteria on other planets

Also: How smoking impacts the lung virome, the association between fecal microbiome profile and phylogeny in deer genera, and the development of the dust microbiome over time in a classroom

Pregnancy and early life

*Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota – Katri Korpela – Scientific Reports

The influence of maternal vaginal flora on the intestinal colonization in newborns and 3-month-old infants – Iwona Gabriel – The Journal of Maternal-Fetal & Neonatal Medicine

Fecal Volatile Organic Compounds in Preterm Infants Are Influenced by Enteral Feeding Composition – Sofia el Manouni el Hassani – Sensors

Multi-site human microbiome

Review: Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Human respiratory microbiome

*Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

Human anal microbiome

Anal microbial patterns and oncogenic HPV in a pilot study of Nigerian men who have sex with men at risk for or living with HIV – Rebecca G Nowak – AIDS Research and Human Retroviruses

Human gut microbiome

*Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – American Journal of Physiology

Intestinal barrier integrity in patients with plaque psoriasis – Mariusz Sikora – The Journal of Dermatology

Review: Mechanisms by which gut microorganisms influence food sensitivities
– Alberto Caminero – Nature Reviews Gastroenterology & Hepatology

Review: Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis – Kayle Dickson – Medical Hypotheses

Review: ADHD-originating in the gut? The emergence of a new explanatory model – Anna M. Sandgren – Medical Hypotheses

Review: Guideline for the Management of Clostridium Difficile Infection in Children and Adolescents With Cancer and Pediatric Hematopoietic Stem-Cell Transplantation Recipients – Caroline Diorio – Journal of Clinical Oncology

Review: Altered Gut Microbiota in Type 2 Diabetes: Just a Coincidence? – Antonio Sircana – Current Diabetes Reports

Review: Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? – Hanne L.P. Tytgat – Trends in Microbiology

Review: Fecal microbiota transplant – a new frontier in inflammatory bowel disease – Sunkara T – Dove Press

Review: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review –  Ticinesi A – Dove Press

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Animal experiments

Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut – András Vida – Molecular Medicine Reports

Lactobacillus reuteri F‐9‐35 Prevents DSS‐Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice – Mao‐cheng Sun – Journal of Food Science

*Cranberries attenuate animal-based diet-induced changes in microbiota composition and functionality: A randomized crossover controlled feeding trial – Jose Rodríguez-Morató – The Journal of Nutritional Biochemistry

*The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLOS ONE

The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet – Huan Wang – Molecules

The influence of gut microbiota dysbiosis to the efficacy of 5-Fluorouracil treatment on colorectal cancer – Lu Yuan – Biomedicine & Pharmacotherapy

Protein deficiency reduces efficacy of oral attenuated human rotavirus vaccine in a human infant fecal microbiota transplanted gnotobiotic pig model – Ayako Miyazaki – Vaccine

In vitro experiments

Butyrate upregulates the TLR4 expression and the phosphorylation of MAPKs and NK‑κB in colon cancer cell in vitro – Tengfei Xiao – Oncology Letters

Animal microbiome

Comparison of the gut microbiota of captive common bottlenose dolphins, Tursiops truncatus in three aquaria – Akihiko Suzuki – Journal of Applied Microbiology

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil – Vinícius C. Cláudio – PLOS ONE

*Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae – Jiaying Li – Frontiers in Microbiology

Probiotics modify body weight together with anxiety states via pro-inflammatory factors in HFD-treated Syrian golden hamster – Ennio Avolio – Behavioural Brain Research

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australas Journal of Animal Sciences

The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency – Chloe Matthews – Gut

MicrobesEvaluation of conjunctival microbiota in clinically normal persian squirrels (Sciurus Anomalus) – Houman Faghihi – Journal of Zoo and Wildlife Medicine

Plant, root, and soil microbiome

Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones – Dongmei Zhou – Microbial Biotechnology

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Soil microbial response to Rhododendron understory removal in southern Appalachian forests: Effects on extracellular enzymes – Ernest D. Osburn – Soil Biology and Biochemistry

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Bacterial diversity in rhizosphere of Paspalum scrobiculatum L. (kodo millet) is revealed with shotgun metagenome sequencing and data analysis – Ratna Prabha – Data in Brief

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Microbial Ecology

Effects of Cd, Cu, Zn and their combined action on microbial biomass and bacterial community structure – Jiuwei Song – Environmental Pollution

Effects of graphene oxides and silver-graphene oxides on aquatic microbial activity – Kwanyoung Ko – Science of The Total Environment

Built environment

*Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten – Anders B. Nygaard – Microbiome

Microbiological analysis of contact lens cases: impact of the hospital environment – Vinicius Targa Villas Bôas – Arquivos Brasileiros de Oftalmologia

Microbes in space

*Nitrogen cycle microorganisms can be reactivated after Space exposure – Ralph E. F. Lindeboom – Scientific Reports

*Desert cyanobacteria under space and planetary simulations: a tool for searching for life beyond Earth and supporting human space exploration – Daniela Billi – International Journal of Astrobiology

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Bioinformatics

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis – Gherman V. Uritskiy – Microbiome

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations  – Alex N Salazar – Bioinformatics

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Microbes in the news

The electrifying energy of gut microbes – Laty A. Cahoon – Nature News and Views

Bacteria and Art

How Anicka Yi’s Science Experiments Are Expanding the Boundaries of Art – Andrew Russeth – W

 

 

August 30, 2018

Today’s digest covers population based studies on regional specificity of the gut microbiome, guidelines on use of fecal microbiota transplant, and review articles on role of the gut microbiome in colorectal cancer, liver tumors and functional gastrointestinal disorders. Also includes articles on how xenobiotics and psychotropic drugs affect the gut microbiota, and link to wonderful bacterial art!

General microbiome

Regional variation limits applications of healthy gut microbiome reference ranges and disease models – Yan He – Nature Medicine

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography – Melanie Deschasaux – Nature Medicine

The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines – Benjamin H Mullish – Gut

Bile Acids, the Microbiome, Immunity, and Liver Tumors – Christoph Schramm – The New England Journal of Medicine

Review: The gut microbiome and colorectal cancer: a review of bacterial pathogenesis – Jessica D. Dahmus – Journal of Gastrointestinal Oncology

Human gut microbiome

Review: The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders – Andrea Shin – Clinical Gastroenterology and Hepatology

Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection – Jillian RM Brown – BMC Gastroenterology

“Cocktail” of Xenobiotics at Human Relevant Levels Reshapes the Gut Bacterial Metabolome in a Species-Specific Manner – Yingdan Zhang – Environmental Science and Technology

Animal experiments

Microbial Sensing by Intestinal Myeloid Cells Controls Carcinogenesis and Epithelial Differentiation – Naoteru Miyata – Cell Reports

Transplacental immune modulation with a bacterial-derived agent protects against allergic airway inflammation – Kyle T Mincham – Journal of Clinical Investigation

Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function – Sofia Cussotto – Pschycopharmocology

Butyrate and Dietary Soluble Fiber Improve Neuroinflammation Associated With Aging in Mice – Stephanie M Matt – Frontiers in Immunonology

Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Convergence between the microcosms of Southeast Asian and North American pitcher plants – Leonora S Bittleston – Elife

Water and extremophile microbiome 

In situ development of a methanotrophic microbiome in deep-sea sediments – S E Ruff – ISME Journal

Probiotics/Prebiotics

Probiotics for management of infantile colic: a systematic review of randomized controlled trials – Radoslaw Dryl – Archives of Medical Science

Bioinformatics

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling – Ari Ugarte – Microbiome

Microbes in the news

The world’s smallest masterpieces? Microscopic version of Leonardo da Vinci’s Mona Lisa and portraits of Albert Einstein and Charles Darwin are recreated using MILLIONS of bacteria – Daily Mail

Non-microbiology picks 

Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015 – Colin F Camerer – Nature Human Behaviour

 

August 18, 2018

The virome of California mosquitoes, effects of climate warming on grassland microbial communities, and a few “bacteria and art” entries including a 92-foot inflatable E. coli sculpture.

General microbiome

Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction – Stephan Noack – Trends in Biotechnology

Growth tradeoffs produce complex microbial communities on a single limiting resource – Michael Manhart – Nature Communications

Human oral microbiome

Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay – Majda Dzidic – The ISME Journal

Animal experiments

Loss of HDAC6 alters gut microbiota and worsens obesity – Arnon D Lieber – The FASEB Journal

Animal microbiome

Pre-print: CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes – Shivanand Hegde – bioRxiv

Plant, root, and soil microbiome

Climate warming leads to divergent succession of grassland microbial communities – Xue Guo – Nature Climate Change

Water and extremophile microbiome

Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams – Scott Hotaling – Microbial Ecology

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration – Sylvain Monteux – The ISME Journal

Phages and viruses

Virome of > 12 thousand Culex mosquitoes from throughout California – Mohammadreza Sadeghi – Virology

Comprehensive comparative analysis of methods and software for identifying viral integrations – Xun Chen – Briefings in Bioinformatics

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe – Alfred Fillol-Salom – The ISME Journal

Metabolomics

Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People – Runmin Wei – Molecular Nutrition & Food Research

More microbes

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea – Michaeline B N Albright – Microbial Ecology

Bacteria art

Linen and Bacteria: The Hidden History of Microbiology – Clara Rodríguez Fernández – Labiotech.eu

Pomona Arts: Sara Parent Ramos: Jumble, Bunch, Grow – Inland Empire

Oxford Natural History exhibition explores benefits of bacteria – BBC News

August 2, 2018

In today’s Microbiome Digest you can read about: the connection of mother’s microbiota and development of psychiatric disorders by M.G. Codagnone; pulmonary microbiome by A.N. Costa; microbiome and allergic diseases by M.Pascal; olfactory communication via microbiota in birds by O. Maraci; global topsoil microbiome by M. Bahram and many more. Enjoy your hot summer read!

Pregnancy and early life

Review: Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease – Martin G.Codagnone – Biological Psychiatry

Human respiratory microbiome

The pulmonary microbiome: challenges of a new paradigm – André Nathan Costa – Jornal Brasileiro de Pneumologia

Oral microbiology

Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries? – Jeffrey A. Banas – BMC Oral Health

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach – Yoshio Nakano – BMC Oral Health

Human skin microbiome

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome – Kang Kang – Cell Reports

Human gut microbiome

Alterations in the Gut Microbiota of Rats Chronically Exposed to Volatilized Cocaine and Its Active Adulterants Caffeine and Phenacetin – Cecilia Scorza – Neurotoxicity Research

Origination, change, and modulation of geriatric disease-related gut microbiota during life – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens – Alexandra E. Livanos – PLOS One

Minireview: Microbiome and Allergic Diseases – Mariona Pascal – Frontiers in Immunology / Mucosal Immunity

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy – Xingming Deng – Frontiers in Microbiology / Antimicrobials, Resistance and Chemotherapy

Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model – Qin Qi – World Journal of Gastroenterology

Helicobacter pylori in human health and disease: Mechanisms for local gastric and systemic effects – Denisse Bravo – World Journal of Gastroenterology

Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species – Valentina Laclare McEneany – The ISME Journal

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance – Aspen T. Reese – mBio

Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs – Celeste Alexander – British Journal of Nutrition

Standardization of gut microbiota analysis: Variability in samples taken at different times from single case and the effect of the freezing the sample – F. Saglam – International Journal of Infectious Diseases

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size – Emily C. Hoedt – The ISME journal

Animal experiments 

A Polysaccharide Isolated from Dictyophora indusiata Promotes Recovery from Antibiotic-Driven Intestinal Dysbiosis and Improves Gut Epithelial Barrier Function in a Mouse Model – Sadia Kanwal – Nutrients

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis – Simon Ghaly – Scientific Reports

Treatment with camu camu (Myrciaria dubia) prevents obesity by altering the gut microbiota and increasing energy expenditure in diet-induced obese mice – Fernando F Anhê – Gut Microbiota

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures – Matej Medvecky – BMC Genomics

Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations – John B. Gorham – European Journal of Nutrition

Animal microbiome 

A prokaryotic-eukaryotic relation in the fat body of Bombus terrestris – Anneleen Parmentier – Environmental Microbiology Reports

Olfactory Communication via Microbiota: What Is Known in Birds? – Öncü Maraci – Genes

Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta) – Alexandria Creasy – Viruses

Plant, root, and soil microbiome

Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field – Pranitha S. Pandit – Antonie van Leeuwenhoek

Long-term effects of untreated wastewater on soil bacterial communities – Tianlin Shen – Science of The Total Environment

Minireview: Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation – Sara Correa-García – Microbial Biotechnology

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana Fusarium wilt disease by reshaping the soil microbiome – Zongzhuan Shen – Biology and Fertility of Soils

Structure and function of the global topsoil microbiome – Mohammad Bahram – Nature

Globally rising soil heterotrophic respiration over recent decades – Ben Bond-Lamberty – Nature

Water and extremophile microbiome

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current – Flavia Flaviani – Frontiers in Microbiology / Aquatic Microbiology

Evaluation of biomethane potential of waste algal biomass collected from eutrophied lake: effect of source of inocula, co-substrate, and VS loading – Pushpendar Kumar – Journal of Applied Phycology

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria – Xiufeng Ma – Environmental Microbiology

Increased biofilm formation due to high-temperature adaptation in marine Roseobacter – Alyssa G. Kent – Nature Microbiology

Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms – Frank Unfried – The ISME Journal

The anchoring effect—long-term dormancy and genetic population structure – Lisa Sundqvist – The ISME Journal

Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments – Stefan Spring – Environmental Microbiology

The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients – Julia M. Otte – Environmental Microbiology

Temporal and spatial dynamics in microbial community composition within a temperate stream network – Norman Hassell – Environmental Microbiology

Diel dynamics and coupling of heterotrophic prokaryotes and dissolved organic matter in epipelagic and mesopelagic waters of the central Red Sea – Francisca C. García – Environmental Microbiology

Probiotics / prebiotics

The effects of a multispecies probiotic on migraine and markers of intestinal permeability–results of a randomized placebo-controlled study – N M de Roos – European Journal of Clinical Nutrition

Phages and viruses

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis – Tanmoy Chakraborty – Virulence

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race – Amelia McKitterick – bioRxiv

Bioinformatics

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea – Johannes Alneberg – Scientific Data

Bacteria & Art

The Beautiful World of Bacteria

 

June 28, 2018

Microbial adaptation to snake and spider venom, a 1.5-year study of fungi in space at the International Space Station, US National Postdoc Survey results.

General microbiome

Quantitative assessment of individual populations within polymicrobial biofilms – Susana Patrícia Lopes – Scientific Reports

Human nearly-sterile sites

Streptococcus mutans in Umbilical Cord Blood, Peripheral Blood, and Saliva from Healthy Mothers – Marcelly Milhomem Mendes – Current Microbiology

Animal microbiome

Pre-print: Microbial adaptation to venom is common in snakes and spiders – E Esmaeilishirazifard – bioRxiv

Plant, root, and soil microbiome

Colonisation dynamics of arbuscular mycorrhizal fungi and dark septate endophytes in the sugarcane crop cycle – Anders Claassens – Rhizosphere

Response Surface Modelling through Box-Behnken approach to optimize bacterial quorum sensing inhibitory action of Tribulus terrestris root extract – Kayeen Vadakkan – Rhizosphere

Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone – Emily B Graham – Science of the Total Environment

Pre-print: Co-culture of soil biofilm isolates enables the discovery of novel antibiotics – Chun-Hui Gao – bioRxiv

Pre-print: Microbial interkingdom interactions in roots promote Arabidopsis survival – Paloma Duran – bioRxiv

Water and extremophile microbiome

Persisting responses of salt marsh fungal communities to the Deepwater Horizon oil spill – Candice Y Lumibao – Science of the Total Environment

Microbes in space

Integrity of the DNA and Cellular Ultrastructure of Cryptoendolithic Fungi in Space or Mars Conditions: A 1.5-Year Study at the International Space Station – Silvano Onofri – Life

Food microbiology

Influence of lactate and acetate removal on the microbiota of French fresh pork sausages – Agnès Bouju-Albert – Food Microbiology

Probiotics/prebiotics

The anxiolytic effect of probiotics: A systematic review and meta-analysis of the clinical and preclinical literature – Daniel J Reis – PLOS ONE

Phages and viruses

Pre-print: Megaphage infect Prevotella and variants are widespread in gut microbiomes – Audra E Devoto – bioRxiv

Bacteria art

Fifty Percent Human – how art brings us in touch with our microbial cohabitants – Sonja Bäumel – Microbial Biotechnology

Scottish fashion student who grows dresses from tea brews up storm in fashion world – Daily Record

artist reimagines the human microbiome as an intricately cut paper coral reef – design bloom

The next big home design trend? Bacteria – Co.Design

Science, career, and publishing

Pre-print: Career Choice, Gender, and Mentor Impact: Results of the U.S. National Postdoc Survey – Sean C McConnell – bioRxiv